Traditionally, a protagonist is the main figure of a piece of literature or drama and has the main part or role. Alternatively, the phrase denotes a primary advocate of or proponent for a cause or movement. The main character can be a hero or a villain in a story - it is just the character with the lead role. In literature, the protagonist is characterized by his/her ability to change or evolve.
It should be pointed out that the protagonist is not always the hero of the story, as implied in the Grand Theft Auto games. They may commit crimes of some sort, (which the protagonists of the GTA games certainly do) but he/she is still considered the lead character, and is known to help out his/her friends, allies or close associates.
The protagonists between Grand Theft Auto III and Grand Theft Auto IV share similar qualities. All protagonists are new to town, either returning after a long time gone (such as Carl Johnson and Toni Cipriani) or have never been to the city before (such as Claude, Tommy Vercetti, Mike, Victor Vance and Niko Bellic). The protagonists usually start with nothing, with minimal influence and reputation, having to do odd jobs around for various small-timers, gaining friends and allies (like Asuka Kasen, Avery Carrington, Wu Zi Mu, and Little Jacob) before moving up the social and ecomonical ladder, attempting to rise through the criminal underworld, although their motives for doing so vary in each game. They eventually start establishing a name for themselves in the town, doing real jobs, making bigger and more powerful friends and business partners, and cutting real deals as their prominence, respect, money, and reputation begins to grow, until they end the game on top of the city, or at least with some powerful business and/or friends.
The opposite of a protagonist is an antagonist, which is the main person working against the protagonist and his actions. Again, this can be a villain or a hero, though usually a villain.
The main antagonists of the Grand Theft Auto games are usually introduced very early in the story, usually the the protagonist's friend or acquaintance until a major, personal betrayal with gunfire (like Catalina, Sonny Forelli, Frank Tenpenny, Jerry Martinez and Dimitri Rascalov) and are usually seen, heard, or mentioned throughout the game, moving against the protagonists' plans or goals, until they are finally confronted in some big event by the protagonist at the end of the game. An abnormal antagonist is Massimo Torini; he makes the least amount of appearances than all the other antagonists in the other games (only 2).
Current list of GTA protagonists
List of Ally Groups
Group reason: While Claude does maintain a close friendship and working relationship with the Yakuza over the course of the game, he always acts freelance and never makes a commitment to any gang. He is quite similar to Niko in this respect.
Protagonist: Tommy Vercetti
Group: Vercetti Gang
Group reason: Tommy founded the Vercetti gang after taking over Ricardo Diaz's empire in Vice City. The actual name "Vercetti Gang" spawned when Tommy bought Kaufman Cabs and Delores tells the employees that the "Vercetti Gang" owns it now. She came up with it as an impromptu excuse because the firm apparently has been owned in the past by other gangs & that's all the firm knows (possibly the Mafia or Cartel, as named by Delores) then the name sticks.
Protagonist: Carl Johnson
Group: Grove Street Families and San Fierro Triads
Group reason: CJ's brother, Sweet started the gang and therefore makes CJ the Underboss and CJ had a friendly relationship with the Triad Leader Woozie.
Protagonist: Toni Cipriani
Group: Leone Family
Group reason: Toni's parents possibly were in the Leone Family (as hinted by his mother in Liberty City Stories), but it is never given how he joined the family. He is close friends with Don Salvatore Leone and is made Caporegime later in the game and keeps his position well into GTA III.
Protagonist: Vic Vance
Group: Vance Crime Family
Group reason: After leaving the Trailer Park Mafia Vic and his brother Lance, who would become Vance Crime Family Underboss, started the gang to make money for their asthmatic brother Pete.
Protagonist: Niko Bellic
Group: None, Niko is a hired gun and works for anyone who pays. He has many connections with groups nonetheless, but he is not a real member for any of them, just doing jobs for people in those groups.
The Jamaican Posse and the McReary Mob have and will always be allied with Niko due to his friendships with Little Jacob and Packie McReary. Niko can also have connections with the North Holland Hustlers, if the player chooses to kill Playboy X instead of Dwayne.
Protagonist: Johnny Klebitz
Group: The Lost Brotherhood
Group reason: Johnny is/was best friends with Billy Grey, the president of the Lost, until the latter was imprisoned and the presidential torch passed to Johnny. Johnny would later go on to execute Grey in the correctional facility.
Protagonist: Luis Fernando Lopez
Group: Northwood Dominican Drug Dealers/None
Group reason: Luis works for Anthony Prince, who isn't a part of any specific organisation. He is also friends with the Northwood Dominican Drug Dealers' members Armando Torres and Henrique Bardas.
Protagonist: Huang Lee
Group: Algonquin Triads
Group reason: Huang's father was head of the gang before his brother Wu Lee killed him for the Yu Jian Sword. In the game's climax, Huang kills Wu and is appointed Triad leader by Hsin Jaoming at the dying breath.