Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 2GC3


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLY 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LYS*     1.3    78.3    +      -       -      +
    107A  GLY*     1.3    58.3    +      -       -      -
    119A  TRP*     4.0     9.5    -      -       -      -
    121A  SER*     3.7     5.7    -      -       -      -
    122A  MET*     2.9    29.8    +      -       -      +
    123A  GLU*     5.2     0.3    -      -       -      +
    139A  VAL      3.1    14.6    -      -       -      -
    141A  ILE*     4.0    15.4    -      -       -      +
    146A  PHE*     4.0     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  GLY*     1.3    75.4    -      -       -      -
    108A  MET*     1.3    60.8    +      -       -      -
    119A  TRP*     3.4    15.0    -      -       -      -
    120A  ILE      3.1    13.9    -      -       -      -
    122A  MET*     3.7    12.7    -      -       -      +
    138A  THR*     3.4     6.8    -      -       -      +
    139A  VAL      3.0    29.1    +      -       -      -
    146A  PHE*     3.9     5.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  TYR*     3.4    49.4    -      -       +      -
    107A  GLY*     1.3    74.8    -      -       -      +
    109A  LEU*     1.3    63.1    +      -       -      +
    110A  LEU*     3.7    23.6    -      -       +      +
    118A  LYS      3.5     1.6    -      -       -      +
    119A  TRP*     3.4    10.5    -      -       -      -
    120A  ILE*     2.8    38.2    +      -       +      +
    122A  MET*     3.9     9.2    -      -       -      -
    128A  VAL*     3.7    18.8    -      -       +      -
    130A  VAL*     3.5    20.4    -      -       +      -
    136A  HIS*     3.9     7.0    -      -       -      -
    137A  ARG      3.3    19.3    -      -       -      +
    138A  THR*     4.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  PHE*     6.3     0.7    -      -       +      -
    108A  MET*     1.3    73.6    -      -       -      +
    110A  LEU*     1.3    59.6    +      -       -      +
    117A  ALA*     5.1     3.8    -      -       +      -
    118A  LYS      3.4    12.8    -      -       -      +
    119A  TRP*     3.8    30.4    -      -       +      -
    136A  HIS*     3.3     2.9    -      -       -      -
    137A  ARG*     2.7    54.7    +      -       +      +
    139A  VAL*     4.4     8.9    -      -       +      +
    168A  PHE*     3.5    21.6    -      -       +      -
    170A  LYS*     3.4    43.1    -      -       +      +
    171A  ILE*     4.7     1.6    -      -       -      -
    172A  VAL*     3.9    21.1    -      -       +      +
    181A  VAL*     4.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  MET*     3.7    33.4    -      -       -      +
    109A  LEU*     1.3    75.0    -      -       -      +
    111A  GLN*     1.3    62.0    +      -       -      +
    117A  ALA*     3.1     5.9    -      -       -      +
    118A  LYS*     2.8    40.1    +      -       +      +
    120A  ILE*     3.7    29.8    -      -       +      -
    128A  VAL*     5.1     0.9    -      -       +      -
    129A  TYR      4.8     0.4    -      -       -      +
    130A  VAL*     3.9    27.6    -      -       +      -
    134A  TRP*     3.6    18.8    -      -       +      -
    135A  ALA      3.0     9.4    -      -       -      +
    168A  PHE*     3.9     2.7    -      -       -      -
      5B  PRO*     3.8    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     3.5     3.5    -      -       +      -
    110A  LEU*     1.3    78.0    -      -       -      +
    112A  THR*     1.3    66.6    +      -       -      +
    115A  GLY*     3.8    10.6    -      -       -      +
    116A  ASP      3.1    16.8    -      -       -      +
    117A  ALA*     3.9     1.8    -      -       -      +
    134A  TRP*     3.5     7.4    -      -       -      -
    135A  ALA*     2.7    45.2    +      -       +      +
    162A  THR*     6.1     1.8    -      -       -      +
    163A  ILE*     4.3     8.4    -      -       +      +
    167A  GLY      3.7    10.1    +      -       -      -
    168A  PHE*     3.4    23.7    -      -       +      -
    169A  SER*     2.9    33.8    +      -       -      -
    187A  TRP*     3.5    25.5    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il