Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 3GSB


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 MET 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  ASN*     4.3     1.1    -      -       -      -
    114A  ILE*     3.8     3.0    -      -       -      +
    115A  GLU*     1.3    80.3    -      -       -      +
    117A  VAL*     1.3    61.0    +      -       -      +
    285A  GLY*     3.3    21.5    -      -       -      -
    286A  GLY      3.4     4.7    +      -       -      -
    288A  ARG*     3.6    39.3    -      -       +      +
    291A  MET*     3.4    32.4    -      -       +      +
    292A  GLN*     3.4    25.4    -      -       -      +
     20B  GLN      4.2     4.5    -      -       -      +
     21B  LYS      3.1    32.1    -      -       -      +
     22B  LEU      3.5     8.3    -      -       -      +
     23B  MET      4.2    11.0    -      -       -      +
     24B  PRO*     3.9    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  ALA*     3.8    29.6    -      -       +      +
    107A  VAL*     4.1    22.4    -      -       +      -
    108A  ASN*     3.2    21.5    -      -       -      +
    114A  ILE*     4.2    11.0    -      -       +      -
    116A  MET*     1.3    72.8    -      -       -      +
    118A  ARG*     1.3    65.3    +      -       -      +
    119A  PHE*     4.3     8.5    -      -       +      -
    283A  ALA*     4.4    14.8    -      -       +      -
    284A  TYR      3.7    13.9    -      -       -      +
    291A  MET*     4.1     0.7    -      -       -      -
     22B  LEU      3.0    10.5    +      -       -      +
     23B  MET*     3.1    16.2    -      -       -      +
     24B  PRO*     3.0    19.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  VAL*     1.3    77.6    -      -       -      +
    119A  PHE*     1.3    78.0    +      -       -      +
    283A  ALA*     3.4     1.8    -      -       -      -
    284A  TYR*     3.1    64.4    +      -       +      +
    291A  MET*     4.0     9.9    -      -       +      -
    294A  VAL*     3.8     8.8    -      -       -      +
    295A  ALA      2.9    27.4    +      -       -      -
    296A  PRO*     3.8     5.7    -      -       -      +
    302A  GLN*     3.3    37.4    +      -       -      +
     23B  MET*     4.6     1.1    -      -       -      -
     24B  PRO*     3.0    32.0    +      -       +      +
     27B  VAL*     3.1    21.5    +      -       -      +
     28B  SER*     3.7    20.5    +      -       -      +
     29B  SER      4.5     0.8    -      -       -      +
     30B  PRO*     4.7     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLU*     3.8    22.4    -      -       +      -
    103A  LEU*     3.8    26.2    -      -       +      -
    104A  ALA*     3.6    31.6    -      -       +      -
    107A  VAL*     4.6     5.8    -      -       +      -
    117A  VAL*     4.9     7.6    -      -       +      -
    118A  ARG*     1.3    89.8    -      -       -      +
    120A  VAL*     1.3    67.3    +      -       -      +
    275A  ILE*     4.0    15.5    -      -       +      -
    281A  VAL*     4.7     2.7    -      -       +      -
    282A  GLY      3.6     5.4    -      -       -      +
    283A  ALA*     4.0    16.2    -      -       +      -
    302A  GLN*     4.8     0.2    -      -       -      +
    307A  SER*     3.7    12.9    -      -       -      -
    308A  GLY      4.6     5.6    -      -       -      +
    313A  MET*     4.1    31.0    -      -       +      -
     23B  MET*     3.8    17.5    -      -       +      -
     28B  SER*     4.1    11.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ARG      4.8     2.0    -      -       -      +
    119A  PHE*     1.3    78.1    -      -       -      +
    121A  ASN*     1.3    63.8    +      -       -      +
    122A  SER      3.5    21.8    -      -       -      +
    125A  GLU*     3.3    29.8    -      -       +      +
    126A  ALA*     3.5    19.7    -      -       +      +
    281A  VAL*     3.7     5.5    -      -       -      +
    282A  GLY      2.8    34.1    +      -       -      +
    283A  ALA*     4.1     1.1    -      -       -      +
    284A  TYR*     4.8     6.5    -      -       +      -
    302A  GLN*     3.7    30.7    -      -       -      +
    303A  ALA      5.3     0.4    -      -       -      +
    307A  SER*     4.0    11.0    -      -       -      +
    153B  HIS*     4.7     1.3    -      -       -      +
----------------------------------------------------------
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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