Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 2VSC


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 92 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     4.0     4.7    -      -       -      -
     43A  LYS*     5.7     2.0    -      -       -      -
     90A  HIS      4.0     0.2    +      -       -      -
     91A  THR*     1.3    74.9    -      -       -      +
     93A  ASN*     1.3    64.2    +      -       -      -
     94A  TYR*     3.5     7.6    -      -       -      -
   1119A  NAG      3.8    22.7    -      -       -      -
    110B  GLU*     3.8    10.5    -      -       -      -
    111B  LEU      2.9    31.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LYS      4.1     0.2    -      -       -      +
     42A  PHE*     3.7    22.0    -      -       -      -
     43A  LYS*     4.3     5.4    +      -       -      +
     92A  GLY*     1.3    68.6    -      -       -      -
     94A  TYR*     1.3    62.4    +      -       -      +
     95A  THR*     5.1     1.3    +      -       -      +
   1119A  NAG      1.5    64.1    +      -       -      +
    108B  ILE*     4.0    20.6    -      -       +      +
    109B  ILE      3.7     2.5    -      -       -      -
    110B  GLU*     3.4    20.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ILE*     3.6    29.8    -      -       +      -
     40A  TRP*     3.9    24.7    -      +       +      -
     41A  LYS      3.3    12.6    -      -       -      -
     42A  PHE*     3.6    24.2    -      +       +      -
     47A  ILE*     4.1    15.3    -      -       +      -
     63A  PHE*     3.5     7.8    -      +       -      -
     80A  LEU*     4.5     0.2    -      -       +      -
     82A  MET*     4.0    13.9    -      -       +      +
     90A  HIS*     2.7    42.0    +      -       -      +
     92A  GLY      3.5    11.4    -      -       -      -
     93A  ASN*     1.3    74.4    -      -       -      +
     95A  THR*     1.3    60.8    +      -       -      +
     96A  CYS      4.1     0.2    -      -       -      -
    107B  THR      3.9     0.3    -      -       -      +
    108B  ILE*     3.2     6.3    -      -       -      +
    109B  ILE*     2.8    39.0    +      -       -      +
    111B  LEU*     3.8    23.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LYS      3.6     1.2    -      -       -      +
     40A  TRP*     3.2     9.3    -      -       -      -
     41A  LYS*     2.8    60.3    +      -       +      +
     93A  ASN*     4.2     1.6    +      -       -      +
     94A  TYR*     1.3    73.7    -      -       -      +
     96A  CYS*     1.3    62.9    +      -       -      +
     97A  GLU*     4.0     1.1    -      -       +      +
    106B  GLU*     3.9    34.3    -      -       +      +
    107B  THR      3.4     9.0    -      -       -      +
    108B  ILE*     3.6    20.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  PHE*     4.3     1.2    -      -       -      -
     23A  CYS*     2.0    48.5    -      -       +      -
     38A  VAL*     5.0     0.7    -      -       -      -
     39A  LYS      3.7     2.9    -      -       -      -
     40A  TRP*     3.6    33.8    -      -       +      -
     78A  ALA*     3.9    12.3    -      -       -      -
     94A  TYR      4.1     0.4    -      -       -      -
     95A  THR*     1.3    72.3    -      -       -      +
     97A  GLU*     1.3    62.0    +      -       -      +
     98A  VAL*     4.0     7.5    +      -       -      -
    106B  GLU*     3.0     6.5    -      -       -      +
    107B  THR*     2.8    40.5    +      -       +      +
    109B  ILE*     4.5     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  TYR*     3.9     4.9    -      -       -      +
     38A  VAL*     3.3     5.7    -      -       -      +
     39A  LYS*     2.8    71.2    +      -       +      +
     41A  LYS*     3.8    28.4    +      -       -      -
     95A  THR*     5.0     0.9    -      -       +      -
     96A  CYS*     1.3    74.0    -      -       -      +
     98A  VAL*     1.3    67.3    +      -       -      +
     99A  THR*     4.3    10.3    +      -       -      +
    104B  GLU*     4.2    15.4    -      -       -      +
    105B  GLY      3.4    10.1    -      -       -      +
    106B  GLU*     3.8    24.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LEU*     3.3    22.7    -      -       +      +
      4A  PHE*     4.3     4.3    -      -       +      -
     25A  VAL*     3.9    24.9    -      -       +      -
     28A  MET*     4.3    10.1    -      -       +      -
     36A  VAL*     4.1    18.6    -      -       +      -
     37A  TYR      3.4     7.4    -      -       -      +
     38A  VAL*     4.5     4.3    -      -       +      -
     73A  LEU*     4.9     2.5    -      -       +      -
     78A  ALA*     3.9    24.9    -      -       +      -
     96A  CYS*     4.0     9.9    -      -       -      -
     97A  GLU*     1.3    78.3    -      -       -      +
     99A  THR*     1.3    67.7    +      -       -      +
    100A  GLU*     5.5     0.2    -      -       +      -
    104B  GLU*     3.4     1.7    -      -       -      +
    105B  GLY      3.1    30.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  GLU      3.6     0.5    -      -       -      +
     36A  VAL*     3.2     8.3    -      -       -      +
     37A  TYR*     2.8    48.4    +      -       -      +
     97A  GLU*     4.3    14.4    +      -       -      +
     98A  VAL*     1.3    78.2    +      -       -      +
    100A  GLU*     1.3    68.6    +      -       -      +
    101A  LEU*     3.9    12.1    -      -       +      +
    102B  THR*     3.5    28.3    -      -       +      -
    103B  ARG      3.4     7.0    -      -       -      +
    104B  GLU*     3.9    12.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LEU*     4.2    12.3    -      -       +      +
     28A  MET*     3.5    21.2    -      -       +      +
     29A  GLU*     2.7    29.9    +      -       -      +
     30A  ALA*     2.8    27.8    +      -       +      +
     35A  GLU*     3.3     6.5    -      -       +      +
     36A  VAL*     4.6     2.2    -      -       +      -
     99A  THR*     1.3    75.1    -      -       -      +
    101A  LEU*     1.3    65.0    +      -       -      +
   1120A   MG      4.3    10.6    -      -       -      -
     29B  GLU*     5.8     0.4    -      -       -      -
    101B  LEU      4.5     0.5    -      -       -      +
    102B  THR*     3.3     3.6    -      -       -      +
    103B  ARG*     2.7    68.7    +      -       +      +
----------------------------------------------------------
 Back to top of page


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