Contacts of the strand formed by residues 191 - 201 (chain A) in PDB entry 3V56


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 191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  GLU      3.6     2.2    +      -       -      -
    190A  THR*     1.3    78.8    -      -       -      +
    192A  TYR*     1.4    67.0    +      -       -      -
    193A  PHE*     3.6    10.0    -      -       -      -
    252A  LYS*     3.4     8.0    -      -       -      +
    253A  LEU      2.9    35.2    +      -       -      +
    283A  LYS*     4.0     7.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLY*     1.4    76.6    -      -       -      -
    193A  PHE*     1.3    63.5    +      -       -      +
    250A  ILE*     4.3     2.7    -      -       +      -
    251A  ALA      3.5     1.8    -      -       -      -
    252A  LYS*     3.7    47.7    +      -       +      +
    283A  LYS*     3.8     2.6    -      -       -      +
    284A  LEU*     2.9    49.9    +      -       +      +
    172B  PHE*     3.3    46.8    -      +       +      -
    173B  LYS      4.8     1.2    +      -       -      -
    174B  ARG*     3.8    35.6    -      -       +      +
    218F  HIS*     3.8    24.4    +      -       -      -
    220F  PHE*     4.4     0.2    -      +       -      -
    254F  GLU*     5.0     2.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ALA*     4.4     3.8    -      -       +      -
    178A  LEU*     3.7    33.4    -      -       +      -
    187A  VAL*     4.0    15.9    -      -       +      -
    189A  GLU      3.4    25.4    -      -       -      -
    191A  GLY*     3.6    25.4    -      -       -      -
    192A  TYR*     1.3    75.0    -      -       -      +
    194A  PHE*     1.3    62.9    +      -       -      +
    195A  ILE*     3.4    24.1    +      -       +      +
    250A  ILE*     3.4     6.8    -      -       -      +
    251A  ALA      2.9    32.2    +      -       -      +
    253A  LEU*     3.8    17.5    -      -       +      -
    281A  ALA*     4.6     2.2    -      -       +      -
    282A  LEU      3.2     7.0    -      -       -      +
    283A  LYS*     3.6    44.9    -      -       +      -
    284A  LEU*     4.6     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  PHE*     1.3    69.9    -      -       -      +
    195A  ILE*     1.3    57.4    +      -       -      +
    196A  TYR*     3.9    24.2    -      +       +      -
    246A  TYR*     4.0     5.2    -      -       -      -
    248A  ALA*     3.6    26.7    -      -       +      -
    249A  GLY*     3.4    20.2    -      -       -      -
    250A  ILE*     4.3    12.6    -      -       +      +
    281A  ALA*     3.3     2.3    -      -       -      -
    282A  LEU*     2.8    58.9    +      -       +      +
    284A  LEU*     4.2    18.4    -      -       +      +
    194B  PHE*     3.8    36.3    -      +       -      -
    196B  TYR*     5.2     2.9    -      +       -      -
    246B  TYR*     4.4     2.9    -      -       -      -
    282B  LEU*     5.4     4.7    -      -       +      -
    194C  PHE*     3.8    24.0    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  PHE*     3.4    24.2    -      -       +      +
    194A  PHE*     1.3    76.4    -      -       -      +
    196A  TYR*     1.3    62.9    +      -       -      +
    212A  ILE*     3.6    30.3    -      -       +      -
    229A  LEU*     4.3     9.6    -      -       +      -
    230A  PHE*     4.3     8.8    -      -       +      -
    248A  ALA*     3.1     5.2    -      -       -      +
    249A  GLY      2.8    33.2    +      -       -      +
    251A  ALA*     4.0    20.2    -      -       +      +
    253A  LEU*     4.0    22.2    -      -       +      -
    259A  LEU*     3.9    23.6    -      -       +      -
    279A  PHE*     4.1     7.9    -      -       +      -
    280A  GLY      3.6    10.3    -      -       -      +
    281A  ALA*     4.2     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  LEU      4.3     1.2    +      -       -      -
    148A  GLN*     2.6    42.6    +      -       -      +
    194A  PHE*     3.9    22.9    -      +       +      -
    195A  ILE*     1.3    73.9    -      -       -      +
    197A  GLY*     1.3    59.4    +      -       -      +
    212A  ILE*     3.8     5.8    -      -       -      -
    246A  TYR*     3.4    24.0    -      -       +      +
    247A  SER      3.6     6.3    -      -       -      -
    248A  ALA*     3.7     5.6    -      -       +      -
    278A  PHE*     4.2    24.7    -      +       -      -
    279A  PHE*     3.3     7.4    -      -       -      -
    280A  GLY*     2.9    60.1    +      -       -      +
    281A  ALA*     3.7     6.3    -      -       -      -
    282A  LEU      4.9     0.2    -      -       -      -
    194C  PHE*     5.5     2.2    -      +       -      -
    248C  ALA      4.5     5.4    -      -       -      -
    249C  GLY*     4.5     7.0    -      -       -      -
    250C  ILE*     3.4    33.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  TYR*     1.3    78.2    -      -       -      +
    198A  GLN*     1.3    59.7    +      -       -      -
    210A  HIS*     3.5    11.3    +      -       -      -
    212A  ILE*     3.7     9.3    -      -       -      +
    246A  TYR*     3.4     6.1    -      -       -      -
    247A  SER      3.1    33.1    +      -       -      +
    261A  LEU*     4.3     7.4    -      -       -      -
    278A  PHE*     3.4    11.7    -      -       -      -
    279A  PHE*     4.2     2.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  GLY*     1.3    74.6    -      -       -      +
    199A  VAL*     1.3    76.8    +      -       -      +
    210A  HIS*     4.2     0.4    -      -       -      -
    244A  SER*     4.0    15.3    +      -       -      -
    245A  CYS      3.2    17.0    -      -       -      +
    246A  TYR*     3.7    17.3    +      -       +      +
    261A  LEU*     4.6     0.6    -      -       -      +
    276A  VAL*     3.0    19.2    +      -       -      +
    277A  THR*     3.2     1.7    -      -       -      +
    278A  PHE*     2.9    58.0    +      -       +      +
    231C  ARG      2.8    28.1    +      -       -      +
    246C  TYR      4.0     1.7    -      -       -      +
    247C  SER*     2.7    29.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  VAL*     4.7     0.7    -      -       +      -
    198A  GLN*     1.3    81.6    -      -       -      +
    200A  LEU*     1.3    62.4    +      -       -      +
    201A  TYR*     3.5    38.9    -      -       +      +
    210A  HIS*     3.5    17.7    -      -       +      +
    244A  SER*     3.3     1.2    -      -       -      -
    245A  CYS      2.9    28.6    +      -       -      -
    261A  LEU*     3.6    26.5    -      -       +      -
    263A  ILE*     4.2     6.5    -      -       +      -
    270A  ILE*     3.7    21.5    -      -       +      -
    276A  VAL      3.9     3.4    -      -       -      -
    277A  THR*     3.6    19.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  VAL*     1.3    70.6    -      -       -      +
    201A  TYR*     1.3    65.8    +      -       -      +
    202A  THR*     4.3    10.1    -      -       +      -
    242A  ASN*     3.9    11.0    -      -       -      +
    243A  ASN      3.6    29.4    -      -       -      +
    244A  SER*     3.8     8.1    -      -       -      +
    270A  ILE*     3.2     7.1    -      -       -      +
    271A  SER*     2.9    48.7    +      -       -      +
    276A  VAL*     3.6    38.9    +      -       +      -
    277A  THR*     3.3     7.5    +      -       -      -
    231C  ARG*     4.3     5.4    -      -       -      +
    233C  ILE*     3.8    25.4    -      -       +      -
     29I  VAL      5.6     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  VAL*     3.5    35.1    -      -       +      +
    200A  LEU*     1.3    72.6    -      -       -      +
    202A  THR*     1.3    61.4    +      -       -      +
    203A  ASP      3.5     0.9    -      -       -      +
    208A  MET*     3.6    36.6    -      -       +      -
    209A  GLY*     3.0    36.1    -      -       -      -
    210A  HIS*     2.6    34.0    +      -       -      +
    234A  GLN*     5.2     2.7    -      -       +      -
    236A  MET*     3.3    21.1    -      -       +      +
    242A  ASN*     3.4     5.4    -      -       -      -
    243A  ASN      2.8    44.7    +      -       -      +
    245A  CYS*     4.2    12.6    -      -       +      -
    263A  ILE*     3.9     6.1    -      -       +      +
    269A  GLN      3.8     1.6    -      -       -      +
    270A  ILE*     3.5    18.2    -      -       +      -
----------------------------------------------------------
 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