Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 2VLR


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 THR 94 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     4.0    19.5    -      -       +      -
     11A  SER      3.6     9.9    -      -       -      +
     12A  VAL*     4.1    14.2    -      -       +      +
     93A  HIS*     1.3    76.7    +      -       -      +
     95A  VAL*     1.3    71.3    +      -       -      +
     96A  GLN*     4.1    16.2    -      -       +      +
    117A  ALA      3.9     0.3    -      -       -      +
    118A  TYR*     3.3     7.7    -      -       -      -
    119A  ASP*     2.7    40.1    +      -       -      -
    120A  GLY      4.8     0.2    +      -       -      -
     31B  HIS*     4.5    16.2    -      -       +      -
     32B  PRO*     4.8    12.0    -      -       -      +
     33B  SER*     5.3     1.7    +      -       -      +
     62B  PHE*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PHE      4.2     0.2    -      -       -      +
     10A  THR*     3.8     0.2    -      -       -      -
     11A  SER*     2.9    43.8    +      -       -      +
     74A  HIS*     5.1    12.8    -      -       +      +
     77A  ASP*     4.9     4.3    -      -       +      -
     78A  LEU*     3.8    25.7    -      -       +      +
     81A  LEU*     3.6    31.9    -      -       +      -
     94A  THR*     1.3    75.0    -      -       -      +
     96A  GLN*     1.3    73.9    +      -       -      +
     97A  ARG*     5.7     0.2    -      -       +      -
    116A  TYR*     4.2    17.9    -      -       +      -
    117A  ALA      3.4    10.8    -      -       -      +
    118A  TYR*     3.8     6.7    -      -       +      -
      9C  LEU*     5.0     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PHE      3.4     8.3    -      -       -      +
     10A  THR*     4.2     7.4    -      -       +      -
     94A  THR*     4.1    11.8    -      -       +      +
     95A  VAL*     1.3    80.1    -      -       -      +
     97A  ARG*     1.3    62.2    +      -       -      +
    116A  TYR*     3.3    10.0    -      -       -      +
    117A  ALA*     3.1    40.4    +      -       +      +
    120A  GLY      4.6     1.6    +      -       -      -
     31B  HIS*     2.9    26.3    +      -       -      -
     56B  PHE*     3.5    22.4    -      -       +      -
     60B  TRP*     2.9    48.0    +      -       +      +
     62B  PHE*     3.5    20.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE*     3.7     0.2    -      -       -      -
      9A  PHE*     2.9    50.7    +      -       +      -
     70A  HIS*     3.5    31.3    +      -       -      -
     73A  THR*     6.0     1.6    -      -       -      +
     74A  HIS*     3.7    24.0    +      -       +      +
     95A  VAL*     5.7     0.4    -      -       +      -
     96A  GLN*     1.3    76.2    -      -       -      +
     98A  MET*     1.3    62.4    +      -       -      +
     99A  TYR*     3.7    16.2    -      -       +      -
    114A  HIS*     3.0    29.5    +      -       +      +
    115A  GLN      3.5    10.3    -      -       -      +
    116A  TYR*     3.2    37.3    +      -       +      -
     56B  PHE*     3.7     6.2    -      -       -      -
     60B  TRP*     4.6     0.9    -      -       -      -
      3C  LEU*     3.6    21.8    -      -       -      +
      5C  PHE      5.4     1.2    +      -       -      -
      6C  VAL*     5.4     5.9    -      -       -      +
      7C  PHE*     3.6    16.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     3.8    23.6    -      -       -      +
      7A  TYR      3.4     9.6    -      -       -      +
      8A  PHE*     3.6    34.5    -      -       +      -
     97A  ARG*     1.3    76.3    -      -       -      +
     99A  TYR*     1.3    71.8    +      -       -      +
    113A  TYR*     3.8    29.8    -      -       +      -
    114A  HIS*     3.4     3.1    -      -       -      -
    115A  GLN*     3.2    56.2    +      -       +      +
     56B  PHE*     4.3     8.5    -      -       +      -
     58B  LYS*     6.3     3.4    -      -       -      -
     60B  TRP*     4.5     8.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     3.8     1.7    -      -       -      -
      7A  TYR*     3.1    43.3    +      +       +      +
      9A  PHE*     3.6    25.2    -      +       -      -
     70A  HIS*     3.1    14.9    +      -       -      -
     97A  ARG*     3.7    35.0    -      -       -      -
     98A  MET*     1.3    81.6    -      -       -      +
    100A  GLY*     1.3    60.3    +      -       -      +
    113A  TYR      3.2    15.9    -      -       -      +
    114A  HIS*     3.8    17.9    -      +       +      -
    159A  TYR*     3.7    36.6    -      +       -      -
    160A  LEU*     4.9     3.1    -      -       +      -
      2C  ILE*     3.4     8.2    -      -       +      +
      3C  LEU*     3.1    33.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     3.3    14.1    -      -       -      -
      6A  ARG*     4.1     8.5    -      -       -      -
      7A  TYR*     6.0     1.6    -      -       -      -
     99A  TYR*     1.3    81.0    -      -       -      +
    101A  CYS*     1.3    58.8    +      -       -      -
    112A  GLY*     3.4     3.8    -      -       -      -
    113A  TYR*     3.1    30.7    +      -       -      +
    160A  LEU*     3.5     8.4    -      -       -      +
    164A  CYS*     3.8    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     3.4     2.9    -      -       -      -
      5A  MET*     3.0    40.4    +      -       -      +
      6A  ARG*     3.8     1.3    -      -       -      +
    100A  GLY*     1.3    72.6    -      -       -      +
    102A  ASP*     1.3    66.8    +      -       -      +
    109A  PHE*     4.8     0.7    -      -       +      -
    111A  ARG      3.4     9.0    -      -       -      +
    112A  GLY*     5.1     0.2    -      -       -      -
    113A  TYR*     5.0     0.2    -      -       -      -
    160A  LEU      3.8    15.7    -      -       -      +
    164A  CYS*     2.1    60.3    -      -       -      -
    165A  VAL*     3.7    14.4    -      -       +      -
    168A  LEU*     4.4     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  HIS      3.5     6.1    -      -       -      +
      4A  SER*     3.4     8.6    -      -       -      -
      6A  ARG*     3.0    29.4    +      -       -      -
    101A  CYS*     1.3    72.3    -      -       -      +
    103A  VAL*     1.3    62.3    +      -       -      +
    109A  PHE*     3.7     4.0    -      -       -      -
    110A  LEU*     2.8    38.7    +      -       +      -
    111A  ARG*     2.8    28.3    +      -       +      +
    113A  TYR*     3.2    25.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  SER*     3.5     7.1    -      -       -      -
      3A  HIS*     2.8    44.8    +      -       +      +
    102A  ASP*     1.3    78.5    -      -       -      +
    104A  GLY*     1.3    61.7    +      -       -      +
    107A  TRP*     3.8    28.7    -      -       +      +
    108A  ARG      3.3    15.0    -      -       -      +
    109A  PHE      4.2     0.2    -      -       -      +
    110A  LEU*     3.6     9.7    -      -       -      +
    165A  VAL*     3.7    33.7    -      -       +      +
    168A  LEU*     3.7    28.5    -      -       +      -
    169A  ARG*     5.8     1.8    -      -       +      -
    172A  LEU*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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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