Contacts of the strand formed by residues 3 - 12 (chain A) in PDB entry 2VLK


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 HIS 3 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  GLY      3.1    30.1    +      -       -      -
      2A  SER*     1.3    77.6    +      -       -      +
      4A  SER*     1.3    63.5    +      -       -      +
     29A  ASP*     3.0    28.3    -      -       -      +
    102A  ASP*     3.1     7.4    -      -       -      +
    103A  VAL*     2.8    44.7    +      -       +      +
    107A  TRP*     3.8    28.3    +      +       -      -
    168A  LEU*     4.1     3.6    -      -       +      -
    172A  LEU*     3.8    31.2    -      -       +      +
    179A  LEU      4.4    10.0    +      -       -      -
    180A  GLN*     5.0     7.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 4 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  HIS*     1.3    77.8    -      -       -      +
      5A  MET*     1.3    62.1    +      -       -      +
      6A  ARG*     3.8    19.1    +      -       -      +
     28A  VAL*     3.5     4.7    -      -       -      -
     29A  ASP*     3.0    45.3    +      -       -      +
    101A  CYS      3.3     5.8    -      -       -      -
    102A  ASP*     3.4    21.3    -      -       -      -
    168A  LEU*     3.7     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     1.3    74.6    -      -       -      +
      6A  ARG*     1.3    67.4    +      -       -      +
      7A  TYR*     3.9    30.3    -      -       +      -
     27A  TYR      3.5    12.3    -      -       -      +
     28A  VAL*     4.8     2.5    -      -       +      -
     33A  PHE*     4.6     3.8    -      -       +      -
    100A  GLY*     3.2     5.4    -      -       -      -
    101A  CYS*     3.0    34.8    +      -       -      +
    159A  TYR*     4.6     0.7    -      -       -      +
    164A  CYS*     3.5    38.1    -      -       -      +
    167A  TRP*     4.0    10.5    -      -       +      -
    168A  LEU*     4.0    22.9    -      -       +      +
    171A  TYR*     3.6    35.2    -      -       -      -
      1C  GLY      4.3     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     3.8    18.0    +      -       -      +
      5A  MET*     1.3    84.8    +      -       -      +
      7A  TYR*     1.3    66.1    +      -       -      +
      8A  PHE*     3.5    27.4    -      -       +      -
     25A  VAL      3.9     0.7    -      -       -      +
     26A  GLY*     3.5     1.9    -      -       -      -
     27A  TYR*     2.9    42.8    +      -       +      +
     29A  ASP      5.9     1.8    -      -       -      +
     98A  MET*     3.7    34.3    -      -       +      +
     99A  TYR      3.5     5.4    -      -       -      -
    101A  CYS      3.8     4.2    +      -       -      +
    102A  ASP*     2.5    36.2    +      -       -      -
    113A  TYR*     3.5    32.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     3.9    22.8    -      -       +      -
      6A  ARG*     1.3    75.1    -      -       -      +
      8A  PHE*     1.3    61.3    +      -       -      +
      9A  PHE*     3.4    24.2    -      +       +      -
     24A  ALA*     6.2     1.3    -      -       +      -
     25A  VAL      3.4     4.5    -      -       -      -
     26A  GLY*     3.7    23.8    -      -       -      -
     33A  PHE*     3.4    20.1    -      +       -      -
     34A  VAL*     4.2    13.1    -      -       +      +
     45A  MET*     5.0     2.6    -      -       +      +
     59A  TYR*     4.8     0.7    +      -       -      -
     63A  GLU*     4.5     1.9    +      -       -      -
     97A  ARG      3.8     0.5    -      -       -      +
     98A  MET*     3.3     8.5    -      -       -      +
     99A  TYR*     2.8    53.1    +      +       +      +
    100A  GLY*     5.7     0.9    -      -       -      -
    159A  TYR*     4.3     0.7    -      -       -      -
    171A  TYR*     4.0     0.7    +      -       -      -
      1C  GLY*     2.8    41.5    +      -       -      -
      2C  ILE*     3.4    25.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     3.5    34.1    -      -       +      -
      7A  TYR*     1.3    73.9    -      -       -      +
      9A  PHE*     1.3    62.2    +      -       -      +
     23A  ILE*     3.8     1.4    -      -       -      +
     24A  ALA*     3.3     3.5    -      -       -      +
     25A  VAL*     2.9    44.4    +      -       +      +
     27A  TYR*     3.6    36.6    -      +       +      -
     97A  ARG      3.6     2.7    -      -       -      -
     98A  MET*     3.6    25.4    -      -       +      -
     55B  SER*     4.1     7.9    -      -       -      +
     56B  PHE*     3.6    50.9    -      +       +      -
     57B  SER      5.2     3.8    -      -       -      -
     63B  TYR*     5.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  TYR*     3.4    27.6    -      +       +      -
      8A  PHE*     1.3    73.3    -      -       -      +
     10A  THR*     1.3    63.0    +      -       -      +
     22A  PHE*     3.5    24.9    -      +       +      -
     23A  ILE      3.3     3.6    -      -       -      -
     24A  ALA*     3.5    28.7    -      -       +      -
     67A  VAL*     4.4     7.6    -      -       +      -
     70A  HIS*     4.1    20.2    -      +       -      -
     74A  HIS*     4.3    14.4    -      +       +      +
     95A  VAL      4.6     0.2    -      -       -      -
     96A  GLN*     3.2     5.0    -      -       -      -
     97A  ARG*     2.8    53.3    +      -       +      +
     99A  TYR*     3.3    42.2    -      +       -      -
     56B  PHE*     3.6     3.5    -      -       -      -
      2C  ILE*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE      5.4     0.2    -      -       -      -
      9A  PHE*     1.3    76.3    -      -       -      +
     11A  SER*     1.3    63.9    +      -       -      +
     12A  VAL*     3.9    20.0    -      -       +      -
     21A  ARG      3.9     0.3    -      -       -      +
     22A  PHE*     3.3     7.6    -      -       -      -
     23A  ILE*     2.8    50.5    +      -       +      +
     94A  THR*     4.1     1.8    -      -       +      -
     95A  VAL      3.5     7.4    -      -       -      +
     96A  GLN*     4.1     3.1    -      -       +      +
     54B  LEU*     4.6    12.6    +      -       +      +
     56B  PHE*     3.5    19.1    -      -       -      -
     62B  PHE*     3.5    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     1.3    75.1    -      -       -      +
     12A  VAL*     1.3    61.9    +      -       -      +
     20A  PRO*     4.3     4.3    -      -       -      +
     21A  ARG      3.2     9.6    +      -       -      -
     22A  PHE*     4.1     7.4    -      -       -      +
     71A  SER      5.5     0.2    +      -       -      -
     74A  HIS*     3.9    30.5    +      -       -      +
     75A  ARG*     4.7     0.5    +      -       -      -
     78A  LEU*     3.1    25.3    -      -       -      +
     93A  HIS      4.0     0.5    -      -       -      +
     94A  THR*     3.5     2.8    -      -       -      +
     95A  VAL*     2.8    41.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     3.9    16.6    -      -       +      -
     11A  SER*     1.3    80.4    +      -       -      +
     13A  SER*     1.3    65.3    +      -       -      +
     14A  ARG*     3.7     6.0    +      -       -      +
     20A  PRO*     3.2     6.6    -      -       -      +
     21A  ARG*     2.9    46.7    +      -       +      +
     78A  LEU*     4.3     0.9    -      -       -      -
     92A  SER*     3.8    17.0    -      -       -      +
     93A  HIS      3.3     6.7    -      -       -      +
     94A  THR*     4.1    13.5    -      -       -      +
     33B  SER*     3.8    22.9    -      -       -      +
     54B  LEU*     5.8     1.1    -      -       +      -
----------------------------------------------------------
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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