Contacts of the strand formed by residues 37 - 45 (chain B) in PDB entry 1ZSV


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 VAL 37 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  LEU*     3.6     7.0    -      -       -      -
     36B  GLU*     1.3    80.6    -      -       -      +
     38B  LEU*     1.3    58.7    +      -       -      +
     39B  LEU*     3.7    24.2    +      -       +      -
     71B  VAL*     3.7     8.5    -      -       +      -
     73B  GLU      3.4     8.1    -      -       -      +
     74B  SER*     3.6    22.0    -      -       -      +
     76B  ASN*     3.7    14.6    -      -       +      +
     79B  LEU*     3.7    21.3    -      -       +      +
     95B  SER      3.8     0.3    -      -       -      +
     96B  ILE*     3.4     6.6    -      -       -      +
     97B  SER*     2.9    47.7    +      -       -      +
     99B  GLY*     5.3     0.4    -      -       -      -
    102B  LEU*     4.3     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  SER*     4.4    21.3    -      -       -      +
     29B  LEU*     3.7    27.4    -      -       +      -
     32B  LEU*     3.6     7.9    -      -       +      +
     37B  VAL*     1.3    71.6    -      -       -      +
     39B  LEU*     1.3    62.4    +      -       -      +
     71B  VAL*     3.5     5.2    -      -       -      -
     72B  VAL*     3.0    46.2    +      -       +      +
     73B  GLU*     2.9    31.3    +      -       +      +
     94B  HIS*     4.6    11.2    -      -       +      -
     95B  SER      3.5    16.6    -      -       -      +
     96B  ILE*     3.8    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL*     3.7    26.7    -      -       +      +
     38B  LEU*     1.3    76.7    -      -       -      +
     40B  GLU*     1.3    59.1    -      -       -      +
     41B  ALA      4.1     0.3    +      -       -      -
     67B  GLN*     4.7     2.1    -      -       -      +
     69B  ALA*     3.8    10.1    -      -       +      -
     70B  LYS      3.5     5.6    -      -       -      +
     71B  VAL*     3.9    18.6    -      -       +      -
     72B  VAL*     4.7     2.0    -      -       -      -
     85B  VAL*     4.0    15.9    -      -       +      -
     87B  ALA*     3.5    31.9    -      -       +      -
     94B  HIS*     3.1     9.4    -      -       -      +
     95B  SER*     2.9    47.8    +      -       -      +
     97B  SER*     4.4     5.8    -      -       -      -
    102B  LEU*     3.8    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LEU      4.0     0.6    +      -       -      -
     39B  LEU*     1.3    73.4    -      -       -      +
     41B  ALA*     1.3    74.0    +      -       -      +
     42B  LEU*     3.5    13.4    +      -       -      +
     69B  ALA*     3.1     3.3    -      -       -      -
     70B  LYS*     2.9    35.8    +      -       +      +
     72B  VAL*     3.7    32.2    -      -       +      +
     93B  THR      3.6     4.9    -      -       -      +
     94B  HIS*     3.7    25.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  GLU*     1.3    80.9    -      -       -      +
     42B  LEU*     1.3    60.9    +      -       -      +
     44B  LEU*     3.9    18.8    -      -       +      -
     67B  GLN*     3.4    38.7    +      -       -      +
     68B  VAL      3.8     3.6    -      -       -      +
     92B  THR      3.7     6.5    -      -       -      +
     93B  THR*     2.9    21.3    +      -       -      +
    329B  ALA*     3.7    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  GLU*     4.2    16.4    -      -       -      +
     41B  ALA*     1.3    77.2    -      -       -      +
     43B  PHE*     1.3    84.6    +      -       +      +
     68B  VAL*     2.9    25.2    +      -       +      +
     70B  LYS*     4.2    21.3    -      -       +      +
     84B  ILE*     3.8    29.6    -      -       +      -
    115B  LEU*     4.1    12.8    -      -       +      -
    328B  LYS*     3.7     2.6    -      -       -      +
    329B  ALA*     3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  LEU*     1.3    94.8    -      -       +      +
     44B  LEU*     1.3    62.5    +      -       -      +
     67B  GLN*     3.2     4.4    -      -       -      +
     68B  VAL*     2.8    35.9    +      -       +      -
    114B  PRO*     6.5     0.4    -      -       +      -
    115B  LEU*     4.1    33.7    -      -       +      -
    116B  SER*     4.0    23.3    -      -       -      -
    119B  LEU*     3.6    17.5    -      -       +      +
    302B  ILE*     5.2     6.1    -      -       +      -
    326B  ILE*     3.8    20.4    -      -       +      -
    327B  VAL      3.4     3.6    -      -       -      -
    328B  LYS*     3.5    39.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ALA*     3.9    15.9    -      -       +      -
     43B  PHE*     1.3    77.8    -      -       -      +
     45B  THR*     1.3    59.9    +      -       -      +
     66B  GLN      3.8     7.4    -      -       -      +
     67B  GLN*     3.5    28.5    -      -       +      +
     90B  GLY      4.3     1.1    -      -       -      +
     91B  TRP*     4.2     3.8    -      -       +      -
     92B  THR      3.6    20.4    -      -       -      +
    119B  LEU*     4.1     2.9    -      -       -      -
    306B  PHE*     4.1    18.2    -      -       +      -
    309B  MET*     3.5    31.6    -      -       +      -
    326B  ILE*     3.6     4.9    -      -       -      +
    327B  VAL*     2.8    48.9    +      -       +      +
    329B  ALA*     4.2    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  LEU*     1.3    75.1    -      -       -      +
     46B  VAL*     1.3    59.6    +      -       -      +
     47B  ASP*     3.0    21.1    +      -       -      +
     49B  TYR*     5.8     0.2    -      -       -      +
     50B  MET*     3.3    12.2    -      -       +      +
     65B  GLY*     5.0     0.3    -      -       -      -
     66B  GLN*     3.2    39.5    +      -       +      +
     91B  TRP*     4.4     1.0    +      -       -      -
    119B  LEU*     4.1    24.4    +      -       +      +
    309B  MET*     3.5    13.8    -      -       -      +
    324B  LYS*     2.7    32.3    +      -       -      -
    325B  THR      4.2     4.0    -      -       -      -
    326B  ILE*     4.4     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