Contacts of the strand formed by residues 36 - 42 (chain B) 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 VAL 36 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  MET*     4.2    14.6    -      -       +      -
     30B  ALA*     3.5    31.4    -      -       +      -
     32B  ASN      4.0     8.7    -      -       -      +
     33B  THR*     3.0    12.1    +      -       -      +
     35B  GLU*     1.3    79.9    -      -       -      +
     37B  TYR*     1.3    70.7    +      -       -      +
     38B  VAL*     4.3     1.3    -      -       +      -
     50B  PHE*     4.0     2.5    -      -       -      -
     52B  GLY*     3.0    27.7    +      -       -      -
     53B  ALA      4.6     0.3    +      -       -      -
     73B  LEU*     3.5    38.1    -      -       +      -
     74B  LEU*     4.2     8.3    -      -       +      -
     98B  VAL*     4.4     3.1    -      -       +      -
     99B  THR      3.4     7.2    -      -       -      +
    100B  GLU*     4.7     2.9    -      -       +      -
    101B  LEU*     5.3     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  GLU      4.1     0.2    +      -       -      -
     36B  VAL*     1.3    75.8    -      -       -      +
     38B  VAL*     1.3    81.8    +      -       -      +
     39B  LYS*     4.1    26.9    -      -       +      -
     49B  THR*     3.9    21.2    +      -       -      +
     50B  PHE      3.4     8.5    -      -       -      -
     51B  ASP*     3.6    40.3    +      -       +      +
     97B  GLU*     3.8     6.4    -      -       -      +
     98B  VAL*     3.4     4.7    -      -       -      +
     99B  THR*     2.9    48.0    +      -       -      +
    101B  LEU*     5.0    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  VAL*     4.3     2.7    -      -       +      -
     37B  TYR*     1.3    84.2    -      -       -      +
     39B  LYS*     1.3    65.6    +      -       -      +
     40B  TRP*     3.9    28.3    -      -       +      +
     48B  TYR*     4.8     2.7    -      -       +      -
     49B  THR*     3.2     5.8    -      -       -      -
     50B  PHE*     2.9    42.4    +      -       +      +
     68B  ILE*     4.3     9.9    -      -       +      -
     73B  LEU*     3.6    42.2    -      -       +      -
     78B  ALA*     4.4    10.5    -      -       +      -
     96B  CYS*     4.9     1.3    -      -       -      -
     97B  GLU      3.4     7.9    -      -       -      +
     98B  VAL*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  TYR*     4.1    22.0    -      -       +      -
     38B  VAL*     1.3    75.8    -      -       -      +
     40B  TRP*     1.3    63.5    +      -       -      +
     41B  LYS*     3.3    25.4    +      -       +      +
     46B  ASP*     3.3    41.2    +      -       +      +
     48B  TYR      3.4     3.6    -      -       -      +
     49B  THR*     4.3     7.6    -      -       +      -
     95B  THR      3.6     1.7    -      -       -      +
     96B  CYS*     3.7     0.9    -      -       -      -
     97B  GLU*     2.8    62.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ILE*     3.8    10.8    -      -       +      -
     21B  ILE*     3.5    40.8    -      -       +      -
     23B  CYS*     3.5    18.6    -      -       +      -
     38B  VAL*     3.9    18.3    -      -       +      +
     39B  LYS*     1.3    73.1    -      -       -      +
     41B  LYS*     1.3    60.6    +      -       -      +
     46B  ASP*     3.4     5.2    -      -       -      +
     47B  ILE*     2.8    43.0    +      -       +      -
     48B  TYR*     2.9    21.4    +      +       +      -
     68B  ILE*     4.0     3.4    -      -       +      +
     78B  ALA      2.9    29.3    +      -       -      -
     80B  LEU*     3.4    42.7    -      -       +      +
     94B  TYR*     3.9    15.5    -      +       +      -
     95B  THR      3.2    15.7    -      -       -      -
     96B  CYS*     3.6    20.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  GLU*     5.4     5.1    +      -       -      -
     39B  LYS*     3.3    32.6    -      -       +      +
     40B  TRP*     1.3    78.5    -      -       -      +
     42B  PHE*     1.3    61.5    +      -       -      +
     44B  GLY*     5.0    10.3    -      -       -      +
     45B  ARG      3.1    13.7    -      -       -      +
     46B  ASP*     3.6    17.3    -      -       -      +
     47B  ILE*     4.3     2.2    -      -       -      -
     93B  ASN      4.1     0.2    -      -       -      +
     94B  TYR*     3.3     9.0    -      -       -      +
     95B  THR*     2.8    56.8    +      -       +      +
     97B  GLU*     3.7    21.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LYS*     1.3    74.5    -      -       -      +
     43B  LYS*     1.3   100.1    +      -       +      +
     44B  GLY      3.1     0.6    +      -       -      -
     45B  ARG*     3.0    29.7    +      -       -      +
     47B  ILE*     4.0    14.5    -      -       +      +
     63B  PHE*     4.2     3.1    -      +       +      -
     89B  SER      5.1     0.7    -      -       -      -
     90B  HIS*     3.5    50.3    -      +       +      -
     91B  THR      3.3    25.1    -      -       -      -
     92B  GLY*     3.9     9.0    -      -       -      -
     93B  ASN      3.7    13.5    -      -       -      -
     94B  TYR*     3.5    35.9    -      +       +      -
----------------------------------------------------------
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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