Contacts of the strand formed by residues 32 - 41 (chain B) in PDB entry 1VI9


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 ASN 32 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  HIS*     4.6    10.9    +      -       -      -
    267A  GLN*     5.1     7.1    +      -       -      +
    269A  VAL*     3.7    16.8    -      -       -      +
      2B  MSE      3.5    34.7    -      -       -      +
      3B  LYS      2.7     9.4    +      -       -      +
      4B  ASN*     3.2    28.1    +      -       -      +
      5B  ILE*     2.9    25.7    +      -       -      +
     27B  ARG*     4.9     1.5    +      -       -      -
     31B  ALA*     1.3    76.5    -      -       -      +
     33B  VAL*     1.3    62.7    +      -       -      +
     34B  TRP*     4.5    10.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL      4.4     0.3    -      -       -      +
      5B  ILE*     3.3     4.5    -      -       +      +
      7B  ALA*     3.8    26.7    -      -       +      -
     19B  ASN*     4.8     0.7    -      -       -      +
     23B  GLU*     4.1    22.0    -      -       +      +
     26B  MSE      3.6    43.5    -      -       +      -
     27B  ARG*     2.9    43.2    +      -       +      +
     31B  ALA*     3.9     1.3    +      -       +      +
     32B  ASN*     1.3    79.7    -      -       -      +
     34B  TRP*     1.3    70.4    +      -       -      +
     35B  PRO*     3.2    11.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL*     3.1    26.7    -      -       +      +
     14A  TYR*     3.6    30.7    -      +       -      -
     15A  GLY      5.0     3.1    -      -       -      -
      4B  ASN*     3.8    31.0    +      -       +      +
      5B  ILE      2.6    18.4    +      -       -      +
      6B  LEU*     3.6    25.8    -      -       +      +
      7B  ALA      2.9    24.0    +      -       -      -
     32B  ASN*     4.5     6.4    -      -       +      +
     33B  VAL*     1.3    79.6    -      -       -      +
     35B  PRO*     1.3    61.1    -      -       -      +
     36B  LEU      3.2     5.2    +      -       -      -
     67B  ILE*     4.1    25.1    -      -       +      -
     72B  LYS      3.5    21.1    -      -       -      -
     73B  LEU*     4.4     7.4    -      -       +      -
     75B  THR*     3.4    16.6    -      -       -      -
     76B  CYS*     3.5    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  HIS*     2.7    49.1    +      -       +      -
     12A  VAL      4.4     2.2    -      -       -      +
     13A  VAL*     3.4    15.9    -      -       -      +
     40A  GLN*     3.6     0.3    -      -       -      +
      7B  ALA      3.7     5.8    -      -       -      +
     19B  ASN*     3.8    19.5    -      -       +      +
     23B  GLU*     4.5    10.5    -      -       +      -
     27B  ARG*     3.8    15.7    -      -       -      +
     33B  VAL*     3.2    21.5    -      -       +      +
     34B  TRP*     1.3    80.3    -      -       -      +
     36B  LEU*     1.3    60.8    -      -       -      +
     37B  ASN*     3.4     8.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL*     3.9    13.0    -      -       +      -
     40A  GLN*     3.9    13.7    -      -       -      +
      6B  LEU*     3.9    10.3    -      -       +      -
      7B  ALA      2.9    11.6    +      -       -      +
      8B  ILE*     3.3    49.2    -      -       +      +
      9B  GLN      3.4     2.3    +      -       -      -
     34B  TRP      3.2     1.8    +      -       -      -
     35B  PRO*     1.3    69.3    -      -       -      +
     37B  ASN*     1.3    63.1    +      -       -      +
     38B  THR      3.6     0.3    +      -       -      -
     59B  HIS*     4.5     0.2    -      -       -      +
     60B  LEU*     3.7    46.7    -      -       +      +
     63B  ILE*     3.8    36.1    -      -       +      -
     64B  VAL*     4.2    10.3    -      -       +      -
     96B  ILE*     4.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  HIS*     3.7    14.5    +      -       -      -
     37A  ASN*     3.8    13.5    -      -       -      +
     40A  GLN*     3.0    39.0    +      -       -      +
      9B  GLN      3.2     4.0    -      -       -      +
     11B  HIS*     3.4    39.6    +      -       +      +
     19B  ASN*     3.0    30.5    +      -       -      +
     35B  PRO*     3.9     7.4    -      -       -      +
     36B  LEU*     1.3    70.8    -      -       -      +
     38B  THR*     1.3    63.1    +      -       -      +
     39B  VAL      3.4     6.7    -      -       -      +
     40B  GLN*     5.1     2.6    +      -       +      -
     55B  MSE      3.3     8.6    -      -       +      +
     60B  LEU*     4.1     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     3.6    32.5    -      -       +      +
      9B  GLN*     2.8    26.8    +      -       -      +
     10B  SER*     3.2     5.2    +      -       -      -
     37B  ASN*     1.3    74.5    -      -       -      +
     39B  VAL*     1.3    64.8    +      -       -      +
     55B  MSE      2.9    24.7    +      -       -      +
     60B  LEU*     4.5     6.7    -      -       +      -
     83B  TYR      3.0    21.8    +      -       -      +
     84B  LEU*     4.4     5.4    -      -       +      -
     85B  GLY      4.4     1.9    +      -       -      -
     89B  GLN*     3.0    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  SER*     3.4    28.7    -      -       -      -
     11B  HIS*     3.1    31.1    +      -       -      +
     37B  ASN*     3.6     5.0    -      -       -      +
     38B  THR*     1.3    83.3    -      -       -      +
     40B  GLN*     1.3    63.0    +      -       -      +
     41B  PHE*     3.5    43.1    -      -       +      -
     53B  CSD      3.4     9.9    -      -       -      +
     54B  VAL*     3.9    14.8    -      -       +      -
     55B  MSE      4.2     5.8    -      -       -      -
     83B  TYR*     4.3     4.0    -      -       +      -
     85B  GLY*     4.1    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     4.1     3.4    -      -       -      +
     37A  ASN*     2.9    53.1    +      -       -      +
     55A  MSE      3.2    19.8    -      -       +      +
     59A  HIS*     3.0    28.5    +      -       -      +
     63A  ILE*     3.7     0.4    -      -       +      +
     11B  HIS*     3.3    23.9    -      -       +      -
     13B  VAL*     4.0    16.8    -      -       +      -
     37B  ASN*     5.1     3.3    +      -       +      -
     39B  VAL*     1.3    73.8    -      -       -      +
     41B  PHE*     1.3    62.0    +      -       -      +
     52B  GLY*     3.2     7.1    -      -       -      -
     53B  CSD      2.9    31.6    +      -       -      -
     55B  MSE      4.9     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ILE*     3.9     3.8    -      -       -      -
     10B  SER*     5.8     0.7    -      -       -      -
     11B  HIS      2.9    10.5    +      -       -      +
     12B  VAL*     3.3     8.5    -      -       +      -
     13B  VAL*     2.8    36.2    +      -       -      +
     39B  VAL*     3.5    39.3    -      -       +      -
     40B  GLN*     1.3    82.1    -      -       -      +
     42B  SER*     1.3    55.8    +      -       -      +
     43B  ASN      3.7    16.8    -      -       -      +
     44B  HIS*     5.8     0.9    -      -       -      -
     45B  THR*     4.9     6.5    -      -       +      -
     50B  TRP*     3.7    38.4    -      +       +      -
     51B  THR      3.3     7.4    -      -       -      +
     52B  GLY      4.3     1.6    -      -       -      -
     53B  CSD      3.8    19.3    -      -       -      -
     54B  VAL*     4.3     9.0    -      -       +      -
     83B  TYR*     4.1    22.2    -      +       -      -
     85B  GLY*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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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