Contacts of the strand formed by residues 49 - 58 (chain B) in PDB entry 2OV2


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 LYS 49 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  GLN*     5.2    16.6    -      -       -      -
     45B  MET*     3.4     4.1    -      -       -      -
     46B  VAL*     2.7    47.8    +      -       +      +
     47B  ASP*     3.9    13.2    -      -       +      +
     48B  GLY*     1.3    81.8    -      -       -      +
     50B  PRO*     1.3    75.2    -      -       +      +
     51B  VAL*     4.1     2.3    -      -       +      +
     74F  GLN*     5.8     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     4.1    24.2    -      -       +      +
      2B  GLN*     4.1    10.4    +      -       -      +
     43B  ASN*     5.5     6.1    -      -       +      +
     44B  VAL      3.4     7.0    -      -       -      +
     45B  MET*     3.8    20.8    -      -       +      -
     48B  GLY      4.4     0.9    -      -       -      +
     49B  LYS*     1.3    91.8    -      -       +      +
     51B  VAL*     1.3    62.9    +      -       -      +
     74F  GLN*     5.4     8.6    +      -       -      +
     38N  GLN*     4.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     4.2     0.7    -      -       -      -
      2B  GLN*     3.4    31.2    -      -       +      +
      4B  ILE*     3.9    31.2    -      -       +      -
     43B  ASN*     3.5     6.3    -      -       -      +
     44B  VAL*     2.7    41.2    +      -       +      +
     46B  VAL*     3.8    32.8    -      -       +      +
     49B  LYS*     4.1     2.5    -      -       +      +
     50B  PRO*     1.3    81.6    -      -       -      +
     52B  ASN*     1.3    70.9    +      -       -      +
     53B  LEU*     3.5     4.3    +      -       +      +
    173B  ILE*     5.5     0.7    -      -       +      -
    177B  LEU*     4.1     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.9    15.9    -      -       +      +
      2B  GLN      2.9    14.7    +      -       -      +
      3B  ALA*     3.3    12.6    -      -       +      +
      4B  ILE      2.8    27.9    +      -       -      +
     41B  SER*     4.3    12.2    -      -       -      -
     42B  ALA      3.4     7.3    +      -       -      +
     43B  ASN*     3.7    15.0    -      -       -      +
     51B  VAL*     1.3    71.1    -      -       -      +
     53B  LEU*     1.3    71.1    +      -       -      +
     54B  GLY*     3.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ILE*     3.8    27.6    -      -       +      +
      6B  CYS*     4.7     4.7    -      -       +      -
     23B  TYR*     3.9    34.5    -      -       +      +
     40B  TYR      4.1     0.2    -      -       -      +
     41B  SER*     3.4     5.2    -      -       -      -
     42B  ALA*     2.7    50.5    +      -       +      +
     44B  VAL*     4.4    11.7    -      -       +      -
     51B  VAL*     3.5     5.7    +      -       +      +
     52B  ASN*     1.3    76.1    +      -       -      +
     54B  GLY*     1.3    57.8    +      -       -      +
     55B  LEU*     4.0    26.6    -      -       +      +
    169B  PHE*     5.1     4.7    -      -       +      -
    172B  ALA*     6.6     0.2    -      -       +      -
    173B  ILE*     4.3    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ILE      2.7    16.2    +      -       -      +
      5B  LYS*     4.8     0.7    -      -       -      -
      6B  CYS*     2.8    33.1    +      -       -      +
     39B  ASN*     5.4     1.3    -      -       -      -
     40B  TYR      3.8     4.5    -      -       -      -
     41B  SER*     4.7     2.9    -      -       -      -
     52B  ASN*     3.7     3.1    +      -       -      -
     53B  LEU*     1.3    71.9    -      -       -      +
     55B  LEU*     1.3    60.2    +      -       -      +
     56B  TRP*     3.6    13.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  CYS*     3.4    26.2    -      -       +      +
     20B  LEU*     4.1    30.3    -      -       +      -
     23B  TYR*     4.9     4.5    -      -       +      -
     24B  THR*     3.5    31.9    -      -       +      -
     38B  ASP      4.0     0.2    -      -       -      +
     39B  ASN*     3.3     5.8    +      -       -      +
     40B  TYR*     2.8    59.8    +      -       +      +
     42B  ALA*     5.2     4.3    -      -       +      -
     53B  LEU*     4.0    25.8    -      -       +      +
     54B  GLY*     1.3    74.6    -      -       -      +
     56B  TRP*     1.3    63.6    +      -       -      +
     57B  ASP      3.8     1.5    +      -       -      -
    169B  PHE*     4.2    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LYS*     3.6    44.0    -      -       +      +
      6B  CYS      3.0    12.4    +      -       -      +
      7B  VAL*     3.7    15.7    -      -       +      -
      8B  VAL*     3.1    28.1    +      -       -      +
     20B  LEU*     4.8     1.8    -      -       -      -
     37B  PHE*     3.4    25.8    -      +       +      -
     38B  ASP      3.9     4.7    -      -       -      -
     39B  ASN*     3.2    19.7    -      -       -      +
     54B  GLY*     3.6    21.5    -      -       -      -
     55B  LEU*     1.3    77.6    -      -       -      +
     57B  ASP*     1.3    60.4    +      -       -      +
     58B  THR*     3.7     3.7    +      -       -      +
     70B  LEU      5.1     0.4    -      -       -      -
     71B  SER*     4.0    11.9    -      -       -      -
      1F  MET*     3.7    36.1    -      -       +      +
     36J  PRO*     5.7     3.4    -      -       +      -
     39J  TRP*     4.0    22.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with ASP 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  VAL*     4.7     1.4    -      -       -      +
     16B  LYS*     3.9    16.5    -      -       -      +
     17B  THR*     2.7    31.4    +      -       -      +
     20B  LEU*     3.7    25.4    -      -       +      +
     35B  THR*     3.5    12.6    +      -       -      +
     37B  PHE*     3.3     5.4    -      -       -      -
     38B  ASP*     2.9    37.6    +      -       +      +
     40B  TYR*     2.8    28.3    +      -       +      +
     55B  LEU      3.8     1.0    +      -       -      -
     56B  TRP*     1.3    69.8    -      -       -      +
     58B  THR*     1.3    66.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     3.9    17.7    -      -       +      -
      8B  VAL      2.7    26.2    +      -       -      +
      9B  VAL*     3.7    13.7    -      -       +      +
     10B  GLY      5.0     0.2    +      -       -      -
     16B  LYS*     3.5    16.1    -      -       -      -
     35B  THR*     3.8    13.9    -      -       -      +
     36B  VAL      4.7     0.7    -      -       -      -
     37B  PHE*     4.6     5.2    -      -       +      -
     56B  TRP      3.9     9.4    -      -       -      +
     57B  ASP*     1.3    82.3    +      -       -      +
     59B  ALA*     1.3    62.2    +      -       -      +
     60B  GLY      3.7     0.5    +      -       -      -
     68B  ARG*     3.8    26.0    -      -       +      +
     71B  SER*     4.0    20.4    -      -       -      +
    200B  GCP      4.1     0.7    +      -       -      -
----------------------------------------------------------
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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