Contacts of the strand formed by residues 62 - 69 (chain B) in PDB entry 3OEH


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 62 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  LEU*     3.9    29.6    -      -       +      -
     55B  VAL      3.2    14.4    -      -       -      +
     56B  GLU*     4.5    20.3    +      -       +      -
     57B  PHE*     4.4     3.9    -      -       -      -
     60B  GLY      3.6    13.9    +      -       -      +
     61B  VAL*     1.3    84.1    -      -       -      +
     63B  GLY*     1.3    59.4    +      -       -      +
     77B  LEU*     3.9     1.6    -      -       -      -
     78B  PHE*     2.8    31.1    +      -       -      +
     93B  THR*     6.0     0.7    -      -       -      +
    113B  LEU*     4.7    19.3    -      -       +      +
    115B  ASN*     4.9    15.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  LEU*     3.2    11.4    -      -       -      +
     55B  VAL*     3.0    32.9    +      -       -      +
     57B  PHE*     4.3     1.6    -      -       -      -
     62B  LYS*     1.3    76.6    -      -       -      +
     64B  MET*     1.3    60.3    +      -       -      -
     75B  ILE*     3.8    14.8    -      -       -      -
     76B  VAL      3.2    14.4    -      -       -      -
     77B  LEU*     4.4     0.2    -      -       -      -
     78B  PHE*     3.8     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  GLU*     4.0    26.0    -      -       +      -
     53B  GLU      3.5     3.1    -      -       -      -
     63B  GLY*     1.3    74.4    -      -       -      +
     65B  ALA*     1.3    62.8    +      -       -      +
     66B  LEU*     3.1    50.8    +      -       +      -
     75B  ILE*     3.2     6.9    -      -       -      +
     76B  VAL*     3.0    42.3    +      -       +      +
     78B  PHE*     4.0    19.3    -      -       +      -
     97B  VAL*     3.4    27.8    -      -       +      -
    246B  TYR*     5.5    16.4    -      -       +      +
    247B  LEU*     6.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ILE*     3.9    18.4    -      -       +      -
     50B  GLN      3.7    20.0    -      -       -      +
     51B  ALA*     4.0     0.9    -      -       -      -
     52B  GLU*     2.9    30.5    +      -       -      +
     53B  GLU      2.9    16.7    +      -       -      +
     64B  MET*     1.3    73.1    -      -       -      +
     66B  LEU*     1.3    62.6    +      -       -      +
     67B  ASN      3.8     0.2    -      -       -      -
     68B  LEU*     4.1     7.6    -      -       +      +
     73B  VAL*     4.0    14.6    -      -       +      -
     74B  GLY      3.7     5.4    -      -       -      -
     75B  ILE*     3.9     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  ALA*     5.4     4.0    -      -       -      +
     52B  GLU*     5.3     6.2    +      -       +      +
     64B  MET*     3.1    27.5    +      -       +      -
     65B  ALA*     1.3    75.2    -      -       -      +
     67B  ASN*     1.3    64.6    +      -       +      +
     68B  LEU*     4.1     4.1    +      -       -      +
     74B  GLY      2.9    12.6    +      -       -      +
     76B  VAL*     3.7    22.0    -      -       +      -
    283B  LEU*     5.1     2.2    -      -       +      -
    287B  LEU*     3.7    38.6    -      -       +      -
    289B  ARG*     4.3    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  ILE*     5.2     4.2    -      -       -      +
     66B  LEU*     1.3    88.1    -      -       +      +
     68B  LEU*     1.3    60.7    +      -       -      +
     69B  GLU*     2.8    31.0    +      -       +      +
     72B  GLN*     5.4     1.4    +      -       -      -
     73B  VAL*     3.6     2.6    -      -       -      +
     74B  GLY*     2.7    52.2    +      -       -      +
    287B  LEU*     4.8    16.8    -      -       -      +
    289B  ARG*     5.3     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ILE*     3.6    33.4    -      -       +      +
     50B  GLN      4.1     2.2    -      -       -      -
     51B  ALA*     3.6    39.5    -      -       +      +
     65B  ALA*     4.1    10.1    -      -       +      -
     66B  LEU      4.1     3.3    +      -       -      +
     67B  ASN*     1.3    71.4    -      -       -      +
     69B  GLU*     1.3    63.3    +      -       -      +
     70B  PRO*     4.7     1.4    -      -       -      +
     72B  GLN      4.5     1.1    -      -       -      -
     73B  VAL*     3.6    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  ASN*     2.8    27.3    -      -       +      +
     68B  LEU*     1.3    79.7    -      -       -      +
     70B  PRO*     1.4    80.3    -      -       +      +
     71B  GLY      3.3     2.6    +      -       -      -
     72B  GLN*     3.0    51.4    +      -       -      +
     73B  VAL*     5.6     0.9    -      -       -      +
----------------------------------------------------------
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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