Contacts of the strand formed by residues 93 - 99 (chain B) in PDB entry 4GKH


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 ASP 93 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  HIS*     2.8    32.0    +      -       -      +
     57B  GLY      3.4     4.5    -      -       -      -
     58B  LYS*     3.8    13.8    -      -       -      +
     62B  ALA*     4.0     4.0    -      -       -      +
     88B  ILE      4.6     0.4    -      -       -      -
     89B  ARG*     3.2     3.3    -      -       -      -
     90B  THR*     2.9    45.5    +      -       -      +
     92B  ASP*     1.3    92.5    +      -       -      +
     94B  ALA*     1.3    60.6    +      -       -      +
     95B  TRP*     4.1    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  LYS      3.6     0.7    -      -       -      +
     56B  HIS*     3.3     7.3    -      -       -      -
     57B  GLY      2.9    31.9    +      -       -      -
     62B  ALA*     3.6    27.4    -      -       -      +
     65B  VAL*     4.1     8.2    -      -       +      +
     66B  THR*     4.0     4.7    -      -       -      +
     87B  PHE*     4.0    11.2    -      -       +      -
     88B  ILE      3.3     7.6    -      -       -      +
     89B  ARG*     3.7    12.8    -      -       -      -
     93B  ASP*     1.3    75.2    -      -       -      +
     95B  TRP*     1.3    62.9    +      -       -      +
     96B  LEU      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     4.4    17.6    -      -       +      +
     41B  TYR*     4.5    12.6    -      +       -      -
     54B  LEU*     3.8    39.3    -      -       +      -
     55B  LYS      3.3     4.3    -      -       -      -
     56B  HIS*     3.3    58.1    +      +       +      -
     86B  HIS      4.0     0.6    -      -       -      +
     87B  PHE*     3.2     8.7    -      -       -      -
     88B  ILE*     2.9    54.9    +      -       +      +
     90B  THR*     5.9     0.9    -      -       +      -
     93B  ASP*     4.1    12.6    -      -       +      +
     94B  ALA*     1.3    79.7    -      -       -      +
     96B  LEU*     1.3    60.5    +      -       -      +
     97B  LEU      4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  PHE      3.5     2.1    -      -       -      +
     54B  LEU*     3.3     5.4    -      -       -      +
     55B  LYS*     2.8    45.9    +      -       +      +
     65B  VAL*     3.6    28.9    -      -       +      +
     68B  GLU*     3.8    33.4    -      -       +      +
     69B  MSE      3.9    16.6    -      -       +      +
     72B  LEU*     4.0     9.2    -      -       +      -
     84B  ILE*     4.3     9.6    -      -       +      -
     86B  HIS      3.8     5.8    -      -       -      +
     87B  PHE*     3.9    17.3    -      -       +      -
     95B  TRP*     1.3    73.2    -      -       -      +
     97B  LEU*     1.3    62.4    +      -       -      +
     98B  THR*     3.9    20.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     4.1     7.6    -      -       +      -
     22B  ASP*     4.0    23.1    -      -       +      -
     23B  LEU*     3.7    33.4    -      -       +      -
     43B  LEU*     4.6     3.4    -      -       +      -
     52B  LEU*     4.0    25.8    -      -       +      -
     53B  PHE      3.4    13.7    -      -       -      +
     54B  LEU*     4.0    18.4    -      -       +      -
     84B  ILE*     3.8     1.6    -      -       -      +
     85B  LYS*     2.8    44.5    +      -       +      -
     86B  HIS*     2.8    25.8    +      -       +      +
     95B  TRP      4.2     0.2    -      -       -      -
     96B  LEU*     1.3    71.9    -      -       -      +
     98B  THR*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  LEU*     3.3     8.8    -      -       -      +
     53B  PHE*     2.8    48.7    +      -       -      +
     72B  LEU*     4.1    18.6    -      -       +      -
     82B  PRO*     4.0    14.6    -      -       +      +
     83B  THR      3.2    14.4    -      -       -      +
     84B  ILE*     4.3     3.8    -      -       -      -
     85B  LYS*     4.2     1.6    -      -       -      +
     96B  LEU*     3.9    27.1    +      -       +      -
     97B  LEU*     1.3    80.8    -      -       -      +
     99B  THR*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  PRO*     5.3    10.3    -      -       +      -
     51B  GLU      4.5     0.9    -      -       -      -
     52B  LEU*     3.8    20.2    -      -       +      -
     53B  PHE*     4.9     1.3    -      -       -      -
     82B  PRO*     3.5    19.8    -      -       -      +
     83B  THR*     3.0    43.1    +      -       +      +
     85B  LYS*     4.8    11.7    -      -       +      -
     98B  THR*     1.3    76.8    +      -       -      +
    100B  ALA*     1.3    68.0    +      -       -      +
    101B  ILE*     3.7     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