Contacts of the strand formed by residues 78 - 83 (chain B) in PDB entry 1A1O


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 TYR 78 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  LEU*     3.7    29.4    -      -       +      -
     40B  LEU      3.1    15.9    -      -       -      +
     41B  LYS*     3.6    44.6    +      -       +      +
     46B  ILE*     4.1    10.1    -      -       +      -
     70B  PHE*     3.6    40.0    -      +       +      +
     71B  THR      3.8    18.8    +      -       -      -
     72B  PRO*     4.8     4.5    -      -       +      -
     73B  THR      5.5     0.4    -      -       -      -
     76B  ASP*     4.0    21.7    +      -       +      +
     77B  GLU*     1.3    82.9    -      -       -      +
     79B  ALA*     1.3    63.9    +      -       -      +
     94B  LYS*     3.6     4.2    -      -       -      +
     95B  TRP*     2.8    49.4    +      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     4.9     5.4    -      -       -      -
     23B  LEU*     5.0     2.2    -      -       -      +
     39B  LEU*     3.5     6.2    -      -       -      +
     40B  LEU*     2.7    45.1    +      -       +      +
     77B  GLU*     6.1     0.9    -      -       +      -
     78B  TYR*     1.3    77.7    -      -       -      +
     80B  CYS*     1.3    61.4    +      -       -      +
     92B  ILE*     3.8    19.5    -      -       +      -
     93B  VAL      3.2    14.6    -      -       -      +
     94B  LYS*     3.8    10.8    -      -       +      +
     95B  TRP      4.3     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ILE*     4.7     2.6    -      -       +      +
      9B  VAL*     3.5    17.7    -      -       +      +
     25B  CYS*     2.2    49.4    -      -       +      -
     37B  VAL*     3.5    20.0    -      -       -      -
     38B  ASP      3.3     6.1    -      -       -      -
     39B  LEU*     4.0     3.1    -      -       +      -
     79B  ALA*     1.3    75.6    -      -       -      +
     81B  ARG*     1.3    62.8    +      -       -      +
     82B  VAL*     4.0     9.7    +      -       -      +
     91B  LYS      3.6     1.6    -      -       -      +
     92B  ILE*     3.4     4.7    -      -       -      -
     93B  VAL*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  GLU      3.5     1.2    -      -       -      +
     37B  VAL*     3.3     4.2    -      -       -      -
     38B  ASP*     2.7    73.6    +      -       +      +
     40B  LEU*     4.1    31.1    -      -       +      +
     43B  GLY      5.2     4.8    +      -       -      -
     45B  ARG*     3.2    20.6    -      -       -      +
     79B  ALA      4.2     0.2    -      -       -      -
     80B  CYS*     1.3    71.5    -      -       -      +
     82B  VAL*     1.3    63.9    +      -       -      +
     83B  ASN*     6.1     0.4    -      -       +      -
     90B  PRO*     4.0    24.0    -      -       +      -
     91B  LYS      3.4     2.7    -      -       -      -
     92B  ILE*     3.7    30.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  PRO*     4.1    17.5    -      -       +      -
      7B  ILE*     3.7    28.9    -      -       +      -
     27B  VAL*     3.8    19.7    -      -       +      -
     35B  ILE*     3.6    32.3    -      -       +      -
     36B  GLU      3.1     3.8    -      -       -      +
     37B  VAL*     4.3     4.7    -      -       +      -
     80B  CYS*     4.0    15.0    -      -       -      -
     81B  ARG*     1.3    79.8    -      -       -      +
     83B  ASN*     1.3    66.4    +      -       -      +
     87B  LEU*     3.6     5.4    -      -       +      +
     90B  PRO*     3.4     4.1    -      -       -      +
     91B  LYS      2.9    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ILE*     3.4     5.7    -      -       -      +
     36B  GLU*     2.8    58.8    +      -       +      +
     81B  ARG*     6.1     0.7    -      -       +      -
     82B  VAL*     1.3    76.9    -      -       -      +
     84B  HIS*     1.3    71.9    +      -       -      +
     87B  LEU*     4.2     7.4    +      -       -      +
     89B  GLN      4.2     2.8    -      -       -      -
     90B  PRO*     3.5    39.1    -      -       +      +
----------------------------------------------------------
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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