Contacts of the strand formed by residues 88 - 94 (chain B) in PDB entry 1AXS


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 ALA 88 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LYS*     3.8    17.0    -      -       +      -
     39B  GLN      3.2    19.3    -      -       -      +
     40B  ARG*     3.5    15.9    -      -       +      +
     41B  PRO*     5.1     3.6    -      -       -      -
     86B  ASP      3.1     7.1    +      -       -      +
     87B  SER*     1.3    77.7    -      -       -      +
     89B  VAL*     1.3    66.0    +      -       -      +
     90B  TYR*     3.5     9.7    -      -       +      -
    108B  SER*     4.5     0.9    -      -       -      -
    109B  VAL      2.9    27.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  VAL      3.9     0.5    -      -       -      +
     38B  LYS*     3.8     0.3    -      -       -      -
     39B  GLN*     3.0    40.9    +      -       -      +
     88B  ALA*     1.3    78.1    -      -       -      +
     90B  TYR*     1.3    65.2    +      -       -      +
     91B  TYR*     3.5    36.4    -      -       +      +
    105B  GLN      5.1     0.4    -      -       -      +
    106B  GLY*     3.8     4.0    -      -       -      -
    107B  THR      3.5    19.1    -      -       -      +
    108B  SER*     4.2    19.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLU*     2.7    21.7    -      -       -      +
     20B  ILE*     3.7    22.7    -      -       +      -
     36B  TRP*     5.1     1.1    -      -       +      -
     37B  VAL      3.6     2.0    -      -       -      -
     38B  LYS*     3.6    32.2    -      -       +      -
     48B  ILE*     3.7    32.8    -      -       +      -
     63B  PHE*     5.6     1.0    -      +       -      -
     80B  MET*     3.8    11.7    -      -       +      -
     82B  LEU*     3.6    27.6    -      -       +      +
     86B  ASP*     2.5    37.1    +      -       -      +
     88B  ALA*     3.5    18.6    -      -       +      -
     89B  VAL*     1.3    73.7    -      -       -      +
     91B  TYR*     1.3    56.9    +      -       -      +
    106B  GLY*     3.1     1.0    -      -       -      -
    107B  THR*     2.9    23.9    +      -       -      +
    109B  VAL*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLN*     3.7     7.3    +      -       -      -
     42A  LYS      4.1     3.3    +      -       -      -
     43A  SER*     3.2    32.6    -      -       -      -
     44A  PRO*     3.7    14.8    -      -       +      -
      6B  GLU*     3.3     6.1    -      -       -      +
     36B  TRP*     3.3    11.0    -      -       -      -
     37B  VAL*     2.9    50.2    +      -       +      +
     39B  GLN*     3.0    38.0    +      -       +      -
     45B  LEU*     4.6     1.1    -      -       +      -
     89B  VAL*     3.5    21.8    -      -       +      +
     90B  TYR*     1.3    75.1    -      -       -      +
     92B  CYS*     1.3    61.9    -      -       -      +
    103B  TRP*     3.9    22.4    -      +       +      -
    104B  GLY      3.9     5.2    -      -       -      +
    105B  GLN      3.5    13.4    +      -       -      -
    106B  GLY*     3.4    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.8     8.0    -      -       -      +
      6B  GLU*     3.3    21.7    +      -       -      -
     22B  CYS*     2.0    48.2    -      -       -      -
     34B  ILE*     4.2     2.0    -      -       +      -
     35B  GLU      3.1     9.6    -      -       -      +
     36B  TRP*     3.6    24.7    -      -       +      -
     37B  VAL*     5.8     0.4    -      -       -      -
     91B  TYR*     1.3    75.6    -      -       -      +
     93B  ALA*     1.3    63.2    +      -       -      +
    103B  TRP*     3.8     0.2    -      -       -      -
    104B  GLY      2.9    25.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.7     4.0    -      -       -      -
     34B  ILE*     3.5     4.8    -      -       -      +
     35B  GLU*     2.7    41.9    +      -       +      +
     37B  VAL*     5.4     1.3    -      -       +      -
     92B  CYS*     1.3    77.9    -      -       -      +
     94B  ARG*     1.3    63.4    +      -       -      +
    101B  ASP*     4.7     0.4    -      -       +      -
    102B  TYR      3.0    16.4    -      -       -      +
    103B  TRP*     3.9    27.1    -      -       +      -
   1004B  HOP      4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  VAL*     3.4    19.8    -      -       +      +
      4B  LEU*     3.5    12.0    -      -       +      +
     27B  TYR*     3.3    60.1    -      -       +      +
     32B  PHE*     3.6    48.2    -      -       +      -
     33B  TRP      3.7     4.7    -      -       -      +
     34B  ILE*     4.5     2.9    -      -       +      -
     35B  GLU*     4.9     0.4    -      -       -      -
     93B  ALA*     1.3    71.8    -      -       -      +
     95B  GLY*     1.3    66.8    +      -       -      +
    100B  PHE*     4.2    17.4    -      -       -      -
    101B  ASP*     3.0    31.9    -      -       -      +
    102B  TYR*     2.8    47.2    +      -       +      +
   1001B  TYR*     5.8     1.0    -      -       -      +
   1002B  ASP*     4.5     1.8    +      -       -      +
   1003B  GLY      4.2     4.1    +      -       -      +
----------------------------------------------------------
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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