Contacts of the strand formed by residues 130 - 134 (chain A) in PDB entry 3I89


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 MET 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  ILE*     3.5     9.9    -      -       -      +
    125A  ASP*     3.4    29.5    +      -       +      -
    128A  CYS      3.2     2.2    -      -       -      -
    129A  ARG*     1.3    91.9    -      -       +      +
    131A  ILE*     1.3    62.7    +      -       -      +
    140A  PHE*     6.1     0.2    -      -       +      -
    142A  VAL*     3.7    22.2    -      -       +      -
    143A  ILE      3.5    10.8    -      -       -      +
    144A  PRO*     4.0     7.6    -      -       +      -
    145A  LEU*     3.4    13.6    -      -       -      +
    169A  PHE*     3.6    25.4    -      -       +      -
    176A  PRO*     3.6    21.5    -      -       +      -
    195A  VAL*     3.6    40.2    -      -       +      +
    197A  LEU*     4.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  PHE*     5.2     1.8    -      -       +      -
     78A  PHE*     3.6    45.8    -      -       +      -
     88A  ILE*     5.1     5.2    -      -       +      -
    123A  ILE      3.4    11.9    -      -       -      +
    124A  ILE*     3.8    18.6    -      -       +      -
    130A  MET*     1.3    82.3    -      -       -      +
    132A  GLY*     1.3    63.0    +      -       -      +
    133A  LEU*     3.5    24.7    -      -       +      +
    141A  LYS      4.2     0.3    -      -       -      +
    142A  VAL*     3.5     4.7    -      -       -      +
    143A  ILE*     2.8    51.7    +      -       +      +
    145A  LEU*     3.9    24.2    -      -       +      -
    152A  LEU*     5.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ILE*     2.7    51.4    +      -       -      +
    131A  ILE*     1.3    73.4    -      -       -      +
    133A  LEU*     1.3    66.2    +      -       -      +
    140A  PHE*     3.4    22.0    -      -       -      -
    141A  LYS      4.0     2.2    -      -       -      -
    142A  VAL*     4.8     0.9    -      -       -      -
    169A  PHE*     4.0     8.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE*     4.4    12.3    -      -       +      -
     80A  LEU*     4.3    19.5    -      -       +      -
    108A  VAL*     4.4     8.5    -      -       +      -
    121A  ILE      3.4     7.4    -      -       -      +
    122A  GLY*     3.6    14.8    -      -       -      -
    131A  ILE*     3.5    25.6    -      -       +      +
    132A  GLY*     1.3    90.6    -      -       -      +
    134A  ARG*     1.3    59.6    +      -       -      +
    135A  LEU*     3.5    26.2    -      -       +      -
    140A  PHE*     3.0    24.2    -      -       -      -
    141A  LYS*     3.2    40.7    +      -       +      +
    143A  ILE*     4.4    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  SER*     2.6    30.1    +      -       -      -
    117A  GLU      2.7    24.2    +      -       -      +
    118A  THR*     3.6     4.0    -      -       -      -
    119A  GLY      3.2    20.6    +      -       -      -
    120A  ILE*     3.5     5.2    -      -       -      -
    121A  ILE*     2.9    63.0    +      -       +      +
    133A  LEU*     1.3    75.3    -      -       -      +
    135A  LEU*     1.3    64.5    +      -       -      +
    136A  TYR      3.7    16.6    -      -       -      +
    137A  ASP*     4.5     2.6    +      -       -      +
    139A  LEU      4.4     7.9    -      -       -      +
    140A  PHE*     4.9     7.2    -      -       +      -
    159A  LEU*     5.5     6.1    -      -       +      -
    164A  VAL*     2.9    44.3    +      -       +      +
    167A  VAL*     5.2     7.2    -      -       +      -
----------------------------------------------------------
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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