Contacts of the strand formed by residues 96 - 104 (chain A) in PDB entry 4OIR


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 THR 96 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     4.4     1.8    -      -       -      -
     94A  LEU*     3.3    14.1    +      -       +      +
     95A  GLN*     1.3    85.1    -      -       +      +
     97A  VAL*     1.3    75.5    +      -       -      +
     98A  THR*     4.9     2.3    +      -       -      -
    143A  ARG*     4.0    19.5    +      -       -      +
    144A  VAL      3.5     7.8    +      -       -      -
    145A  ASP*     3.3    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PHE*     3.5    28.5    -      -       +      -
     94A  LEU*     3.5    24.2    -      -       +      -
     96A  THR*     1.3    84.1    +      -       -      +
     98A  THR*     1.3    68.3    +      -       -      +
     99A  LEU*     3.5    26.9    +      -       +      -
    117A  VAL*     4.5    13.0    -      -       +      -
    120A  VAL*     3.7    17.5    -      -       +      -
    142A  VAL      3.7     0.7    -      -       -      +
    143A  ARG*     3.7     1.4    -      -       -      -
    144A  VAL*     2.9    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  THR*     4.9     2.3    +      -       -      -
     97A  VAL*     1.3    78.9    +      -       -      +
     99A  LEU*     1.3    62.2    +      -       -      +
    100A  LEU*     3.7    27.6    +      -       +      +
    117A  VAL*     4.7     6.6    -      -       -      +
    141A  GLU*     4.2    13.0    -      -       +      +
    142A  VAL      3.1    16.1    +      -       -      +
    143A  ARG*     4.4     5.4    -      -       -      +
    160A  ASP*     3.7    21.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LEU*     3.9    21.3    -      -       +      -
     87A  VAL*     4.5    11.4    -      -       +      -
     97A  VAL*     3.5    26.4    +      -       +      +
     98A  THR*     1.3    72.3    -      -       -      +
    100A  LEU*     1.3    60.4    +      -       -      +
    114A  PHE*     3.5    45.6    -      -       +      -
    115A  LEU      5.1     4.7    -      -       -      +
    117A  VAL*     4.9     7.6    -      -       +      -
    120A  VAL*     4.3    15.7    -      -       +      -
    122A  ILE*     4.3    13.5    -      -       +      -
    140A  MET      4.0     0.2    -      -       -      +
    141A  GLU*     3.5     4.3    -      -       -      -
    142A  VAL*     2.9    42.1    +      -       +      +
    144A  VAL*     4.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  THR*     3.8    20.9    -      -       +      +
     99A  LEU*     1.3    82.8    -      -       -      +
    101A  LEU*     1.3    62.0    +      -       -      +
    102A  LYS*     5.9     8.1    -      -       -      +
    114A  PHE*     3.4     4.2    -      -       -      -
    115A  LEU*     2.9    58.4    +      -       +      +
    117A  VAL*     5.8     1.1    -      -       +      +
    140A  MET      3.7     4.0    -      -       -      +
    141A  GLU*     3.8    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  LEU*     1.3    74.6    -      -       -      +
    102A  LYS*     1.3    65.2    +      -       -      +
    103A  ALA*     3.9    17.3    -      -       +      +
    109A  VAL*     3.7    34.1    -      -       +      -
    110A  LYS      4.3     5.6    -      -       -      +
    113A  ASP*     4.2    15.0    -      -       +      +
    114A  PHE*     3.7    38.3    -      -       +      -
    115A  LEU*     5.3     0.4    -      -       -      -
    129A  ILE*     4.1     6.5    -      -       +      -
    138A  LEU*     4.2    17.5    -      -       +      +
    139A  ASN*     3.1     8.0    -      -       -      +
    140A  MET*     2.9    50.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  LEU*     5.9     9.1    -      -       -      +
    101A  LEU*     1.3    75.3    -      -       -      +
    103A  ALA*     1.3    63.6    +      -       -      +
    113A  ASP*     4.8     7.6    +      -       -      +
    115A  LEU*     5.5    15.5    -      -       +      +
    138A  LEU      3.7     3.4    -      -       -      +
    139A  ASN*     3.3    39.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  LEU*     3.9    12.8    -      -       +      +
    102A  LYS*     1.3    77.3    -      -       -      +
    104A  GLU*     1.3    68.5    +      -       -      +
    107A  LYS*     4.0    14.1    -      -       +      +
    109A  VAL*     3.7    31.6    -      -       +      -
    113A  ASP*     5.4     1.6    -      -       +      -
    132A  LEU*     3.9     3.1    -      -       +      -
    137A  ARG*     3.8     2.9    -      -       -      +
    138A  LEU      2.9    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ALA*     1.3    80.9    -      -       -      +
    105A  GLY*     1.3    71.2    +      -       -      +
    106A  PRO      4.5     0.5    -      -       -      +
    107A  LYS*     3.6    16.8    -      -       -      +
    132A  LEU*     3.9     3.5    -      -       -      +
    135A  GLY      6.0     0.7    -      -       -      -
    136A  GLY      3.3    13.5    -      -       -      +
    137A  ARG*     3.5    27.0    +      -       +      -
----------------------------------------------------------
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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