Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 4OI0


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 ARG 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LYS*     3.6    29.8    -      -       -      +
    114A  GLY      3.8     8.5    +      -       -      +
    115A  PRO*     1.3    80.0    -      -       -      +
    117A  LEU*     1.3    60.6    +      -       -      +
    208A  ALA*     6.2     0.6    -      -       -      +
    212A  ASN*     2.9    30.8    +      -       -      +
    215A  ILE*     3.3    25.7    -      -       -      +
    225A  GLY*     5.6     0.6    -      -       -      -
    226A  MET*     3.4    42.7    -      -       +      +
    228A  ILE*     4.9     0.7    -      -       +      -
    249A  PHE*     2.8    33.4    +      -       -      +
    250A  GLU*     4.1    14.1    +      -       -      +
    251A  VAL*     3.7    18.6    -      -       +      +
    252A  ASP*     2.9    34.8    +      -       -      +
    253A  VAL*     3.1     9.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ILE*     3.6    30.1    -      -       +      -
     94A  MET*     4.1    27.4    -      -       +      -
    115A  PRO*     6.4     0.2    -      -       +      -
    116A  ARG*     1.3    74.2    -      -       -      +
    118A  LEU*     1.3    58.5    +      -       -      +
    119A  LEU*     3.9    23.3    -      -       +      -
    134A  LEU*     4.2    12.8    -      -       +      -
    226A  MET      2.8    14.9    +      -       -      +
    227A  ILE*     3.6     5.5    -      -       +      -
    228A  ILE*     2.8    38.7    +      -       -      +
    251A  VAL*     4.7     0.2    -      -       -      -
    253A  VAL*     3.3    24.5    -      -       +      -
    255A  ILE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ARG      4.3     0.2    -      -       -      -
    117A  LEU*     1.3    75.4    -      -       -      +
    119A  LEU*     1.3    59.0    +      -       -      +
    120A  VAL*     3.8    22.0    -      -       +      -
    228A  ILE*     3.6    35.0    -      -       +      +
    230A  THR*     3.7    17.9    -      -       +      -
    242A  ILE*     3.9    24.7    -      -       +      +
    245A  ALA*     4.4    11.4    -      -       +      -
    246A  ALA*     4.0    19.1    -      -       +      +
    251A  VAL*     4.1    11.0    -      -       +      +
    253A  VAL      2.9    13.3    +      -       -      +
    254A  VAL*     3.4    14.0    -      -       +      +
    255A  ILE      2.8    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  LEU*     3.9    10.7    -      -       +      -
    118A  LEU*     1.3    71.0    -      -       -      +
    120A  VAL*     1.3    53.6    +      -       -      +
    127A  LYS*     3.7    19.6    -      -       +      +
    130A  VAL*     3.7    24.9    -      -       +      -
    131A  SER*     3.5    42.6    -      -       -      +
    134A  LEU*     4.3     4.9    -      -       +      -
    227A  ILE*     3.9    15.3    -      -       +      -
    228A  ILE      2.9    13.4    +      -       -      +
    229A  ASN*     4.8     1.8    -      -       -      +
    230A  THR*     2.8    34.0    +      -       -      +
    255A  ILE*     3.6    17.3    -      -       +      -
    257A  LEU*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  LEU*     3.8    28.9    -      -       +      -
    119A  LEU*     1.3    80.2    -      -       -      +
    121A  GLY*     1.3    59.6    +      -       -      +
    127A  LYS*     3.7     6.7    -      -       -      -
    230A  THR*     3.6    14.1    -      -       +      +
    242A  ILE*     3.8    24.0    -      -       +      -
    254A  VAL*     3.9     9.0    -      -       +      -
    255A  ILE      2.9    10.9    +      -       -      +
    256A  VAL*     3.7    28.0    -      -       +      -
    257A  LEU*     2.9    31.2    +      -       -      +
    262A  LEU*     3.9    11.4    -      -       +      -
    266A  LEU*     4.1     5.8    -      -       +      -
----------------------------------------------------------
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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