Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 1GMO


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 PHE 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LYS*     2.7    38.1    +      -       -      -
     48A  THR      2.8    24.5    +      -       -      +
     49A  THR*     3.6    28.3    -      -       +      -
     88A  VAL*     4.0    11.7    -      -       +      -
     89A  PHE      3.7     0.2    -      -       -      -
     90A  ASP*     3.3    31.0    -      -       +      -
     93A  ARG*     5.9     7.4    -      -       -      -
     95A  GLN*     5.9     0.2    -      -       -      -
     97A  LEU*     5.6     7.4    -      -       +      -
    112A  PHE      5.3     0.4    -      -       -      -
    113A  GLY*     3.4    11.4    +      -       -      +
    114A  HIS      3.3     3.1    -      -       -      +
    115A  GLU*     1.3   119.5    -      -       +      +
    117A  ASP*     1.3    56.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LYS*     3.8    22.7    +      -       +      -
     45A  SER      4.1     1.8    -      -       -      -
     46A  ALA*     3.4     9.3    -      -       -      +
     47A  LYS      3.2    13.2    +      -       -      -
     48A  THR      3.6     3.1    -      -       -      -
     88A  VAL*     3.2     6.3    -      -       -      +
     89A  PHE*     3.1    40.9    +      -       +      +
     91A  LYS*     6.1     1.7    -      -       -      +
    114A  HIS      5.7     0.3    -      -       -      +
    115A  GLU      5.8     0.4    -      -       -      -
    116A  PHE*     1.3    81.0    -      -       -      +
    118A  LEU*     1.3    61.1    +      -       -      +
    119A  TYR*     3.5    21.5    +      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     43A  LYS      3.4     0.9    -      -       -      +
     44A  LYS*     3.2     2.6    -      -       -      -
     45A  SER*     2.7    56.9    +      -       -      +
     48A  THR*     3.6    23.0    +      -       +      +
     50A  LEU*     3.8    39.0    -      -       +      -
     86A  ALA*     4.5     2.9    -      -       +      -
     87A  PHE      3.7     4.5    -      -       -      +
     88A  VAL*     3.7    21.3    -      -       +      -
    103A  SER*     4.5     4.5    -      -       -      -
    110A  LYS*     5.9     0.7    -      -       +      -
    117A  ASP*     1.3    69.4    -      -       -      +
    119A  TYR*     1.3    85.8    +      -       -      +
    120A  GLU*     4.0    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ILE*     3.1    42.5    -      -       +      +
     42A  PHE*     4.1    16.0    -      -       +      -
     43A  LYS      3.7     3.4    -      -       -      -
     44A  LYS*     2.9    44.3    +      -       +      -
     67A  ALA*     4.3    10.8    -      -       +      +
     86A  ALA*     3.3     3.3    -      -       -      +
     87A  PHE*     2.8    79.5    +      +       +      +
     89A  PHE*     5.3     2.2    -      -       +      -
    117A  ASP*     3.5    33.1    +      -       +      -
    118A  LEU*     1.3    81.0    -      -       -      +
    120A  GLU*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     3.2     8.6    -      -       -      -
     43A  LYS*     2.9    57.6    +      -       -      +
     45A  SER*     4.4     8.0    +      -       -      -
     85A  LYS      4.5     0.7    -      -       -      +
     86A  ALA*     3.9     8.3    -      -       +      -
    102A  ASN*     3.4    15.0    -      -       +      +
    103A  SER*     2.4    48.5    +      -       -      +
    104A  MET*     4.3     1.8    -      -       -      +
    118A  LEU*     4.0    18.4    -      -       +      -
    119A  TYR*     1.3    75.6    -      -       -      +
    121A  ASN*     1.3    63.8    +      -       -      +
    122A  LYS      3.4     0.7    +      -       -      -
    125A  ILE*     3.6    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  GLU      5.1     1.2    -      -       -      +
     42A  PHE*     3.6    24.6    -      -       +      -
     74A  CYS*     5.1     4.6    +      -       -      -
     75A  THR*     5.5     5.3    -      -       -      +
     84A  CYS      3.8    13.3    +      -       -      +
     85A  LYS      2.8    28.1    +      -       -      +
    120A  GLU*     1.3    69.9    -      -       -      +
    122A  LYS*     1.3    66.0    +      -       -      +
    123A  ASP*     2.8    30.3    +      -       -      +
    124A  TYR*     3.0    35.1    +      -       +      +
    125A  ILE*     3.8     7.4    +      -       -      +
----------------------------------------------------------
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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