Contacts of the strand formed by residues 42 - 45 (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 42 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  THR      2.9    29.4    -      -       -      -
     39A  ILE*     3.4    16.8    -      -       -      +
     40A  HIS*     3.2     8.6    -      -       -      +
     41A  GLU*     1.3    85.9    -      -       +      +
     43A  LYS*     1.3    60.8    +      -       -      +
     44A  LYS*     3.8     3.0    +      -       -      +
     71A  ALA*     3.9    16.6    -      -       +      -
     74A  CYS*     3.8    24.5    -      -       -      -
     75A  THR*     3.6    24.5    -      -       +      -
     85A  LYS      5.5     0.4    -      -       -      -
     86A  ALA*     5.5     0.2    -      -       -      -
     87A  PHE*     3.9    23.1    -      +       -      -
    119A  TYR*     4.1    19.3    -      +       +      -
    120A  GLU      3.2    26.5    -      -       -      +
    121A  ASN*     3.6    20.0    -      -       +      -
    122A  LYS*     4.1     7.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     1.3    70.5    -      -       -      +
     44A  LYS*     1.3    65.6    +      -       -      +
     45A  SER*     4.2    10.3    +      -       -      +
    104A  MET*     4.4     8.9    -      -       -      +
    118A  LEU      3.4     2.9    -      -       -      +
    119A  TYR*     4.5     1.1    -      -       -      -
    120A  GLU*     2.9    48.4    +      -       +      +
    122A  LYS*     4.6     4.6    -      -       +      +
    125A  ILE*     3.7    21.1    -      -       +      +
    137A  LYS*     3.0    28.8    +      -       -      +
    139A  THR*     3.6    28.7    -      -       +      -
    171A  ASP*     3.4    23.4    +      -       -      -
    173A  GLN*     6.3     0.2    -      -       -      -
    176A  TYR*     3.7    28.0    -      -       -      +
    178A  ARG*     4.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE      3.8     4.6    +      -       -      +
     43A  LYS*     1.3    80.0    -      -       -      +
     45A  SER*     1.3    66.3    +      -       -      +
     46A  ALA*     4.0     9.9    -      -       +      +
    117A  ASP*     3.8    19.2    +      -       -      -
    118A  LEU      3.2     4.0    -      -       -      -
    119A  TYR*     2.9    45.3    +      -       +      +
    174A  GLU*     5.2     7.8    -      -       -      +
    176A  TYR*     4.4     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  LYS*     4.2    10.9    +      -       -      -
     44A  LYS*     1.3    78.4    +      -       -      +
     46A  ALA*     1.3    69.0    +      -       -      +
     48A  THR*     3.1    15.6    +      -       -      -
    117A  ASP*     4.8     0.2    -      -       -      -
    118A  LEU*     2.7    45.9    +      -       -      +
    120A  GLU*     4.4    10.2    +      -       -      -
    173A  GLN*     6.1     2.3    -      -       -      +
----------------------------------------------------------
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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