Contacts of the strand formed by residues 116 - 121 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47H  LYS*     2.9    20.1    +      -       -      -
     48H  THR      2.9    21.3    -      -       -      +
     49H  THR*     3.5    28.9    -      -       +      -
     88H  VAL*     3.7    19.3    -      -       +      -
     89H  PHE      3.5     1.8    -      -       -      -
     90H  ASP*     3.4    34.3    -      -       +      -
     97H  LEU*     5.1     9.6    -      -       +      -
    111H  GLU*     5.9     1.6    -      -       -      -
    112H  PHE      4.5     2.5    -      -       -      -
    113H  GLY*     2.7    25.3    +      -       -      +
    114H  HIS      4.5     1.6    -      -       -      +
    115H  GLU*     1.3    98.7    -      -       +      +
    117H  ASP*     1.3    70.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 117 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44H  LYS*     5.3     5.0    -      -       -      +
     45H  SER      4.1     4.0    -      -       -      -
     46H  ALA*     3.8    16.3    +      -       -      +
     47H  LYS*     3.7    11.8    +      -       -      +
     48H  THR      4.0     2.5    -      -       -      -
     88H  VAL*     3.4     1.7    -      -       -      -
     89H  PHE*     3.0    36.8    +      -       +      +
    114H  HIS      5.4     1.0    -      -       -      +
    115H  GLU      4.9     1.9    -      -       -      +
    116H  PHE*     1.3    88.5    -      -       -      +
    118H  LEU*     1.3    60.0    +      -       -      +
    119H  TYR*     3.2    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43H  LYS      3.6     0.2    -      -       -      +
     44H  LYS*     3.1     6.8    -      -       -      +
     45H  SER*     2.7    58.3    +      -       -      +
     48H  THR*     3.7    26.2    +      -       +      +
     49H  THR*     5.0     4.0    -      -       -      +
     50H  LEU*     5.0     7.6    -      -       +      +
     86H  ALA*     4.6     7.9    -      -       +      -
     87H  PHE      4.0     4.5    -      -       -      +
     88H  VAL*     3.4    25.1    -      -       +      -
     99H  PHE*     5.1     2.7    -      -       +      -
    102H  ASN*     6.5     0.2    -      -       -      -
    103H  SER*     4.6     4.3    -      -       -      +
    110H  LYS*     4.5    13.0    -      -       +      -
    117H  ASP*     1.3    71.4    -      -       -      +
    119H  TYR*     1.3    69.2    +      -       -      +
    120H  GLU*     3.9    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 119 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  ILE*     4.1    25.9    -      -       +      +
     42H  PHE*     3.6    23.0    -      -       +      -
     43H  LYS      3.8     3.1    -      -       -      -
     44H  LYS*     4.5    15.9    -      -       +      -
     67H  ALA*     4.0    17.2    -      -       +      +
     86H  ALA*     3.2     3.2    -      -       -      -
     87H  PHE*     2.9    75.6    +      +       +      +
     89H  PHE*     4.3     6.8    -      -       +      -
    117H  ASP*     3.2    48.8    +      -       +      +
    118H  LEU*     1.3    76.7    -      -       -      +
    120H  GLU*     1.3    63.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42H  PHE*     3.4     4.0    -      -       -      -
     43H  LYS*     2.9    59.0    +      -       -      +
     45H  SER*     4.7     4.0    +      -       -      -
     85H  LYS      3.9     4.3    -      -       -      +
     86H  ALA*     3.9    10.8    -      -       +      -
    102H  ASN*     3.5     8.2    -      -       +      +
    103H  SER*     2.4    45.7    +      -       -      +
    104H  MET*     3.8     7.3    -      -       -      +
    110H  LYS*     5.4     2.1    +      -       -      -
    118H  LEU*     3.9    25.4    -      -       +      +
    119H  TYR*     1.3    75.0    -      -       -      +
    121H  ASN*     1.3    65.1    +      -       -      +
    122H  LYS      3.2     1.2    +      -       -      -
    125H  ILE*     3.8    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 121 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41H  GLU      4.9     1.4    -      -       -      +
     42H  PHE*     3.8    26.5    -      -       +      -
     74H  CYS*     4.6     6.9    +      -       -      -
     75H  THR*     5.4     3.4    +      -       -      +
     84H  CYS      3.4    16.5    +      -       -      +
     85H  LYS*     2.8    30.8    +      -       -      +
    102H  ASN*     5.0     0.2    +      -       -      -
    120H  GLU*     1.3    70.1    -      -       -      +
    122H  LYS*     1.3    63.9    +      -       -      +
    123H  ASP*     2.7    46.4    +      -       -      +
    124H  TYR*     2.9    24.0    +      -       +      +
    125H  ILE*     3.5    10.1    -      -       -      +
----------------------------------------------------------
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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