Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 4GGA


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 VAL 370 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  TRP*     3.5     8.4    -      -       -      -
    364A  CYS*     2.9    37.3    +      -       +      +
    367A  GLN*     3.0    35.3    +      -       +      +
    368A  SER      3.3     0.6    -      -       -      -
    369A  ASN*     1.3    83.0    -      -       +      +
    371A  LEU*     1.3    62.3    +      -       -      +
    384A  ILE*     3.7    27.8    -      -       +      -
    385A  TRP      3.3     6.3    -      -       -      +
    386A  ASN*     5.2     2.5    -      -       +      -
    393A  LEU*     4.5    10.1    -      -       +      -
    407A  TRP*     3.8    20.9    -      -       +      -
    430A  TYR*     4.0    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 371 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  ALA*     3.9    22.7    -      -       +      -
    333A  VAL*     4.2     6.3    -      -       +      -
    335A  VAL*     4.1    19.5    -      -       +      -
    351A  PHE*     4.9     0.4    -      -       +      -
    361A  VAL*     4.1     2.7    -      -       +      -
    362A  ALA      3.6    23.1    -      -       -      +
    363A  TRP*     3.8    26.5    -      -       +      -
    369A  ASN      3.8     0.4    +      -       -      -
    370A  VAL*     1.3    77.4    -      -       -      +
    372A  ALA*     1.3    64.3    +      -       -      +
    373A  THR*     3.9    21.1    -      -       +      -
    384A  ILE*     3.4     2.9    -      -       -      +
    385A  TRP*     2.8    50.2    +      -       +      -
    387A  VAL*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 372 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  VAL*     3.5     0.9    +      -       -      -
    362A  ALA*     2.8    39.3    +      -       -      +
    371A  LEU*     1.3    75.0    -      -       -      +
    373A  THR*     1.3    65.7    +      -       -      +
    382A  ILE*     5.1     0.7    -      -       +      -
    383A  ARG      3.4     3.8    -      -       -      -
    384A  ILE*     3.5    23.1    -      -       +      -
    405A  ILE*     4.2    12.6    -      -       +      +
    407A  TRP*     3.6    19.9    -      -       +      +
    414A  LEU*     3.8    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 373 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  VAL*     4.0    16.8    -      -       +      -
    354A  HIS*     2.8    28.1    +      -       -      -
    358A  VAL*     3.8     7.4    -      -       +      -
    360A  ALA      3.1    11.2    -      -       -      +
    361A  VAL*     4.4     8.5    -      -       +      -
    371A  LEU*     3.9    19.5    -      -       +      -
    372A  ALA*     1.3    79.7    -      -       -      +
    374A  GLY*     1.3    59.9    +      -       -      +
    382A  ILE*     3.3     4.3    -      -       -      -
    383A  ARG      2.8    33.8    +      -       -      -
    385A  TRP*     2.9    26.3    +      -       -      +
    405A  ILE*     3.6     7.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  HIS*     3.9     4.3    -      -       -      -
    357A  ALA      3.7     0.3    -      -       -      +
    358A  VAL*     3.5    20.9    -      -       -      +
    359A  LYS      3.7     0.2    +      -       -      -
    360A  ALA*     2.9    30.1    +      -       -      +
    373A  THR*     1.3    76.6    -      -       -      +
    375A  GLY*     1.3    61.3    +      -       -      -
    381A  HIS      3.3     7.6    -      -       -      -
    382A  ILE*     4.5     0.2    -      -       -      -
    402A  VAL*     3.7    17.4    -      -       -      +
    405A  ILE*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  HIS*     3.6     9.4    +      -       -      -
    356A  GLY      4.7     0.7    -      -       -      -
    357A  ALA      3.3     8.5    -      -       -      -
    374A  GLY*     1.3    73.0    -      -       -      -
    376A  GLY*     1.3    68.0    +      -       -      +
    379A  ASP*     3.4    19.3    -      -       -      -
    380A  ARG      3.7     5.1    +      -       -      -
    381A  HIS      3.0    12.1    +      -       -      -
    402A  VAL*     3.0    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