Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 1GZD


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 THR 334 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327A  ILE*     5.6     1.6    -      -       -      +
    332A  CYS*     3.3     6.4    -      -       -      +
    333A  GLU*     1.3    91.7    -      -       +      +
    335A  HIS*     1.3    67.1    +      -       -      +
    376A  PRO*     3.9     4.9    -      -       -      +
    377A  ILE*     3.0    32.1    -      -       +      +
    379A  TRP*     3.2    21.7    +      -       +      +
    400A  MET      5.2     1.5    +      -       -      -
    401A  ILE*     3.7    19.9    -      -       -      +
    402A  PRO*     3.7    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  GLY*     5.8     6.1    -      -       -      -
    327A  ILE*     6.3     0.2    -      -       +      -
    334A  THR*     1.3    81.9    -      -       -      +
    336A  ALA*     1.3    67.8    +      -       -      +
    337A  MET*     4.1    18.6    -      -       +      +
    355A  ASP*     5.7     1.1    -      -       -      -
    376A  PRO*     4.1    19.1    -      -       +      -
    377A  ILE      3.0     2.8    +      -       -      +
    378A  VAL*     3.3    29.5    -      -       +      +
    379A  TRP*     3.3     6.3    +      -       -      -
    402A  PRO*     3.6    24.8    +      -       +      +
    403A  CYS      4.9     0.9    -      -       -      -
    404A  ASP*     2.9    42.5    +      -       -      -
    474A  ASN*     5.1     2.5    -      -       -      -
    496A  LYS*     3.7    24.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  HIS*     1.3    76.8    -      -       -      +
    337A  MET*     1.3    64.9    +      -       -      +
    338A  LEU*     3.9    18.4    -      -       +      -
    379A  TRP*     3.2    35.3    -      -       +      +
    394A  ILE*     5.2     0.4    -      -       +      -
    401A  ILE*     4.3     1.3    -      -       +      +
    402A  PRO      3.1     7.4    +      -       -      +
    403A  CYS*     3.5    21.0    -      -       -      -
    404A  ASP      2.9    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  HIS*     4.0    17.9    +      -       +      +
    336A  ALA*     1.3    76.5    -      -       -      +
    338A  LEU*     1.3    67.1    +      -       -      +
    339A  PRO*     3.2    14.4    -      -       +      +
    347A  PHE*     3.6    32.3    -      -       +      +
    348A  ALA*     4.1    16.0    -      -       +      +
    351A  PHE*     3.7    27.1    -      -       +      -
    378A  VAL*     3.8    24.5    -      -       +      -
    379A  TRP      2.9     9.7    +      -       -      +
    380A  GLY*     3.7    12.8    -      -       -      -
    404A  ASP*     3.8    11.0    -      -       +      +
    406A  LEU*     5.0     3.4    -      -       +      -
    493A  TYR*     3.6    28.9    -      -       +      +
    496A  LYS*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  ALA*     3.9    18.6    -      -       +      -
    337A  MET*     1.3    85.5    -      -       -      +
    339A  PRO*     1.3    65.3    -      -       -      +
    340A  TYR*     3.4    14.0    -      -       +      -
    380A  GLY*     4.1    10.3    -      -       -      -
    381A  GLU      3.9    15.9    -      -       -      +
    383A  GLY      5.3     0.4    -      -       -      +
    390A  PHE*     4.1    13.2    -      -       +      -
    391A  TYR*     3.3    36.6    -      -       +      +
    394A  ILE*     4.7     5.2    -      -       +      -
    403A  CYS*     4.1    16.6    -      -       +      -
    404A  ASP      2.7    18.7    +      -       -      +
    405A  PHE*     3.6    23.1    -      -       +      -
    406A  LEU*     3.2    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  MET*     3.2    15.7    -      -       +      +
    338A  LEU*     1.3    85.4    -      -       -      +
    340A  TYR*     1.3    58.5    +      -       -      +
    341A  ASP      2.9     8.8    +      -       -      -
    344A  LEU*     3.9    49.4    -      -       +      +
    347A  PHE*     4.4    12.3    -      -       +      -
    348A  ALA*     5.2     3.8    -      -       +      +
    381A  GLU      4.3     5.4    -      -       -      +
    382A  PRO*     3.1    17.4    -      -       +      +
    383A  GLY      3.0    16.6    +      -       -      -
    406A  LEU*     3.5    23.1    -      -       +      +
----------------------------------------------------------
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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