Contacts of the strand formed by residues 377 - 382 (chain A) in PDB entry 6Q6Q


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 CYS 377 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  MET*     3.8    22.7    -      -       -      -
    372A  LEU*     3.3    42.4    +      -       -      +
    375A  GLY      4.3     0.2    -      -       -      -
    376A  ASN*     1.3    77.6    -      -       -      +
    378A  THR*     1.3    56.4    +      -       -      +
    391A  PRO*     3.5     4.5    -      -       -      +
    392A  LEU*     2.6    51.3    +      -       +      +
    414A  VAL*     4.4     4.9    -      -       +      -
    415A  ASN      3.5    17.7    -      -       -      +
    416A  ILE*     4.0    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376A  ASN      4.9     4.9    -      -       -      +
    377A  CYS*     1.3    78.4    -      -       -      +
    379A  LEU*     1.3    63.4    +      -       -      +
    380A  ASN      4.2     0.2    -      -       -      -
    389A  GLN*     3.7    26.8    -      -       -      +
    390A  ILE      3.5     7.0    -      -       -      +
    391A  PRO*     4.2    14.8    -      -       +      -
    414A  VAL*     3.3     7.4    -      -       -      +
    415A  ASN*     2.6    64.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     4.2    19.1    -      -       +      -
    378A  THR*     1.3    74.7    -      -       -      +
    380A  ASN*     1.3    62.3    +      -       -      +
    381A  LEU*     3.3    16.5    +      -       +      +
    389A  GLN*     3.3     4.2    -      -       -      -
    390A  ILE*     2.8    44.1    +      -       +      +
    392A  LEU*     4.1    19.5    -      -       +      -
    396A  PHE*     3.5    46.0    -      -       +      -
    405A  LEU*     5.3     0.4    -      -       +      -
    411A  LEU*     3.8    18.6    -      -       +      -
    413A  SER      3.7     2.0    -      -       -      -
    414A  VAL*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  THR*     4.8     2.4    -      -       -      +
    379A  LEU*     1.3    68.7    -      -       -      +
    381A  LEU*     1.3    63.0    +      -       -      +
    388A  ARG      3.6     4.9    -      -       -      -
    389A  GLN*     3.6    18.2    -      -       -      +
    411A  LEU*     4.2     0.2    -      -       -      -
    412A  VAL*     3.0    32.7    +      -       +      +
    413A  SER*     2.5    40.9    +      -       -      +
    415A  ASN*     2.9    37.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379A  LEU*     3.9    29.2    -      -       +      +
    380A  ASN*     1.3    73.8    -      -       -      +
    382A  LEU*     1.3    57.4    +      -       -      +
    383A  SER      4.3     0.2    -      -       -      -
    387A  LYS*     3.6     3.6    -      -       -      +
    388A  ARG*     2.7    74.8    +      -       +      +
    390A  ILE*     3.6    26.5    -      -       +      -
    405A  LEU*     3.6    38.1    -      -       +      -
    409A  GLU*     3.4    15.9    -      -       -      +
    410A  ILE      3.2     7.9    -      -       -      +
    411A  LEU*     3.9    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  LEU*     3.7    33.2    -      -       +      -
    253A  LEU*     3.2    30.6    -      -       +      +
    380A  ASN      3.8     1.0    +      -       -      -
    381A  LEU*     1.3    74.7    -      -       -      +
    383A  SER*     1.3    73.3    +      -       -      +
    386A  GLY*     3.8     8.5    -      -       -      +
    387A  LYS*     3.6    33.2    -      -       +      +
    409A  GLU*     3.7     2.2    -      -       -      -
    410A  ILE*     2.9    30.2    +      -       -      +
    412A  VAL*     3.6    22.4    -      -       +      -
----------------------------------------------------------
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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