Contacts of the strand formed by residues 304 - 308 (chain T) in PDB entry 6QX2


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 304 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259T  ILE      3.7     1.7    -      -       -      +
    260T  VAL*     3.5     3.3    -      -       -      -
    261T  VAL*     2.9    50.6    +      -       +      +
    264T  ILE*     5.5     0.9    -      -       +      -
    270T  LYS*     4.1    15.3    -      -       +      -
    273T  MET*     4.8    12.8    -      -       +      -
    274T  ILE*     3.9    31.4    -      -       +      -
    277T  ILE*     5.5     1.6    -      -       +      -
    292T  LEU*     4.4    14.4    -      -       +      -
    293T  ARG      3.6    11.4    -      -       -      +
    294T  ASP*     3.9    14.1    -      -       -      +
    302T  VAL*     4.5     6.1    -      -       +      -
    303T  ARG*     1.3    72.3    -      -       -      +
    305T  VAL*     1.3    61.6    +      -       -      +
    306T  ILE*     4.2     7.5    +      -       +      +
    327T  LEU*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 305 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258T  ARG*     3.6    21.8    -      -       +      -
    259T  ILE      3.6     4.0    -      -       -      +
    260T  VAL*     4.9     2.7    -      -       +      -
    291T  ASP      4.6     0.2    -      -       -      -
    292T  LEU*     3.4     4.9    -      -       -      +
    293T  ARG*     2.8    66.8    +      -       -      +
    295T  GLU*     3.4    34.8    -      -       +      +
    303T  ARG*     3.9    22.7    -      -       +      +
    304T  VAL*     1.3    74.6    -      -       -      +
    306T  ILE*     1.3    65.1    +      -       -      +
    307T  ASP*     3.4    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 306 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258T  ARG*     3.3     1.6    -      -       -      -
    259T  ILE*     2.9    58.1    +      -       +      +
    261T  VAL*     4.8    11.2    -      -       +      -
    277T  ILE*     4.3    15.3    -      -       +      -
    289T  ILE*     3.6    43.3    -      -       +      -
    291T  ASP      3.5     3.8    -      -       -      +
    292T  LEU*     3.7    20.4    -      -       +      -
    304T  VAL*     4.8     7.2    -      -       +      +
    305T  VAL*     1.3    74.2    -      -       -      +
    307T  ASP*     1.3    63.9    +      -       -      +
    308T  VAL*     3.8     3.0    +      -       +      +
    321T  LEU*     3.6    27.6    -      -       +      -
    327T  LEU*     5.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 307 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252T  ARG*     3.7    31.1    +      -       -      +
    258T  ARG*     3.6    11.5    -      -       -      +
    289T  ILE*     3.5     6.8    -      -       -      +
    290T  THR*     2.9    43.4    +      -       -      +
    291T  ASP*     3.0    19.8    +      -       +      +
    293T  ARG*     3.0    28.9    +      -       -      -
    305T  VAL*     3.4    20.6    -      -       -      +
    306T  ILE*     1.3    71.3    -      -       -      +
    308T  VAL*     1.3    56.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 308 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252T  ARG*     2.7    25.0    +      -       -      -
    256T  ARG*     4.5     0.5    -      -       -      +
    257T  GLN*     3.5    23.9    +      -       +      +
    258T  ARG*     4.6     2.9    -      -       -      -
    259T  ILE*     4.2    21.1    -      -       +      -
    288T  GLY      3.4     4.0    -      -       -      +
    289T  ILE*     5.4     0.2    -      -       +      -
    290T  THR*     3.9     0.9    -      -       -      -
    306T  ILE*     4.0    11.9    -      -       +      +
    307T  ASP*     1.3    76.9    -      -       -      +
    309T  ARG*     1.3    74.0    +      -       -      +
    310T  LYS      3.7     0.3    +      -       -      -
    312T  ALA*     3.7    16.4    -      -       +      +
    314T  ALA*     4.2    17.3    -      -       +      -
    317T  ILE*     3.5    33.4    -      -       +      -
----------------------------------------------------------
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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