Contacts of the strand formed by residues 311 - 319 (chain A) in PDB entry 6VSB


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 GLY 311 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310A  LYS*     1.3    78.8    -      -       -      +
    312A  ILE*     1.3    60.9    +      -       -      -
    313A  TYR*     3.7    10.4    -      -       -      -
    597A  VAL      3.6     1.9    -      -       -      +
    598A  ILE*     3.7     0.2    -      -       -      -
    599A  THR      2.9    32.0    +      -       -      -
    664A  ILE*     3.6    23.8    -      -       -      -
    665A  PRO*     6.1     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  GLY*     1.3    72.1    -      -       -      -
    313A  TYR*     1.3    70.9    +      -       -      +
    596A  SER*     3.7    23.3    -      -       -      +
    597A  VAL      3.3     6.7    -      -       -      +
    598A  ILE*     3.6    28.7    -      -       +      -
    611A  LEU*     4.0    19.5    -      -       +      -
    613A  GLN*     5.3     2.2    -      -       -      +
    664A  ILE*     3.7     4.4    -      -       +      +
    665A  PRO*     3.7    29.4    -      -       +      +
    666A  ILE*     4.7     5.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  THR*     4.9    11.1    -      -       +      +
    302A  THR*     6.1     1.3    -      -       +      -
    303A  LEU*     4.2    29.4    -      -       +      -
    308A  VAL*     4.8     9.2    -      -       +      -
    309A  GLU*     2.9    50.8    +      -       -      +
    310A  LYS      3.0    17.0    +      -       -      -
    311A  GLY*     3.7    13.7    -      -       -      -
    312A  ILE*     1.3    79.2    -      -       -      +
    314A  GLN*     1.3    64.7    +      -       -      +
    315A  THR      3.9     0.7    +      -       -      -
    596A  SER*     3.1     5.3    -      -       -      -
    597A  VAL*     3.0    46.1    +      -       +      +
    599A  THR*     5.4     2.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  THR*     4.3    10.6    +      -       -      +
    313A  TYR*     1.3    75.6    -      -       -      +
    315A  THR*     1.3    63.1    +      -       -      +
    316A  SER*     4.2     6.9    +      -       -      +
    317A  ASN*     4.1    19.8    +      -       -      +
    594A  GLY*     4.1    16.0    -      -       -      -
    595A  VAL      3.8    14.1    -      -       -      +
    596A  SER*     3.8    11.2    +      -       -      +
    613A  GLN*     5.1     7.2    +      -       -      +
    735B  SER*     4.6    11.0    +      -       -      -
    764B  ASN*     4.4    20.4    +      -       -      +
    768B  THR*     4.3    14.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  GLU*     2.5    55.5    +      -       +      +
    299A  THR*     3.6    22.2    -      -       +      -
    302A  THR*     3.3    20.4    +      -       -      +
    313A  TYR      3.9     1.0    +      -       -      +
    314A  GLN*     1.3    75.8    -      -       -      +
    316A  SER*     1.3    67.2    +      -       -      +
    595A  VAL*     3.3    17.1    +      -       +      +
    597A  VAL*     5.0     8.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  GLU*     2.9    24.0    +      -       -      -
    314A  GLN*     3.9     7.6    -      -       -      +
    315A  THR*     1.3    81.3    -      -       -      +
    317A  ASN*     1.3    70.9    +      -       -      +
    594A  GLY*     3.9     2.8    -      -       -      -
    595A  VAL*     3.1    38.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  GLN*     4.1    11.7    +      -       -      +
    316A  SER*     1.3    90.7    +      -       -      +
    318A  PHE*     1.3    68.0    +      -       -      +
    319A  ARG*     5.2     7.0    -      -       -      +
    592A  PHE*     5.5     3.0    -      -       +      -
    593A  GLY*     3.1    31.7    +      -       -      +
    594A  GLY*     3.3     8.1    -      -       -      +
    595A  VAL*     4.3     1.0    -      -       -      +
    737B  ASP*     3.3    45.4    +      -       -      +
    764B  ASN*     5.0     5.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  ASN*     1.3    79.5    -      -       -      +
    319A  ARG*     1.3    80.1    +      -       -      +
    320A  VAL*     5.8     2.9    -      -       +      -
    591A  SER*     4.7     5.4    -      -       -      -
    592A  PHE*     3.3     7.4    -      -       -      +
    593A  GLY*     2.8    61.7    +      -       -      +
    594A  GLY      3.5    21.3    -      -       -      -
    595A  VAL*     4.1     5.8    -      -       +      -
    612A  TYR*     3.7    38.1    -      +       +      -
    613A  GLN      4.3     1.1    -      -       -      -
    615A  VAL*     3.6    32.8    -      -       +      -
    620A  VAL      4.9    14.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  ASN*     5.2     5.2    -      -       -      +
    318A  PHE*     1.3    90.4    +      -       -      +
    320A  VAL*     1.3    68.5    +      -       -      +
    321A  GLN*     3.5    33.6    +      -       -      +
    590A  CYS*     5.7     2.2    -      -       -      +
    591A  SER      4.1     1.6    -      -       -      -
    592A  PHE*     3.8    17.1    -      -       +      -
    737B  ASP*     3.3    18.8    +      -       -      -
    739B  THR*     6.0     1.0    -      -       -      +
    740B  MET*     3.3    38.8    -      -       -      +
    745B  ASP*     2.9    41.0    +      -       -      +
----------------------------------------------------------
 Back to top of page


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