Contacts of the strand formed by residues 309 - 317 (chain A) in PDB entry 6M85


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 309 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  ARG*     5.2     3.5    +      -       -      -
    300A  GLU*     5.7     3.1    -      -       +      -
    301A  GLY*     3.5    19.1    -      -       -      +
    302A  MET*     4.1    14.5    -      -       +      +
    308A  MET*     1.3    75.5    -      -       -      +
    310A  THR*     1.3    65.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  ARG*     4.4    21.8    +      -       -      +
    193A  THR*     5.8     4.0    -      -       +      -
    194A  LEU*     5.1     9.6    -      -       +      +
    299A  LEU      3.9     0.6    -      -       -      +
    300A  GLU*     3.3     8.4    -      -       -      +
    301A  GLY      2.8    32.7    +      -       -      -
    303A  VAL*     3.3    21.2    -      -       +      +
    306A  THR*     4.3     4.5    +      -       -      -
    308A  MET      3.1    15.2    +      -       -      -
    309A  THR*     1.3    77.1    +      -       -      +
    311A  GLN*     1.3    73.6    +      -       -      +
    312A  ALA*     4.0     3.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  ARG*     5.2     4.0    -      -       -      +
    298A  ILE*     4.1    23.4    -      -       +      +
    299A  LEU      3.6     3.8    -      -       -      -
    300A  GLU*     2.7    31.6    +      -       +      +
    310A  THR*     1.3    80.5    -      -       -      +
    312A  ALA*     1.3    59.3    +      -       -      +
    313A  ARG*     3.0    50.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  GLN*     6.5     0.9    -      -       +      -
    194A  LEU*     3.8    41.0    -      -       +      +
    196A  PHE*     3.8    14.6    -      -       +      -
    298A  ILE*     3.5     5.7    -      -       -      +
    299A  LEU*     2.9    34.1    +      -       +      +
    310A  THR*     4.0     5.1    -      -       +      +
    311A  GLN*     1.3    74.7    -      -       -      +
    313A  ARG*     1.3    61.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  VAL*     4.5     8.5    -      -       +      -
     48A  LYS      4.2     0.3    -      -       -      +
     49A  ASN      3.9     4.0    +      -       -      +
     50A  GLY*     2.8    68.9    +      -       -      +
     51A  GLN*     4.7     1.6    -      -       -      +
     52A  CYS*     4.5    17.6    -      -       -      +
    196A  PHE*     3.5    10.3    -      -       -      -
    296A  VAL*     5.0     4.5    -      -       +      -
    297A  VAL      3.5     4.3    -      -       -      +
    298A  ILE*     4.1    19.7    -      -       +      -
    311A  GLN*     3.0    49.0    +      -       +      +
    312A  ALA*     1.3    77.0    -      -       -      +
    314A  SER*     1.3    64.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  VAL*     4.3     3.6    -      -       -      +
     47A  LYS      4.1     7.4    -      -       -      -
     48A  LYS*     2.7    30.9    +      -       -      +
    196A  PHE*     3.6    31.6    -      -       -      +
    197A  SER      4.9     3.1    +      -       -      -
    296A  VAL*     3.6     8.7    -      -       -      +
    297A  VAL*     3.0    35.4    +      -       -      +
    313A  ARG*     1.3    76.2    -      -       -      +
    315A  SER*     1.3    70.8    +      -       -      +
    316A  TYR*     5.1     2.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ARG*     3.2    13.8    +      -       -      -
     46A  VAL*     2.9    29.6    -      -       -      -
     47A  LYS      4.0     4.4    +      -       -      -
     48A  LYS*     2.8    28.6    +      -       -      +
    294A  GLU*     2.6    32.1    +      -       -      +
    295A  ILE      3.4     6.1    -      -       -      -
    296A  VAL*     4.9     0.9    -      -       -      -
    314A  SER*     1.3    84.2    +      -       -      +
    316A  TYR*     1.3    68.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LYS*     3.5    10.5    -      -       -      -
    196A  PHE*     3.9     8.1    -      -       +      +
    197A  SER*     2.8    45.8    +      -       -      -
    198A  HIS      3.4    10.5    -      -       -      -
    199A  ASN*     3.5     9.9    -      -       -      -
    200A  ALA*     3.6    19.7    -      -       +      -
    213A  TRP*     3.5    28.3    -      +       +      +
    293A  PHE      4.2     0.2    -      -       -      +
    295A  ILE*     2.7    52.0    +      -       +      +
    297A  VAL*     3.7    32.8    -      -       +      -
    314A  SER*     5.1     2.2    -      -       -      -
    315A  SER*     1.3    83.9    +      -       -      +
    317A  LEU*     1.3    66.5    +      -       -      +
    318A  ALA      3.9     0.2    +      -       -      -
    320A  GLU*     3.5     6.1    -      -       +      -
    321A  ILE*     4.3    14.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  CYS      5.4     9.2    -      -       -      +
     42A  ARG      4.9    11.0    -      -       -      +
     43A  ASN      5.4     0.9    -      -       -      +
     44A  ARG*     3.3    46.8    -      -       +      +
    292A  ASP*     5.1     8.1    -      -       -      +
    293A  PHE      3.5    13.7    -      -       -      +
    294A  GLU*     4.2    19.1    -      -       +      +
    316A  TYR*     1.3    75.7    -      -       -      +
    318A  ALA*     1.3    60.7    +      -       -      +
    319A  SER*     3.1    18.4    -      -       -      +
    320A  GLU*     2.7    35.7    +      -       -      +
    321A  ILE*     3.5     9.4    +      -       -      +
----------------------------------------------------------
 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