Contacts of the strand formed by residues 314 - 320 (chain D) in PDB entry 4OMD


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 314 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274D  PHE*     3.6    33.4    -      -       +      -
    289D  PHE*     3.2    16.2    -      -       +      -
    291D  TRP*     3.9    17.4    -      -       +      +
    308D  TYR      2.6    27.7    +      -       -      +
    309D  THR*     3.6     2.9    +      -       -      -
    311D  SER*     3.4     5.9    +      -       -      +
    312D  ILE      4.2     3.8    -      -       -      +
    313D  TYR*     1.3    85.3    -      -       -      +
    315D  LEU*     1.3    60.0    +      -       -      +
    316D  SER      3.5     0.3    +      -       -      -
    337D  LEU*     5.7     0.3    -      -       -      +
    394D  GLN*     4.3     6.1    +      -       -      +
    534D  MET*     5.2     1.0    -      -       -      +
    606D   NA      2.2    43.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 315 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288D  ILE*     3.7    26.7    -      -       +      -
    289D  PHE      2.8    24.4    +      -       -      +
    290D  VAL*     3.7     6.4    -      -       +      -
    291D  TRP      3.0    22.0    +      -       -      +
    313D  TYR      5.0     0.9    -      -       -      +
    314D  THR*     1.3    73.0    -      -       -      +
    316D  SER*     1.3    63.0    +      -       -      +
    317D  ILE*     3.5    15.6    +      -       +      +
    337D  LEU*     4.2    14.8    -      -       +      -
    378D  ILE*     3.7    21.8    -      -       +      -
    390D  TRP      5.6     1.1    -      -       -      +
    393D  MET*     4.4     8.7    -      -       +      -
    394D  GLN*     3.9    32.3    -      -       +      +
    397D  VAL*     4.1    21.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 316 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291D  TRP*     3.5     7.9    -      -       -      -
    293D  SER*     3.5    18.4    -      -       -      -
    303D  CYS*     5.3     0.3    -      -       -      +
    309D  THR*     3.2    44.6    -      -       -      +
    314D  THR      3.5     4.8    +      -       -      -
    315D  LEU*     1.3    71.4    -      -       -      +
    317D  ILE*     1.3    63.8    +      -       -      +
    318D  SER      4.3     0.2    -      -       -      -
    335D  SER*     4.1     3.4    +      -       -      -
    336D  THR*     3.6    21.5    +      -       -      +
    337D  LEU*     3.0    28.2    +      -       -      +
    338D  ALA      3.6     0.7    +      -       -      -
    606D   NA      3.9     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 317 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290D  VAL*     4.0     5.8    -      -       +      -
    291D  TRP      2.8    15.4    +      -       -      +
    292D  ALA*     3.9     3.5    -      -       -      -
    293D  SER*     3.2    21.9    +      -       -      -
    315D  LEU*     3.6    24.5    -      -       +      +
    316D  SER*     1.3    82.7    +      -       -      +
    318D  SER*     1.3    74.6    +      -       -      +
    337D  LEU*     5.3     1.3    -      -       +      -
    338D  ALA*     3.4    24.9    -      -       +      +
    339D  THR*     4.3     0.4    -      -       -      +
    340D  THR*     3.8    28.5    -      -       +      +
    367D  THR*     4.2     3.6    +      -       -      -
    370D  SER*     4.0    12.1    -      -       -      +
    371D  ALA*     4.4     5.4    -      -       -      -
    374D  ALA*     3.6    23.3    -      -       +      -
    378D  ILE*     6.1     0.7    -      -       +      -
    397D  VAL*     5.8     1.3    -      -       +      -
    429D  LEU*     5.0     4.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 318 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  SER*     3.0    19.0    +      -       -      -
    317D  ILE*     1.3    78.1    -      -       -      +
    319D  SER*     1.3    65.3    +      -       -      +
    330D  SER*     5.1     4.3    -      -       -      -
    331D  GLU      4.2     7.1    +      -       -      -
    336D  THR*     3.2    23.8    +      -       -      +
    338D  ALA      2.9     7.7    +      -       -      -
    339D  THR*     3.4    10.0    -      -       -      +
    340D  THR      3.1    23.9    +      -       -      +
    367D  THR*     5.4     0.2    -      -       -      -
    370D  SER*     3.6     2.7    +      -       -      -
    422D  HIS      5.2     0.2    +      -       -      -
    423D  SER      3.2    25.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 319 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318D  SER*     1.3    74.8    -      -       -      +
    320D  ALA*     1.3    61.4    +      -       -      +
    327D  PRO*     3.3    17.7    -      -       -      +
    329D  TYR*     3.5    38.6    -      -       -      -
    330D  SER*     4.7     6.3    +      -       -      -
    339D  THR*     3.5     4.2    -      -       -      +
    340D  THR      3.3     4.3    -      -       -      -
    342D  SER*     3.7     6.5    -      -       -      -
    367D  THR*     3.7     9.4    -      -       -      -
    370D  SER*     2.6    24.6    +      -       -      -
    423D  SER      4.5     1.7    -      -       -      +
    424D  TYR*     3.5    15.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 320 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319D  SER*     1.3    75.7    -      -       -      +
    321D  THR*     1.3    65.9    +      -       -      +
    324D  GLY*     5.0     0.7    -      -       -      -
    325D  ASN      3.5     7.4    -      -       -      +
    327D  PRO*     3.9     4.3    -      -       -      -
    339D  THR*     3.7    15.7    -      -       +      -
    340D  THR      3.3     4.4    +      -       -      +
    341D  TYR*     3.4    12.0    -      -       +      -
    342D  SER      3.0    24.2    +      -       -      +
    406D  LEU*     3.9    21.3    -      -       +      -
    424D  TYR*     3.9    13.0    -      -       +      +
    428D  LEU*     4.3     1.8    -      -       +      -
----------------------------------------------------------
 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