Contacts of the strand formed by residues 561 - 573 (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 GLY 561 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460D  ASP*     3.4    11.1    +      -       -      +
    461D  ILE*     3.0    26.9    +      -       -      +
    462D  GLY      4.7     1.6    -      -       -      +
    494D  SER*     3.0    17.7    -      -       -      -
    495D  TYR*     3.7     7.7    -      -       -      -
    560D  TYR*     1.3    79.6    -      -       -      +
    562D  THR*     1.3    66.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 562 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458D  PRO*     3.9    20.6    -      -       +      -
    459D  LYS      3.2    15.5    -      -       -      +
    460D  ASP*     4.1     8.5    +      -       -      -
    461D  ILE*     3.9     5.4    -      -       -      +
    493D  LEU*     3.2     3.1    -      -       -      -
    494D  SER*     2.9    40.2    +      -       -      -
    561D  GLY*     1.3    76.9    +      -       -      -
    563D  LEU*     1.3    71.4    +      -       -      +
    564D  THR*     3.7    14.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 563 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455D  LEU*     3.6    22.2    -      -       +      +
    458D  PRO*     3.5     2.1    -      -       -      +
    459D  LYS*     2.8    39.6    +      -       +      +
    461D  ILE*     4.0     4.0    -      -       +      +
    465D  LEU*     3.7    28.7    -      -       +      -
    467D  VAL*     4.3     9.4    -      -       +      -
    491D  LEU*     4.5    10.5    -      -       +      -
    492D  THR      3.7     9.9    -      -       -      +
    493D  LEU*     3.9    15.7    -      -       +      -
    549D  LEU*     4.1    14.6    -      -       +      -
    551D  ILE*     3.9    20.4    -      -       +      -
    562D  THR*     1.3    71.4    -      -       -      +
    564D  THR*     1.3    58.2    +      -       -      +
    565D  LYS      3.6    20.4    -      -       -      +
    566D  PHE*     4.4     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 564 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455D  LEU*     3.7    12.3    -      -       -      +
    457D  GLU      5.6     0.5    -      -       -      -
    458D  PRO*     4.4    18.1    -      -       +      +
    492D  THR*     2.8    32.1    +      -       -      +
    493D  LEU*     4.8     0.6    -      -       -      -
    494D  SER*     5.7     1.6    -      -       -      +
    562D  THR*     3.7    22.6    +      -       +      +
    563D  LEU*     1.3    78.1    -      -       -      +
    565D  LYS*     1.3    62.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 565 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232C  THR*     6.4     2.2    -      -       -      -
    233C  ASP*     6.0     9.4    -      -       +      -
    269C  LEU*     6.1     2.5    -      -       -      -
    453D  ASP*     4.2    10.3    -      -       -      +
    455D  LEU*     3.7     6.5    -      -       -      +
    490D  ARG*     3.3    23.3    +      -       -      +
    491D  LEU*     3.3     4.9    -      -       -      -
    492D  THR*     2.8    60.4    +      -       -      +
    530D  ASP*     3.1    29.0    +      -       -      +
    563D  LEU*     3.6     7.0    -      -       -      +
    564D  THR*     1.3    80.9    -      -       -      +
    566D  PHE*     1.3    64.3    +      -       -      +
    567D  THR*     3.6    21.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 566 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453D  ASP*     3.7     2.0    +      -       -      +
    454D  ILE*     3.0    63.6    +      -       +      +
    455D  LEU*     4.0    16.6    +      -       +      +
    467D  VAL*     4.2    14.8    -      -       +      -
    469D  LYS*     5.8     1.6    -      -       +      -
    489D  ALA*     3.9    24.7    -      -       +      -
    490D  ARG      3.4     2.2    -      -       -      -
    491D  LEU*     3.2    21.1    -      -       +      -
    505D  LEU*     4.2    14.4    -      -       +      -
    547D  TRP*     5.7     6.7    -      -       +      -
    548D  VAL      5.6     0.4    -      -       -      -
    549D  LEU*     3.8    39.3    -      -       +      -
    563D  LEU*     4.4     4.3    -      -       +      -
    565D  LYS*     1.3    77.5    -      -       -      +
    567D  THR*     1.3    68.2    +      -       -      +
    568D  LEU*     4.7     9.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 567 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234C  ALA*     4.5     1.7    -      -       +      +
    269C  LEU*     4.1    13.7    -      -       +      +
    451D  ILE*     3.7    30.3    -      -       +      -
    452D  ILE      3.6    10.8    -      -       -      +
    453D  ASP*     2.9    21.6    +      -       -      +
    488D  GLN      3.7     0.5    -      -       -      +
    489D  ALA*     3.6     2.3    -      -       -      -
    490D  ARG*     2.8    50.3    +      -       -      +
    565D  LYS*     3.6    19.8    -      -       -      +
    566D  PHE*     1.3    74.2    -      -       -      +
    568D  LEU*     1.3    63.7    +      -       -      +
    569D  VAL*     3.8     5.0    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 568 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450D  CYS      3.7     2.4    -      -       -      +
    452D  ILE*     2.8    61.5    +      -       +      +
    454D  ILE*     4.4    11.7    -      -       +      -
    471D  VAL*     4.4     6.3    -      -       +      -
    487D  ALA*     5.3     1.1    -      -       +      -
    488D  GLN      3.5    15.0    -      -       -      +
    489D  ALA*     4.8     0.7    -      -       -      +
    505D  LEU*     4.5    16.8    -      -       +      -
    547D  TRP*     3.8    55.9    -      -       +      +
    566D  PHE*     4.0     8.8    +      -       +      -
    567D  THR*     1.3    72.3    -      -       -      +
    569D  VAL*     1.3    61.8    +      -       -      +
    570D  LEU*     3.8    21.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 569 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269C  LEU*     4.2    11.7    -      -       +      -
    449D  LYS*     3.8    28.9    -      -       +      -
    450D  CYS      3.6     4.3    -      -       -      +
    451D  ILE*     4.6     5.6    -      -       +      -
    487D  ALA*     3.4     5.0    -      -       -      -
    488D  GLN*     2.9    50.4    +      -       +      +
    490D  ARG*     4.0    30.3    -      -       +      -
    567D  THR*     4.3     8.1    -      -       +      -
    568D  LEU*     1.3    78.7    -      -       -      +
    570D  LEU*     1.3    64.0    +      -       -      +
    571D  TYR*     3.6    25.3    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 570 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449D  LYS*     3.3     4.5    -      -       -      +
    450D  CYS*     2.7    45.6    +      -       +      +
    452D  ILE*     3.8    25.8    -      -       +      -
    471D  VAL*     4.9     2.7    -      -       +      -
    473D  ALA*     4.0    17.9    -      -       +      -
    481D  ILE*     3.2    14.2    -      -       +      +
    484D  LEU*     3.8    16.6    -      -       +      -
    487D  ALA*     4.6     2.9    -      -       +      -
    543D  PRO*     3.8    19.3    -      -       +      -
    547D  TRP*     3.9    24.2    -      -       +      -
    568D  LEU*     3.8    24.0    -      -       +      -
    569D  VAL*     1.3    76.9    -      -       -      +
    571D  TYR*     1.3    62.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 571 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272C  GLU*     4.1     3.8    +      -       -      -
    276C  ARG*     4.4     1.1    -      -       -      -
    312D  ILE*     3.8    23.7    -      -       +      +
    447D  GLN*     3.6    29.6    -      -       +      +
    448D  ARG      3.2     6.5    -      -       -      -
    449D  LYS*     3.6    30.0    +      -       +      -
    481D  ILE*     3.6     3.3    -      -       -      +
    484D  LEU*     3.3     8.3    -      -       -      +
    485D  GLU*     2.8    24.9    +      -       +      +
    486D  HIS*     3.1    39.9    +      -       +      +
    488D  GLN*     3.2    38.2    +      -       +      -
    569D  VAL*     3.6    16.4    -      -       +      -
    570D  LEU*     1.3    76.7    -      -       -      +
    572D  GLY*     1.3    60.0    +      -       -      +
    602D  FMT      3.7    25.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 572 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447D  GLN*     3.8     1.9    -      -       -      +
    448D  ARG*     2.8    42.5    +      -       -      +
    481D  ILE*     3.6     6.6    -      -       -      +
    483D  ARG      3.4    10.1    -      -       -      -
    485D  GLU*     4.0    19.0    +      -       -      -
    571D  TYR*     1.3    77.1    -      -       -      +
    573D  THR*     1.3    66.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 573 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391D  ARG*     3.5    25.1    -      -       -      +
    395D  HIS*     6.1     0.7    -      -       -      -
    444D  VAL*     5.1     2.5    -      -       +      -
    445D  ALA*     3.7    28.0    -      -       +      +
    446D  PRO      3.9     5.6    -      -       -      +
    448D  ARG*     4.6     5.2    -      -       -      +
    480D  HIS      4.3     1.3    -      -       -      -
    481D  ILE*     3.4     5.3    -      -       -      -
    482D  THR      2.8    22.5    +      -       -      -
    483D  ARG*     3.0    37.0    +      -       -      +
    485D  GLU*     4.2     5.4    +      -       -      +
    572D  GLY*     1.3    78.9    -      -       -      +
    574D  ALA*     1.3    66.5    +      -       -      +
----------------------------------------------------------
 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