Contacts of the strand formed by residues 465 - 476 (chain A) in PDB entry 2ID5


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 465 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  ARG*     3.8     9.2    -      -       -      -
    385A  ALA*     3.6     4.6    -      -       -      +
    461A  ALA*     5.0     0.2    -      -       -      -
    462A  ASN*     2.7    36.9    +      -       -      +
    463A  ALA      3.1     1.9    -      -       -      -
    464A  GLY*     1.3    79.9    -      -       -      +
    466A  ASN*     1.3    62.3    +      -       -      -
     94D  LEU*     4.0    14.1    -      -       -      -
     96D  PRO*     5.2     2.2    -      -       -      -
     97D  LEU      5.6     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  ARG*     5.0     0.5    +      -       -      -
    385A  ALA      4.0     6.7    -      -       -      +
    460A  ALA      3.1    12.6    -      -       -      +
    461A  ALA*     3.9     1.8    -      -       +      -
    465A  GLY*     1.3    76.2    -      -       -      +
    467A  ASP*     1.3    65.6    +      -       -      +
    468A  SER*     5.5     0.5    +      -       -      -
     93D  LYS      5.3     2.3    -      -       -      +
     94D  LEU*     3.4    42.8    -      -       -      +
    118D  ILE*     3.4    32.9    +      -       +      +
    120D  LEU*     3.8    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  ALA      3.6    14.6    -      -       -      +
    386A  ARG*     3.6    14.3    -      -       -      +
    387A  ILE*     2.9    24.0    +      -       +      +
    390A  ARG*     2.6    42.4    +      -       -      -
    459A  ILE*     3.3     6.3    -      -       -      +
    460A  ALA*     2.7    31.7    +      -       +      +
    466A  ASN*     1.3    79.6    -      -       -      +
    468A  SER*     1.3    68.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  ILE*     3.9     1.8    -      -       -      -
    390A  ARG*     4.3     3.8    +      -       -      -
    457A  LEU*     4.0    24.2    -      -       -      +
    458A  CYS      2.9    11.7    -      -       -      -
    459A  ILE*     4.4     5.6    -      -       -      -
    466A  ASN*     5.5     0.5    +      -       -      -
    467A  ASP*     1.3    84.9    +      -       -      +
    469A  MET*     1.3    70.5    +      -       -      +
    470A  PRO*     4.5     2.6    -      -       -      +
    117D  VAL*     4.1    26.0    -      -       -      +
    118D  ILE*     5.0     6.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  ILE*     4.0    19.1    -      -       +      -
    389A  ASP      3.4    24.5    -      -       -      +
    390A  ARG*     3.5    44.9    -      -       -      +
    391A  LYS      3.4    22.7    -      -       -      +
    392A  ALA*     3.7    12.1    -      -       +      +
    393A  GLN*     4.9     5.2    -      -       +      +
    407A  CYS*     5.4     0.4    -      -       -      -
    457A  LEU*     3.7     3.8    -      -       -      -
    458A  CYS*     2.8    40.5    +      -       +      +
    468A  SER*     1.3    78.4    -      -       -      +
    470A  PRO*     1.3    80.1    -      -       +      +
    471A  ALA*     4.9     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392A  ALA*     4.1     7.9    -      -       +      +
    393A  GLN*     4.0    14.6    +      -       -      +
    455A  THR*     4.0    18.2    -      -       +      -
    456A  TYR      3.5     6.1    -      -       -      +
    457A  LEU*     4.3    12.3    -      -       +      -
    468A  SER      4.5     2.2    -      -       -      +
    469A  MET*     1.3   107.4    -      -       +      +
    471A  ALA*     1.3    60.7    +      -       -      +
    472A  HIS*     4.1    16.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  GLN*     3.7    16.2    -      -       +      +
    405A  PHE*     3.7    28.9    -      -       +      -
    419A  TRP*     3.8    26.7    -      -       +      -
    455A  THR*     3.3     1.7    -      -       -      -
    456A  TYR*     2.6    38.9    +      -       +      +
    470A  PRO*     1.3    75.1    -      -       -      +
    472A  HIS*     1.3    62.9    +      -       -      +
    473A  LEU      4.1     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392A  ALA*     4.2    14.3    -      -       +      +
    393A  GLN      3.0    18.3    +      -       -      -
    394A  GLN*     3.5    22.9    +      -       +      -
    395A  VAL      3.3    25.8    +      -       -      +
    405A  PHE*     3.6     5.6    -      -       -      -
    454A  GLY      3.4     3.1    -      -       -      -
    455A  THR*     2.8    38.2    +      -       +      -
    470A  PRO*     4.1    16.3    -      -       +      +
    471A  ALA*     1.3    73.6    -      -       -      +
    473A  LEU*     1.3    61.1    +      -       -      +
    474A  HIS*     3.6    19.5    -      +       -      +
    491A  NAG      3.8    11.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395A  VAL*     3.8    28.5    -      -       +      +
    397A  VAL*     3.8    22.4    -      -       +      -
    403A  VAL*     3.9     8.5    -      -       +      -
    405A  PHE*     3.7    14.5    -      -       +      -
    445A  VAL*     4.4    21.8    -      -       +      -
    448A  ALA*     5.2     0.4    -      -       +      -
    452A  ASP*     3.4    28.3    -      -       +      +
    453A  ASN*     3.0    16.6    -      -       -      +
    454A  GLY      2.8    24.4    +      -       -      +
    456A  TYR*     4.1    12.3    -      -       +      -
    472A  HIS*     1.3    71.6    -      -       -      +
    474A  HIS*     1.3    60.1    +      -       -      +
    475A  VAL*     3.9    17.0    -      -       +      -
    491A  NAG      3.9     3.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394A  GLN*     3.4    34.3    +      -       +      +
    395A  VAL      3.1    16.0    +      -       -      -
    396A  PHE*     3.5    40.9    -      +       +      +
    397A  VAL      3.0    25.6    +      -       -      +
    453A  ASN*     3.7     4.0    -      -       -      -
    472A  HIS*     3.6    14.3    -      +       +      +
    473A  LEU*     1.3    72.2    -      -       -      +
    475A  VAL*     1.3    62.1    +      -       -      +
    476A  ARG*     3.8     6.1    +      -       +      +
    491A  NAG      3.5    35.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  VAL*     3.3    25.8    -      -       +      +
    399A  GLU*     3.8    30.5    -      -       +      +
    448A  ALA*     4.0     4.9    -      -       +      -
    449A  GLN      3.4    31.9    -      -       -      +
    450A  VAL*     4.3    14.8    -      -       +      +
    453A  ASN*     3.5    20.1    +      -       +      +
    473A  LEU*     3.9    20.6    -      -       +      -
    474A  HIS*     1.3    72.4    -      -       -      +
    476A  ARG*     1.3    62.6    +      -       -      +
    477A  SER      4.1     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  PHE*     3.3    43.7    -      -       -      +
    397A  VAL      3.1     8.0    +      -       -      +
    398A  ASP*     3.6    22.9    -      -       -      +
    399A  GLU*     3.2    25.5    +      -       -      +
    474A  HIS*     4.3     9.8    -      -       +      +
    475A  VAL*     1.3    74.6    -      -       -      +
    477A  SER*     1.3    62.0    +      -       -      +
----------------------------------------------------------
 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