Contacts of the strand formed by residues 284 - 298 (chain A) in PDB entry 4R2G


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 ILE 284 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  ILE*     4.0    20.0    -      -       +      -
    273A  ARG      3.8     6.3    -      -       -      +
    274A  SER*     4.2    11.0    -      -       -      -
    277A  PHE*     4.0    25.8    -      -       +      +
    282A  LYS      4.1     8.3    -      -       -      +
    283A  THR*     1.3    71.0    -      -       -      +
    285A  ILE*     1.3    73.7    +      -       -      +
    286A  VAL*     3.9     7.7    +      -       +      +
    349A  LEU*     4.6     5.6    -      -       +      -
    353A  PHE*     4.6     1.6    -      -       +      -
    453A  LEU*     3.8     1.4    -      -       -      -
    454A  LEU*     2.9    43.7    +      -       +      +
    455A  THR*     5.3     0.7    -      -       -      -
    456A  ARG*     4.2    15.5    -      -       +      +
    468A  PHE*     3.6    34.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  MET*     4.1    15.5    -      -       +      -
     96A  TRP*     3.9    26.5    -      -       +      -
    260A  LEU*     4.5     4.5    -      -       +      -
    272A  ILE*     3.4     2.9    -      -       -      -
    273A  ARG*     2.9    52.8    +      -       +      +
    283A  THR*     3.5     3.6    +      -       +      +
    284A  ILE*     1.3    74.0    -      -       -      +
    286A  VAL*     1.3    69.7    +      -       -      +
    287A  GLN*     5.7     0.7    -      -       +      -
    452A  LEU      3.7     8.3    -      -       -      +
    453A  LEU*     3.8    15.5    -      -       +      -
    477A  ASP*     3.5    33.4    -      -       +      +
    480A  ARG*     4.2     1.3    -      -       +      -
    481A  SER*     4.1    22.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260A  LEU*     4.6     1.2    -      -       -      +
    270A  VAL*     4.4     2.7    -      -       +      -
    271A  VAL      3.8     2.7    -      -       -      +
    272A  ILE*     3.8    26.9    -      -       +      -
    284A  ILE*     4.1     9.9    -      -       +      +
    285A  ILE*     1.3    85.2    -      -       -      +
    287A  GLN*     1.3    62.9    +      -       -      +
    288A  LEU*     3.6    22.0    -      -       +      -
    345A  ILE*     3.9    19.1    -      -       +      -
    349A  LEU*     6.3     0.2    -      -       +      -
    451A  GLY*     3.0     7.3    -      -       -      -
    452A  LEU*     2.9    42.1    +      -       +      +
    454A  LEU*     3.9    27.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  SER*     2.6    32.0    +      -       -      +
    265A  LEU      3.5     3.0    +      -       -      -
    266A  ALA*     3.4    29.3    -      -       +      +
    270A  VAL*     3.2     7.3    -      -       -      +
    271A  VAL*     2.9    45.9    +      -       +      +
    273A  ARG*     2.8    33.3    +      -       -      +
    285A  ILE*     5.7     1.6    -      -       +      -
    286A  VAL*     1.3    75.3    -      -       -      +
    288A  LEU*     1.3    64.3    +      -       -      +
    450A  THR      4.0     7.2    -      -       -      +
    481A  SER      4.7    12.2    +      -       -      +
    482A  GLU*     4.9     0.2    +      -       -      -
    484A  TYR*     3.7    21.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     2.7    29.2    -      -       +      +
    266A  ALA*     3.3    12.6    +      -       -      -
    270A  VAL*     4.1     8.3    -      -       +      -
    286A  VAL*     3.6    28.7    -      -       +      +
    287A  GLN*     1.3    77.2    -      -       -      +
    289A  ASN*     1.3    56.9    +      -       -      +
    290A  GLU      3.7    15.5    -      -       -      +
    292A  VAL*     5.1     2.7    -      -       +      +
    341A  THR*     3.9    22.4    -      -       +      +
    344A  GLN*     5.7     0.7    -      -       -      +
    345A  ILE*     4.0    12.8    -      -       +      -
    449A  ILE*     3.5    28.9    -      -       +      +
    450A  THR      3.7    11.9    +      -       -      +
    451A  GLY      4.0     6.7    -      -       -      +
    452A  LEU*     3.9    18.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     3.6     9.9    -      -       -      +
    266A  ALA*     3.7    15.9    -      -       -      +
    267A  GLU      4.6     1.2    -      -       -      -
    268A  GLU*     2.6    35.6    +      -       -      +
    269A  LYS*     4.5     1.3    -      -       -      -
    270A  VAL*     3.5    20.4    -      -       +      +
    288A  LEU*     1.3    74.5    -      -       -      +
    290A  GLU*     1.3    70.7    +      -       +      +
    344A  GLN*     3.9    18.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     3.6    11.2    -      -       +      -
    288A  LEU*     3.7    16.3    -      -       -      +
    289A  ASN*     1.3    87.7    +      -       +      +
    291A  SER*     1.3    67.3    +      -       -      +
    292A  VAL*     4.0     4.5    +      -       +      +
    341A  THR*     4.7     4.8    +      -       -      +
    344A  GLN*     4.3    20.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     3.4    21.8    -      -       -      +
    290A  GLU*     1.3    81.5    -      -       -      +
    292A  VAL*     1.3    62.4    +      -       -      +
    293A  LYS*     4.2     6.8    +      -       -      -
    337A  GLN*     4.9     6.6    +      -       -      +
    448A  ASN*     3.4    28.8    +      -       -      +
    449A  ILE      3.5    11.7    -      -       -      -
    450A  THR*     4.4     5.8    -      -       -      -
    520A  NAG      3.8    16.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  LEU*     5.2     1.3    -      -       +      -
    290A  GLU*     4.7     3.4    -      -       +      +
    291A  SER*     1.3    76.9    -      -       -      +
    293A  LYS*     1.3    63.7    +      -       -      +
    333A  ILE*     3.6    30.5    -      -       +      -
    334A  SER      5.3     0.2    -      -       -      +
    337A  GLN*     3.6    34.8    -      -       +      +
    338A  TRP*     4.2    11.0    -      -       +      +
    341A  THR*     3.1    32.1    -      -       +      +
    448A  ASN*     3.9     0.9    -      -       -      -
    449A  ILE*     2.4    52.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  SER*     4.2     6.0    +      -       -      -
    292A  VAL*     1.3    85.8    -      -       -      +
    294A  ILE*     1.3    60.8    +      -       -      +
    295A  ASN*     4.8     1.5    +      -       -      +
    332A  ASN      3.7     3.7    -      -       -      +
    333A  ILE*     3.7    11.8    -      -       -      +
    334A  SER      4.6     1.9    +      -       -      -
    337A  GLN*     3.8    24.0    +      -       -      +
    446A  SER*     5.3     4.5    -      -       -      -
    447A  SER      4.7     1.1    -      -       -      -
    448A  ASN*     3.8    24.6    -      -       +      +
    520A  NAG      5.9     3.4    -      -       -      -
      1T  NAG      4.0    54.5    +      -       -      +
      2T  NAG      4.8     6.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  LEU*     4.0     6.5    -      -       +      -
    261A  LEU*     3.6    20.6    -      -       +      -
    293A  LYS*     1.3    76.0    -      -       -      +
    295A  ASN*     1.3    64.6    +      -       -      +
    296A  CYS*     4.2     8.0    -      -       -      -
    331A  CYS*     4.2    20.0    -      -       +      -
    332A  ASN      3.2     9.6    -      -       -      +
    333A  ILE*     3.9    21.8    -      -       +      -
    374A  HIS*     3.6    32.1    -      -       +      +
    416A  LEU*     4.6     1.1    -      -       +      -
    445A  CYS      3.9     1.2    -      -       -      +
    446A  SER*     3.2     2.9    -      -       -      -
    447A  SER*     2.5    66.7    +      -       -      +
    449A  ILE*     3.8    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ILE*     1.3    76.9    -      -       -      +
    296A  CYS*     1.3    63.1    +      -       -      +
    331A  CYS*     3.2     3.3    -      -       -      -
    332A  ASN*     2.8    35.9    +      -       +      -
    445A  CYS      3.9     1.5    -      -       -      -
    446A  SER*     2.3    35.3    -      -       -      -
      1S  NAG      3.3    27.4    -      -       +      +
      1T  NAG      1.5    59.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ILE*     4.2    12.8    -      -       -      -
    295A  ASN*     1.3    75.8    -      -       -      +
    297A  THR*     1.3    65.7    +      -       -      +
    330A  HIS      3.3     2.7    -      -       -      +
    331A  CYS*     2.2    50.0    -      -       -      -
    376A  PHE*     3.3    27.6    -      -       +      -
    378A  CYS*     5.4     0.2    -      -       -      -
    383A  PHE*     4.2     7.2    -      -       +      -
    444A  ARG*     3.4     2.6    -      -       -      +
    445A  CYS*     2.9    44.2    +      -       -      +
    447A  SER*     6.0     0.7    -      -       -      -
      1S  NAG      5.3     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  CYS*     1.3    78.3    -      -       -      +
    298A  ARG*     1.3    69.7    +      -       -      +
    299A  PRO*     3.7    10.8    -      -       +      +
    327A  ARG*     6.1     0.2    -      -       -      +
    329A  ALA*     3.1     6.8    -      -       -      +
    330A  HIS*     3.0    61.3    +      -       +      +
    383A  PHE*     3.5     8.0    -      -       -      -
    442A  GLN*     4.5     3.8    +      -       -      +
    443A  ILE      3.4    13.1    +      -       -      -
    444A  ARG*     3.9    20.0    +      -       -      +
      1S  NAG      4.5    11.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  THR*     1.3    75.7    +      -       -      +
    299A  PRO*     1.3    67.9    +      -       +      +
    300A  SER*     2.6    48.2    +      -       -      +
    301A  ASN*     3.5    11.9    -      -       -      +
    302A  ASN*     4.0    17.0    -      -       -      +
    327A  ARG      5.7     0.4    -      -       -      +
    329A  ALA*     3.8    10.5    -      -       +      +
    381A  GLU*     2.4    30.6    +      -       -      -
    383A  PHE*     3.6     5.0    -      -       +      -
    420A  ILE*     3.5    28.0    -      -       +      -
    438A  PRO*     4.8     5.1    -      -       -      +
    439A  ILE      5.4     0.4    +      -       -      -
    440A  LYS*     5.2     3.0    -      -       -      +
    441A  GLY      3.2    28.5    +      -       -      +
    442A  GLN*     4.2     1.0    -      -       -      +
    443A  ILE*     3.4    36.0    +      -       +      +
----------------------------------------------------------
 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