Contacts of the strand formed by residues 279 - 288 (chain A) in PDB entry 3I7L


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 ARG 279 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     2.8    44.7    +      -       -      +
    255A  GLN*     3.0    40.5    +      -       -      +
    256A  SER*     4.0     7.1    -      -       -      +
    273A  LEU      3.7     1.9    -      -       -      +
    274A  GLY*     4.3     1.4    -      -       -      -
    275A  ASP*     3.2    38.3    +      -       -      +
    277A  GLU*     3.7    28.5    -      -       +      +
    278A  GLY*     1.3    80.3    -      -       -      +
    280A  LEU*     1.3    60.3    +      -       -      +
    281A  PHE*     3.5    24.9    -      -       +      -
    304A  LEU*     4.2    15.5    -      -       +      +
    306A  GLY      3.2    11.7    -      -       -      +
    307A  GLU*     4.4     7.9    -      -       +      +
    308A  THR*     5.3     0.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  LEU*     4.1    26.2    -      -       +      -
    273A  LEU      3.3    25.1    -      -       -      +
    274A  GLY*     4.9     0.9    -      -       -      -
    278A  GLY      3.7     0.2    +      -       -      -
    279A  ARG*     1.3    73.3    -      -       -      +
    281A  PHE*     1.3    74.6    +      -       -      +
    304A  LEU*     3.7     4.7    -      -       -      +
    305A  LEU*     2.8    33.6    +      -       +      +
    306A  GLY      2.8    16.0    +      -       -      +
    308A  THR*     4.1    29.8    -      -       +      +
    314A  LEU*     4.1    13.5    -      -       +      -
    322A  VAL*     4.9     9.6    -      -       +      -
    334A  VAL*     5.3     0.4    -      -       +      -
    336A  LEU*     4.4    20.4    -      -       +      -
    347A  VAL*     4.9     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     4.1    11.0    -      -       +      -
    253A  ILE*     3.8    25.6    -      -       +      -
    258A  ILE*     5.2     4.7    -      -       +      -
    272A  LEU*     3.5    10.4    -      -       -      +
    273A  LEU*     3.1    51.7    +      -       +      -
    275A  ASP*     3.6    28.7    -      -       +      -
    279A  ARG*     3.5    37.5    -      -       +      -
    280A  LEU*     1.3    81.1    -      -       -      +
    282A  MET*     1.3    62.0    +      -       -      +
    283A  LEU      4.1     0.7    -      -       -      -
    302A  VAL*     3.4    27.4    -      -       +      -
    303A  GLU      3.2     4.3    -      -       -      +
    304A  LEU*     3.7    28.7    -      -       +      -
    305A  LEU*     4.2     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  VAL*     4.2     7.4    -      -       +      -
    270A  ARG*     3.9    38.6    -      -       +      +
    271A  TYR      3.2    21.1    -      -       -      +
    272A  LEU*     3.9    13.9    -      -       +      -
    281A  PHE*     1.3    75.1    -      -       -      +
    283A  LEU*     1.3    62.6    +      -       -      +
    284A  LEU*     3.8    29.2    +      -       +      +
    301A  ARG      3.6     0.3    -      -       -      +
    302A  VAL*     3.0     6.1    -      -       -      -
    303A  GLU*     2.7    38.2    +      -       +      +
    305A  LEU*     3.7    33.4    -      -       +      +
    336A  LEU*     4.2     9.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  ILE*     4.9     5.8    -      -       +      -
    230A  ILE*     4.4    25.1    -      -       +      -
    232A  ILE*     5.1     1.6    -      -       +      -
    237A  ILE*     4.2    22.9    -      -       +      -
    248A  ILE*     4.8     0.7    -      -       +      -
    269A  SER      3.8     0.5    -      -       -      +
    270A  ARG*     3.2     5.5    -      -       -      +
    271A  TYR*     2.8    52.2    +      -       +      +
    273A  LEU*     3.4    36.9    -      -       +      +
    281A  PHE      4.1     0.6    -      -       -      -
    282A  MET*     1.3    72.7    -      -       -      +
    284A  LEU*     1.3    61.0    +      -       -      +
    285A  LEU*     4.3     7.0    -      -       +      -
    300A  LEU*     4.4    17.7    -      -       +      -
    301A  ARG      3.2    17.0    -      -       -      +
    302A  VAL*     4.3    12.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  SER      3.5     1.6    -      -       -      +
    270A  ARG*     3.5    30.5    -      -       +      -
    282A  MET*     3.8    20.9    -      -       +      +
    283A  LEU*     1.3    75.9    -      -       -      +
    285A  LEU*     1.3    65.6    +      -       -      +
    286A  GLU*     3.6     3.6    +      -       -      +
    300A  LEU*     3.4     5.0    -      -       -      +
    301A  ARG*     2.6    72.0    +      -       +      +
    303A  GLU*     3.3    35.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  VAL*     3.8    23.6    -      -       +      -
    226A  PHE*     3.8    25.6    -      -       +      -
    230A  ILE*     3.8    24.5    -      -       +      -
    239A  TYR*     5.3     2.2    -      -       +      -
    268A  GLY      2.9    23.3    -      -       -      +
    269A  SER*     2.5    25.4    +      -       -      +
    271A  TYR*     4.7     4.7    -      -       +      -
    283A  LEU*     4.3    12.6    -      -       +      +
    284A  LEU*     1.3    73.8    -      -       -      +
    286A  GLU*     1.3    59.8    +      -       -      +
    287A  LYS*     3.0    13.3    +      -       -      +
    297A  LEU*     3.7     7.9    -      -       +      -
    300A  LEU*     3.2    27.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  LEU      3.6     3.6    +      -       -      +
    285A  LEU*     1.3    68.2    -      -       -      +
    287A  LYS*     1.3    74.1    +      -       -      +
    297A  LEU*     3.6     4.4    -      -       -      -
    298A  LYS*     2.7    71.0    +      -       +      +
    299A  ASP*     2.9    32.3    +      -       +      +
    301A  ARG*     5.6    12.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  PRO*     5.6     2.5    -      -       -      -
    226A  PHE*     3.6    31.9    -      -       +      -
    267A  ASN*     3.8    30.5    +      -       -      +
    269A  SER*     4.3     8.3    -      -       -      -
    285A  LEU      3.0     6.5    +      -       -      +
    286A  GLU*     1.3    87.0    +      -       -      +
    288A  GLU*     1.3    67.7    +      -       -      +
    295A  VAL*     4.7    23.6    -      -       +      -
    296A  THR      3.5     9.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  LYS*     1.3    84.2    -      -       -      +
    289A  GLU*     1.3    69.8    +      -       -      +
    290A  GLN*     3.8    16.9    +      -       -      +
    295A  VAL*     3.9     2.7    -      -       -      -
    296A  THR*     3.1    58.6    +      -       +      +
    298A  LYS*     4.0    31.5    -      -       +      +
----------------------------------------------------------
 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