Contacts of the strand formed by residues 276 - 282 (chain B) in PDB entry 4COO


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 276 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  ASP      2.9    16.5    +      -       -      +
    250B  MET*     3.3    18.2    -      -       +      +
    251B  LEU      2.8    32.6    +      -       -      +
    274B  GLY      4.3     6.5    -      -       -      +
    275B  CYS*     1.3    74.2    -      -       -      +
    277B  ILE*     1.3    57.9    +      -       -      +
    278B  ILE*     3.7    10.6    -      -       +      +
    321B  ASP*     3.5    24.9    +      -       -      +
    322B  LYS*     3.6    37.2    -      -       -      +
    363B  GLU*     3.5    25.3    +      -       -      -
    364B  LEU*     6.2     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 277 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  LEU*     3.6    22.2    -      -       +      +
    261B  ILE*     3.8    31.2    -      -       +      -
    265B  ALA*     4.0    22.4    -      -       +      -
    268B  LEU*     4.2    17.0    -      -       +      -
    269B  LYS*     4.1     9.9    -      -       +      -
    275B  CYS*     3.8    11.0    -      -       -      +
    276B  ARG*     1.3    78.5    -      -       -      +
    278B  ILE*     1.3    63.7    +      -       -      +
    319B  VAL      3.5    28.0    -      -       -      +
    320B  VAL*     3.9     3.9    -      -       -      +
    321B  ASP*     2.8    40.8    +      -       -      +
    322B  LYS      3.3     8.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 278 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  MET*     3.8    39.9    -      -       +      -
    251B  LEU      2.8    12.7    +      -       -      +
    252B  VAL*     3.4     8.2    -      -       +      +
    253B  ALA      3.0    27.0    +      -       -      +
    261B  ILE*     3.8     4.6    -      -       -      +
    276B  ARG*     3.7    27.8    -      -       +      +
    277B  ILE*     1.3    83.2    -      -       -      +
    279B  GLY*     1.3    62.7    +      -       -      +
    322B  LYS*     3.3    13.0    -      -       +      +
    324B  PHE*     3.5    35.2    -      -       +      -
    356B  VAL*     4.0    15.5    -      -       +      -
    360B  ALA*     4.1     4.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 279 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  ALA      3.5     6.1    -      -       -      -
    261B  ILE*     3.5    13.0    -      -       -      -
    278B  ILE*     1.3    74.0    -      -       -      +
    280B  VAL*     1.3    64.0    +      -       -      +
    320B  VAL*     3.7     7.3    -      -       -      +
    322B  LYS      2.9    10.6    +      -       -      -
    323B  TRP*     3.3    21.5    -      -       -      -
    324B  PHE      2.9    26.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 280 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  VAL*     3.7    21.5    -      -       +      -
    253B  ALA      3.0    10.0    +      -       -      +
    254B  SER*     3.4    15.0    -      -       -      -
    255B  VAL*     3.0    30.5    +      -       -      +
    279B  GLY*     1.3    77.2    -      -       -      -
    281B  ASP*     1.3    62.4    +      -       -      +
    282B  PRO*     4.5     1.6    -      -       -      +
    306B  ILE*     5.0     1.1    -      -       +      +
    323B  TRP*     4.5     1.6    -      -       -      -
    324B  PHE      3.6     2.5    -      -       -      +
    326B  SER*     3.6    23.1    -      -       -      +
    352B  SER*     4.0    15.7    -      -       -      +
    353B  THR*     4.3     4.9    -      -       -      -
    356B  VAL*     3.7    42.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255B  VAL      4.5     0.4    -      -       -      +
    280B  VAL*     1.3    75.8    -      -       -      +
    282B  PRO*     1.3    68.6    -      -       -      +
    285B  SER*     2.6    32.8    +      -       -      -
    287B  LEU*     3.2    15.5    +      -       -      +
    288B  ALA*     3.1    28.7    +      -       +      -
    307B  GLY*     3.7     1.9    +      -       -      -
    323B  TRP*     4.0    16.8    -      -       +      -
    324B  PHE      3.1     6.7    +      -       -      +
    325B  LYS*     2.8    29.4    +      -       +      +
    326B  SER*     2.9    22.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 282 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281B  ASP*     1.3    95.2    -      -       -      +
    283B  GLU*     1.3    65.8    +      -       -      +
    285B  SER*     3.0    17.8    +      -       -      -
    301B  TYR*     3.5    47.3    -      -       +      +
    303B  VAL*     5.7     2.0    -      -       +      -
    306B  ILE*     3.6    26.5    -      -       +      +
    307B  GLY*     3.6    15.3    -      -       -      +
    325B  LYS*     3.2    10.8    +      -       -      -
    326B  SER*     3.4    13.4    -      -       -      +
    327B  ASN*     6.1     0.4    -      -       -      -
    328B  ASP*     6.0     0.4    -      -       -      +
----------------------------------------------------------
 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