Contacts of the strand formed by residues 22 - 31 (chain B) in PDB entry 4C02


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 THR 22 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  GLY      3.8     0.9    +      -       -      -
     21B  GLN*     1.3    70.7    -      -       -      +
     23B  CYS*     1.3    66.6    +      -       -      +
     24B  VAL*     3.8     2.1    +      -       +      +
     48B  LYS*     3.8    36.1    -      -       +      -
     49B  PHE*     3.6     8.3    -      -       -      +
     50B  ARG*     3.8    20.4    -      -       -      +
    107B  LEU*     3.4     6.6    -      -       -      -
    108B  GLU*     3.0    52.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PRO*     3.9    10.1    -      -       -      -
     22B  THR*     1.3    72.8    -      -       -      +
     24B  VAL*     1.3    60.9    +      -       -      +
     25B  VAL*     4.0     1.8    -      -       +      -
     47B  PHE      3.4     1.4    -      -       -      +
     48B  LYS*     3.1     7.4    -      -       -      -
     49B  PHE*     2.8    57.9    +      -       +      +
     51B  ILE*     3.2    38.6    -      -       -      -
     64B  ALA*     5.1     2.2    -      -       -      -
    104B  LEU*     4.3    11.0    -      -       +      -
    106B  ASN      3.9     4.0    -      -       -      -
    107B  LEU*     3.8    16.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  THR*     4.3     2.9    -      -       +      +
     23B  CYS*     1.3    75.4    -      -       -      +
     25B  VAL*     1.3    64.8    +      -       -      +
     46B  PRO*     3.7    25.8    -      -       +      -
     47B  PHE      3.4     3.8    -      -       -      +
     48B  LYS*     4.0    20.0    -      -       +      -
    104B  LEU*     3.7     0.7    -      -       -      +
    105B  LEU*     2.8    36.8    +      -       +      +
    106B  ASN*     2.9    26.8    +      -       +      +
    108B  GLU*     3.7    38.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  CYS*     4.4     0.7    -      -       +      -
     24B  VAL*     1.3    80.8    -      -       -      +
     26B  HIS*     1.3    67.4    +      -       -      +
     27B  TYR*     4.4     0.9    -      -       +      -
     46B  PRO*     3.5     4.5    -      -       -      +
     47B  PHE*     2.8    63.9    +      -       +      +
     49B  PHE*     4.2    17.7    -      -       +      -
     60B  PHE*     4.2    18.6    -      -       +      -
     64B  ALA*     5.3     3.1    -      -       +      -
    102B  VAL*     4.0    11.9    -      -       +      -
    103B  GLU      3.1    13.9    -      -       -      +
    104B  LEU*     3.9    19.5    -      -       +      -
    105B  LEU*     4.0     7.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  VAL*     1.3    73.2    -      -       -      +
     27B  TYR*     1.3    59.1    +      -       -      +
     40B  SER*     2.9    37.6    +      -       -      +
     41B  ARG*     3.8    30.2    +      -       +      +
     44B  ASN*     4.4     6.4    +      -       -      -
     45B  LYS      3.8     4.9    -      -       -      -
     46B  PRO*     3.6    35.1    -      -       +      +
    101B  ASP      3.9     0.6    -      -       -      +
    102B  VAL*     3.3     4.0    -      -       -      +
    103B  GLU*     2.8    48.8    +      -       +      +
    105B  LEU*     3.6    22.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  LEU*     3.3    27.2    +      -       +      +
    200A  VAL*     4.7     0.9    +      -       -      +
     25B  VAL*     4.4     0.9    -      -       +      -
     26B  HIS*     1.3    75.6    -      -       -      +
     28B  THR*     1.3    65.6    +      -       -      +
     29B  GLY      4.1     9.6    -      -       -      -
     38B  ASP*     2.6    44.6    +      -       +      -
     39B  SER*     3.4     1.6    +      -       -      -
     40B  SER*     2.8    41.7    +      -       -      -
     41B  ARG*     3.5     4.2    +      -       -      +
     43B  ARG*     2.8    24.7    +      -       -      -
     47B  PHE*     3.6    42.0    -      +       +      -
     60B  PHE*     4.0    23.8    -      +       +      -
    100B  PHE*     4.2     7.2    -      +       +      -
    101B  ASP      3.2     9.4    -      -       -      +
    102B  VAL*     4.3     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  TYR*     1.3    73.9    +      -       -      +
     29B  GLY*     1.3    61.8    +      -       -      +
     30B  MET*     3.8    17.5    -      -       +      +
     36B  LYS*     4.1    30.5    -      -       +      -
     38B  ASP      3.6     7.4    -      -       -      +
     39B  SER*     3.4    14.2    +      -       -      +
     41B  ARG*     2.9    25.8    +      -       -      +
     99B  ILE      3.7     1.0    -      -       -      +
    100B  PHE*     3.3     2.8    -      -       -      -
    101B  ASP*     2.8    37.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  TYR*     4.1     2.6    -      -       -      -
     28B  THR*     1.3    72.3    -      -       -      +
     30B  MET*     1.3    62.9    +      -       -      +
     36B  LYS*     3.4     5.5    -      -       -      +
     37B  PHE*     2.8    40.0    +      -       -      -
     38B  ASP      2.7    18.1    +      -       -      +
     99B  ILE      3.4     5.6    -      -       -      -
    100B  PHE*     3.7    16.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  THR*     3.8    29.6    -      -       +      +
     29B  GLY*     1.3    77.9    -      -       -      +
     31B  LEU*     1.3    67.6    +      -       -      +
     34B  GLY*     3.8    23.1    -      -       -      +
     35B  LYS      3.1     8.1    -      -       -      +
     36B  LYS*     3.8    12.8    -      -       +      -
     37B  PHE*     3.3    12.7    -      -       -      -
     74B  LYS*     6.3     0.4    -      -       +      -
     98B  LEU*     3.5     1.2    -      -       -      -
     99B  ILE*     2.7    60.3    +      -       +      +
    101B  ASP*     4.4    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  MET*     1.3    79.3    -      -       -      +
     32B  GLN*     1.3    60.9    +      -       -      +
     33B  ASN*     3.1    18.2    -      -       -      +
     34B  GLY*     2.9    20.4    +      -       -      -
     35B  LYS*     2.8    24.4    +      -       +      +
     37B  PHE*     3.7    21.8    -      -       +      -
     91B  VAL      4.4     7.0    -      -       -      +
     92B  ILE*     4.0     9.6    -      -       +      -
     93B  PRO*     4.0    23.1    -      -       +      -
     96B  ALA*     4.7     3.6    -      -       +      -
     97B  THR      4.2     3.4    -      -       -      +
     98B  LEU*     3.8    18.2    -      -       +      -
     99B  ILE*     4.3     5.0    -      -       -      +
   1109B  EDO      3.7    28.3    -      -       -      +
----------------------------------------------------------
 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