Contacts of the strand formed by residues 982 - 992 (chain A) in PDB entry 1K3A


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 MET 982 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    974A  GLU*     3.4    35.9    -      -       -      +
    976A  GLY*     3.4    25.8    -      -       -      +
    977A  GLN*     3.4    32.0    +      -       +      +
    981A  GLY*     1.3    71.3    -      -       -      -
    983A  VAL*     1.3    66.1    +      -       -      +
    984A  TYR*     3.4    39.2    -      -       +      +
   1004A  THR*     2.8    40.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 983 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  ACP      3.4    56.5    -      -       +      +
    974A  GLU*     3.8     0.2    -      -       -      -
    975A  LEU*     2.8    27.3    +      -       +      -
    976A  GLY      2.8    22.0    +      -       -      +
    978A  GLY*     4.1     4.5    -      -       -      +
    981A  GLY      4.0     9.2    -      -       -      +
    982A  MET*     1.3    79.6    -      -       -      +
    984A  TYR*     1.3    68.7    +      -       -      +
   1001A  ALA*     4.8     0.4    -      -       +      -
   1002A  ILE      3.3    16.2    -      -       -      +
   1003A  LYS*     4.2    21.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 984 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    971A  MET*     3.3    44.4    -      -       +      -
    973A  ARG*     3.3    10.5    -      -       -      +
    974A  GLU*     3.7    34.6    +      -       +      -
    975A  LEU*     3.8     7.5    -      -       -      +
    982A  MET*     3.4    32.0    -      -       +      +
    983A  VAL*     1.3    73.9    -      -       -      +
    985A  GLU*     1.3    65.1    +      -       -      +
   1001A  ALA*     3.4     3.3    -      -       -      -
   1002A  ILE*     2.5    45.4    +      -       +      +
   1004A  THR*     3.6    26.9    +      -       +      -
   1044A  PRO*     6.4     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 985 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    971A  MET*     3.8     2.3    -      -       -      -
    972A  SER*     2.9    26.4    +      -       -      -
    973A  ARG*     2.7    58.7    +      -       +      +
    975A  LEU*     3.7    20.5    -      -       +      +
    984A  TYR*     1.3    75.0    -      -       -      +
    986A  GLY*     1.3    64.0    +      -       -      +
    999A  ARG*     2.9    34.5    +      -       -      -
   1000A  VAL      3.5     3.6    -      -       -      +
   1002A  ILE*     4.5     1.1    -      -       -      -
   1051A  LEU*     3.8    25.1    -      -       +      +
   1053A  THR*     5.8     0.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 986 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    970A  THR      3.1    15.0    -      -       -      -
    972A  SER*     3.7     9.4    -      -       -      -
    984A  TYR      4.1     0.6    +      -       -      -
    985A  GLU*     1.3    81.5    -      -       -      +
    987A  VAL*     1.3    69.9    +      -       -      +
    999A  ARG*     3.5     4.3    -      -       -      +
   1000A  VAL*     2.9    32.0    +      -       -      +
   1002A  ILE*     4.0     5.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 987 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    968A  LYS      3.8     1.3    -      -       -      +
    969A  ILE*     3.4     3.1    -      -       -      +
    970A  THR*     2.9    45.0    +      -       -      +
    972A  SER*     4.7     7.2    -      -       -      +
    986A  GLY*     1.3    80.2    -      -       -      +
    988A  ALA*     1.3    65.4    +      -       -      +
    989A  LYS*     5.3     5.2    -      -       +      +
    997A  GLU*     3.6    42.0    -      -       +      +
    998A  THR      3.3     9.2    -      -       -      +
    999A  ARG*     4.7    11.9    -      -       +      -
   1000A  VAL*     3.9     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 988 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    968A  LYS      3.2     5.2    -      -       -      -
    969A  ILE*     4.0    20.4    -      -       +      -
    987A  VAL*     1.3    76.2    -      -       -      +
    989A  LYS*     1.3    63.1    +      -       -      +
    990A  GLY      4.1     0.2    +      -       -      -
    991A  VAL*     4.0    11.6    -      -       +      +
    997A  GLU*     3.2     1.7    -      -       -      -
    998A  THR*     2.7    39.3    +      -       -      -
   1000A  VAL*     4.0    21.8    -      -       +      -
   1048A  ILE*     4.0    13.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 989 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    964A  VAL*     6.1     0.3    -      -       -      +
    968A  LYS*     2.9    50.9    +      -       +      +
    970A  THR*     5.7     7.5    -      -       -      +
    987A  VAL*     5.3     4.2    -      -       +      +
    988A  ALA*     1.3    75.1    -      -       -      +
    990A  GLY*     1.3    65.4    +      -       -      +
    991A  VAL*     3.4     7.6    +      -       -      +
    996A  PRO      3.4    11.0    -      -       -      +
    997A  GLU*     4.0    23.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 990 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    968A  LYS*     5.8     0.7    -      -       -      -
    988A  ALA      4.1     0.6    +      -       -      -
    989A  LYS*     1.3    72.7    -      -       -      +
    991A  VAL*     1.3    61.5    +      -       -      +
    992A  VAL      3.5     4.0    -      -       -      -
    995A  GLU      4.1     7.4    +      -       -      -
    996A  PRO*     2.8    18.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 991 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    964A  VAL*     4.4    14.1    -      -       +      -
    969A  ILE*     5.6     0.9    -      -       +      -
    988A  ALA*     4.0    18.1    +      -       +      +
    989A  LYS      3.9     9.2    -      -       -      +
    990A  GLY*     1.3    79.2    -      -       -      +
    992A  VAL*     1.3    69.6    +      -       +      +
    995A  GLU      4.7     0.6    +      -       -      -
    998A  THR*     3.7    26.9    +      -       -      +
   1036A  LEU*     4.0    35.0    -      -       +      +
   1048A  ILE*     3.6    25.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 992 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    990A  GLY*     4.6     2.4    -      -       -      -
    991A  VAL*     1.3    89.3    +      -       +      +
    993A  LYS*     1.3    77.1    +      -       +      +
    994A  ASP      3.6     0.2    +      -       -      -
    995A  GLU*     3.1    41.8    +      -       +      +
    998A  THR*     3.6    27.9    +      -       +      +
   1036A  LEU*     4.0    21.3    -      -       +      -
----------------------------------------------------------
 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