Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1C9T


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 GLN 81 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  VAL      3.0    13.5    -      -       -      +
     66C  ARG*     3.2     2.0    -      -       -      -
     67C  LEU*     3.0    46.1    +      -       +      +
     70C  GLU*     4.6     1.0    +      -       -      -
     79C  ASN*     5.4     6.9    +      -       -      +
     80C  GLU*     1.3    82.5    -      -       -      +
     82C  PHE*     1.3    65.0    +      -       -      +
     83C  ILE*     3.8     7.9    -      -       +      +
    112C  ALA*     4.3     5.4    -      -       -      +
    113C  SER*     2.8    38.2    +      -       -      -
    115C  ASN*     6.1     0.4    -      -       -      +
    118C  VAL*     3.1    28.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  ASN*     5.8     5.8    -      -       -      -
     64C  GLN*     5.6    15.9    -      -       +      +
     65C  VAL      3.3     5.8    -      -       -      +
     66C  ARG*     3.4    43.3    -      -       +      -
     70C  GLU*     4.2     1.8    -      -       -      -
     76C  VAL*     6.3     0.2    -      -       +      -
     80C  GLU*     3.4    34.1    -      -       +      -
     81C  GLN*     1.3    77.1    -      -       -      +
     83C  ILE*     1.3    61.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  GLN*     3.5     3.5    -      -       -      -
     65C  VAL*     2.8    42.0    +      -       -      +
     67C  LEU*     3.7    24.2    -      -       +      -
     81C  GLN*     4.5    10.1    -      -       +      +
     82C  PHE*     1.3    77.9    -      -       -      +
     84C  SER*     1.3    79.3    +      -       -      +
     85C  ALA      3.8     0.2    +      -       -      -
    108C  LEU*     3.7    20.4    -      -       +      -
    109C  LYS*     4.4     1.1    -      -       +      -
    110C  SER*     3.7    43.3    -      -       -      +
    111C  ALA      4.7     1.6    -      -       -      +
    112C  ALA*     4.1    14.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63C  ILE      4.1     5.6    -      -       -      -
     64C  GLN*     4.6    13.4    +      -       -      +
     82C  PHE      4.3     0.4    +      -       -      -
     83C  ILE*     1.3    82.0    -      -       -      +
     85C  ALA*     1.3    56.3    +      -       -      +
    108C  LEU*     3.6     1.3    -      -       -      -
    109C  LYS*     2.7    64.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  GLY*     5.7     3.3    -      -       -      -
     63C  ILE*     3.3    28.5    +      -       +      +
     65C  VAL*     4.9     3.1    -      -       +      -
     83C  ILE      3.8     0.2    +      -       -      -
     84C  SER*     1.3    74.8    -      -       -      +
     86C  SER*     1.3    64.7    +      -       -      +
     87C  LYS      4.8     0.2    -      -       -      +
     88C  SER*     3.9    16.2    +      -       -      +
    106C  ILE*     3.6    28.5    -      -       +      -
    107C  LYS      3.4     4.5    -      -       -      +
    108C  LEU*     4.4     2.2    -      -       -      +
    109C  LYS*     5.8     0.8    -      -       -      -
    109F  LYS*     4.8     2.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  ALA*     1.3    75.3    -      -       -      +
     87C  LYS*     1.3    76.1    +      -       -      +
     88C  SER*     4.2     0.3    +      -       -      -
    107C  LYS*     2.6    18.2    +      -       -      -
    108C  LEU      4.3     3.1    -      -       -      -
    109C  LYS*     3.6    21.4    -      -       -      +
     64F  GLN*     4.1     2.9    -      -       -      +
     84F  SER*     2.7    23.7    +      -       -      -
    109F  LYS*     3.0    36.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  TRP*     5.0     1.0    -      -       +      -
     86C  SER*     1.3   100.2    -      -       -      +
     88C  SER*     1.3    62.6    +      -       -      +
     89C  ILE*     3.7    23.3    +      -       +      -
    105C  LEU      4.0     0.2    -      -       -      +
    106C  ILE*     3.6     2.3    -      -       -      +
    107C  LYS*     2.8    52.7    +      -       +      +
    245C  ASN*     3.9    22.7    +      -       +      +
     64F  GLN*     3.1    10.1    -      -       -      +
     82F  PHE*     3.2    32.1    +      -       +      +
     83F  ILE*     4.8     3.8    -      -       -      +
     84F  SER*     3.8    15.3    -      -       -      +
    109F  LYS*     5.3     3.6    -      -       -      -
    110F  SER*     6.0     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  TYR*     3.7    31.3    -      -       -      -
     60C  LYS      4.9     4.4    +      -       -      -
     62C  GLY*     5.7     1.2    +      -       -      -
     63C  ILE*     4.9    10.7    +      -       -      +
     85C  ALA*     3.9    19.8    +      -       -      +
     86C  SER      4.2     0.6    +      -       -      -
     87C  LYS*     1.3    73.4    +      -       -      +
     89C  ILE*     1.3    61.1    +      -       -      +
     90C  VAL      3.6     3.0    +      -       -      -
    104C  MET*     4.8     4.0    -      -       -      -
    105C  LEU      3.6     5.2    -      -       -      -
    106C  ILE*     4.4    11.5    -      -       -      +
     34F  ASN*     5.2     0.3    -      -       -      +
     38F  GLY*     5.7     0.3    -      -       -      -
     64F  GLN*     2.7    32.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  TRP*     3.7    20.6    -      -       +      -
     87C  LYS*     3.7    17.2    -      -       +      -
     88C  SER*     1.3    71.6    -      -       -      +
     90C  VAL*     1.3    70.9    +      -       -      +
     92C  PRO*     6.0     0.2    -      -       +      -
    104C  MET*     3.4     2.5    -      -       -      -
    105C  LEU*     2.7    40.4    +      -       +      +
    237C  TRP*     3.7    11.1    -      -       +      -
    241C  THR*     3.7    16.6    -      -       +      -
    245C  ASN*     3.5    38.1    -      -       +      +
     64F  GLN*     4.9     3.8    -      -       -      +
     82F  PHE*     4.6    28.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56C  ALA*     3.8    19.1    -      -       +      +
     59C  TYR*     3.4    46.4    -      -       +      -
     88C  SER      3.6     1.6    +      -       -      -
     89C  ILE*     1.3    82.0    -      -       -      +
     91C  HIS*     1.3    75.8    +      -       -      +
     92C  PRO*     3.3     7.3    -      -       -      +
     94C  TYR*     4.0    14.6    -      -       +      -
    104C  MET*     3.8    14.6    -      -       +      -
    237C  TRP*     4.4     0.4    -      -       -      -
     38F  GLY*     4.1    23.5    -      -       -      +
----------------------------------------------------------
 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