Contacts of the strand formed by residues 81 - 90 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  VAL      3.0    13.9    -      -       -      +
     66B  ARG*     3.2     2.3    -      -       -      -
     67B  LEU*     3.1    39.3    +      -       +      +
     70B  GLU*     4.6     1.4    +      -       -      -
     79B  ASN*     5.4     6.7    +      -       -      +
     80B  GLU*     1.3    82.2    -      -       -      +
     82B  PHE*     1.3    63.9    +      -       -      +
     83B  ILE*     3.8     8.6    -      -       +      +
    112B  ALA*     4.3    10.2    -      -       -      +
    113B  SER*     2.8    39.1    +      -       -      -
    115B  ASN*     6.1     0.6    -      -       -      +
    118B  VAL*     3.2    27.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  ASN*     5.9     4.3    -      -       -      -
     64B  GLN*     5.6    17.7    -      -       +      +
     65B  VAL      3.4     5.4    -      -       -      -
     66B  ARG*     3.4    44.9    -      -       +      -
     70B  GLU*     4.2     2.0    -      -       -      -
     76B  VAL*     6.3     0.4    -      -       +      -
     80B  GLU*     3.4    33.7    -      -       +      -
     81B  GLN*     1.3    76.6    -      -       -      +
     83B  ILE*     1.3    62.8    +      -       -      +
     84B  SER      4.3     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  GLN*     3.5     3.7    -      -       -      -
     65B  VAL*     2.8    42.6    +      -       -      +
     67B  LEU*     3.9    23.6    -      -       +      -
     81B  GLN*     4.5    10.5    -      -       +      +
     82B  PHE*     1.3    78.8    -      -       -      +
     84B  SER*     1.3    78.4    +      -       -      +
    108B  LEU*     3.8    20.4    -      -       +      -
    109B  LYS*     4.4     1.3    -      -       +      -
    110B  SER*     3.7    44.2    -      -       -      +
    111B  ALA      4.7     1.1    -      -       -      +
    112B  ALA*     4.1    13.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ILE      4.2     5.4    -      -       -      -
     64B  GLN*     4.6    13.5    +      -       -      +
     82B  PHE      4.3     0.4    +      -       -      -
     83B  ILE*     1.3    82.6    -      -       -      +
     85B  ALA*     1.3    60.8    +      -       -      +
    108B  LEU*     3.6     2.0    -      -       -      +
    109B  LYS*     2.8    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  GLY*     5.8     2.8    -      -       -      -
     63B  ILE*     3.4    27.6    +      -       +      +
     65B  VAL*     4.8     3.6    -      -       +      -
     83B  ILE      3.7     0.2    +      -       -      -
     84B  SER*     1.3    74.2    -      -       -      +
     86B  SER*     1.3    66.3    +      -       -      +
     87B  LYS      4.8     0.2    -      -       -      +
     88B  SER*     3.9    15.1    +      -       -      +
    106B  ILE*     3.5    30.1    -      -       +      -
    107B  LYS      3.3     4.9    -      -       -      +
    108B  LEU*     4.3     1.8    -      -       -      +
    109B  LYS*     4.8     1.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ALA*     1.3    74.2    -      -       -      +
     87B  LYS*     1.3    83.2    +      -       -      +
     88B  SER      4.2     0.7    +      -       -      -
    107B  LYS*     2.6    18.8    +      -       -      -
    108B  LEU      4.3     3.1    -      -       -      -
    109B  LYS*     3.6    27.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TRP*     4.8     0.6    -      -       +      -
     86B  SER*     1.3   101.5    -      -       -      +
     88B  SER*     1.3    60.7    +      -       -      +
     89B  ILE*     3.7    23.7    +      -       +      -
    105B  LEU      4.0     0.5    -      -       -      +
    106B  ILE*     3.6     1.6    -      -       -      +
    107B  LYS*     2.8    51.1    +      -       +      +
    245B  ASN*     4.1    27.0    +      -       +      +
    111F  ALA*     5.3     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  TYR*     3.6    37.2    -      -       -      -
     60B  LYS      4.9     3.9    +      -       -      -
     62B  GLY*     5.7     1.6    +      -       -      -
     63B  ILE*     4.8    11.3    +      -       -      +
     85B  ALA*     3.9    19.8    +      -       -      +
     86B  SER      4.2     0.8    +      -       -      -
     87B  LYS*     1.3    73.1    +      -       -      +
     89B  ILE*     1.3    62.0    +      -       -      +
     90B  VAL*     3.6     2.0    +      -       -      +
    104B  MET*     4.8     4.5    -      -       -      -
    105B  LEU      3.6     5.2    -      -       -      -
    106B  ILE*     4.4    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TRP*     3.8    14.6    -      -       +      -
     87B  LYS*     4.1    17.3    -      -       +      -
     88B  SER*     1.3    70.1    -      -       -      +
     90B  VAL*     1.3    70.3    +      -       -      +
    104B  MET*     3.5     2.7    -      -       -      -
    105B  LEU*     2.7    40.8    +      -       +      +
    237B  TRP*     3.7    18.8    -      -       +      -
    241B  THR*     3.8    14.6    -      -       +      -
    245B  ASN*     3.4    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  ALA*     3.8    19.7    -      -       +      +
     59B  TYR*     3.4    46.4    -      -       +      -
     88B  SER      3.6     1.6    +      -       -      +
     89B  ILE*     1.3    81.2    -      -       -      +
     91B  HIS*     1.3    77.5    +      -       -      +
     92B  PRO*     3.3     7.3    -      -       -      +
     94B  TYR*     4.0    14.6    -      -       +      -
    104B  MET*     4.0    11.9    -      -       +      -
    237B  TRP*     4.4     0.7    -      -       -      -
----------------------------------------------------------
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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