Contacts of the strand formed by residues 91 - 100 (chain B) in PDB entry 6S1M


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 CYS 91 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  GLY*     3.4    16.4    -      -       -      +
     80B  LYS*     4.7     6.7    -      -       +      +
     85B  LEU*     3.6    37.9    -      -       +      -
     86B  GLN      6.0     1.1    -      -       -      -
     89B  GLU*     3.4    25.8    -      -       -      +
     90B  LYS*     1.3    75.2    -      -       -      +
     92B  CYS*     1.3    61.7    +      -       -      +
     93B  VAL*     4.9     3.7    -      -       -      +
    161B  VAL      3.9     0.2    -      -       -      +
    162B  PHE*     3.2    12.7    -      -       -      -
    163B  GLY      2.9    42.0    +      -       -      +
    164B  SER*     4.8     2.5    -      -       -      -
    165B  VAL*     5.5     1.1    -      -       -      -
    171B  PHE*     4.9     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  ALA*     4.1     6.7    -      -       +      -
     73B  TRP*     3.8    23.6    -      -       +      -
     78B  GLY*     3.0     9.9    +      -       -      +
     79B  VAL*     3.3    29.0    -      -       +      +
     80B  LYS*     3.1    27.0    +      -       -      +
     91B  CYS*     1.3    75.6    -      -       -      +
     93B  VAL*     1.3    68.5    +      -       -      +
     94B  VAL*     4.5     2.3    +      -       -      +
    160B  ALA*     4.1    16.2    -      -       -      -
    161B  VAL      3.1    12.3    -      -       -      +
    162B  PHE*     4.5     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  LYS      4.1    15.0    -      -       -      +
     82B  LEU*     4.1    24.9    -      -       +      +
     85B  LEU*     4.5    10.3    -      -       +      -
     91B  CYS*     4.9     3.6    -      -       -      +
     92B  CYS*     1.3    80.6    -      -       -      +
     94B  VAL*     1.3    69.0    +      -       -      +
     95B  GLY      4.1     1.0    +      -       -      -
    135B  LEU*     3.9    17.5    -      -       +      -
    137B  ASP*     5.9     1.3    -      -       -      +
    159B  LEU      3.9     0.7    -      -       -      +
    160B  ALA*     3.3     2.1    -      -       -      -
    161B  VAL*     2.9    43.9    +      -       +      +
    171B  PHE*     3.7    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  LEU*     4.9     6.3    -      -       +      +
     62B  ARG*     4.4    28.4    +      -       +      +
     65B  LEU*     4.0    30.7    -      -       +      -
     66B  GLU*     4.7    17.5    -      -       +      +
     69B  ALA*     6.1     0.2    -      -       +      -
     79B  VAL*     5.2     5.2    -      -       +      -
     80B  LYS      5.0     1.4    +      -       -      -
     92B  CYS*     4.7     7.6    -      -       -      +
     93B  VAL*     1.3    83.2    -      -       -      +
     95B  GLY*     1.3    60.8    +      -       -      +
    137B  ASP*     3.8    15.8    -      -       -      +
    158B  VAL*     4.8     5.2    -      -       +      -
    159B  LEU      3.5     8.5    -      -       -      +
    160B  ALA*     3.9    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  LEU*     4.3     6.5    -      -       -      -
     93B  VAL      4.1     1.2    +      -       -      -
     94B  VAL*     1.3    74.7    -      -       -      +
     96B  THR*     1.3    62.4    -      -       -      -
    135B  LEU*     3.7    20.6    -      -       -      +
    136B  GLU      3.8     8.1    -      -       -      -
    137B  ASP*     5.1     2.7    -      -       -      -
    157B  THR      4.1     0.2    -      -       -      +
    158B  VAL*     3.4     9.2    -      -       -      +
    159B  LEU*     3.0    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1065A  LEU*     5.5     3.4    -      -       +      -
   1066A  HIS*     3.9    16.2    -      -       +      +
     54B  TYR*     4.9    13.6    +      -       +      -
     57B  ARG*     6.2     3.1    -      -       -      +
     58B  LEU*     3.4    29.5    -      -       -      +
     95B  GLY*     1.3    71.2    -      -       -      -
     97B  LEU*     1.3    75.6    +      -       -      +
    134B  VAL      3.6     0.3    -      -       -      +
    135B  LEU*     3.7     4.1    -      -       -      +
    136B  GLU*     2.9    40.7    +      -       +      +
    156B  GLY*     4.5    15.5    -      -       -      +
    157B  THR      3.7     8.7    -      -       -      +
    158B  VAL*     4.5     4.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1065A  LEU*     4.8     3.8    -      -       -      +
     96B  THR*     1.3    86.7    -      -       -      +
     98B  PHE*     1.3    62.7    +      -       -      +
    133B  LEU*     3.7    42.2    -      -       +      -
    134B  VAL      3.6    15.9    -      -       -      +
    135B  LEU*     4.6     2.2    -      -       +      +
    136B  GLU*     5.6     0.2    -      -       -      +
    144B  LEU*     4.5    12.3    -      -       +      -
    148B  ILE*     6.1     3.6    -      -       +      -
    153B  LEU*     3.8    35.4    -      -       +      -
    154B  VAL      3.9    18.4    -      -       -      +
    155B  THR*     4.0     1.9    +      -       -      -
    156B  GLY      3.6    11.4    +      -       -      -
    157B  THR*     3.0    20.5    +      -       -      +
    159B  LEU*     4.3    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1060A  ARG*     4.4    27.1    -      -       +      -
   1065A  LEU*     4.0    25.1    -      -       +      -
     96B  THR      5.1     0.4    -      -       -      +
     97B  LEU*     1.3    76.0    -      -       -      +
     99B  LYS*     1.3    74.5    +      -       -      +
    100B  ALA*     3.8    19.3    +      -       +      -
    133B  LEU*     3.7     3.2    -      -       -      -
    134B  VAL*     2.9    49.5    +      -       +      +
    136B  GLU*     4.5    17.7    -      -       +      +
    141B  ARG*     5.2     7.0    -      -       -      -
    155B  THR*     3.9    17.0    -      -       +      -
    380B  ASP*     4.8    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  PHE*     1.3    86.2    -      -       -      +
    100B  ALA*     1.3    61.5    +      -       -      +
    101B  MET*     3.3    38.4    +      -       +      +
    104B  GLN*     5.3     1.4    -      -       -      +
    127B  ILE*     4.5     5.9    -      -       -      +
    131B  ASP*     3.3    28.0    +      -       +      +
    132B  GLU      3.5    11.2    -      -       -      +
    133B  LEU*     3.8    14.4    -      -       +      -
    150B  VAL      3.3    22.6    +      -       -      -
    151B  SER*     3.7    15.8    +      -       -      +
    153B  LEU      3.3    25.1    +      -       -      +
    154B  VAL*     4.6     3.1    -      -       -      -
    155B  THR*     3.6    28.4    -      -       +      +
    355B  TYR*     4.1     8.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  PHE*     3.8    22.1    +      -       +      +
     99B  LYS*     1.3    70.2    -      -       -      +
    101B  MET*     1.3    58.6    +      -       -      +
    102B  PRO*     3.5    10.0    -      -       -      +
    131B  ASP*     3.8     2.9    -      -       -      +
    132B  GLU*     2.9    43.0    +      -       +      +
    134B  VAL*     5.2     6.5    -      -       +      -
    143B  LYS*     6.0     0.9    -      -       -      +
----------------------------------------------------------
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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