Contacts of the strand formed by residues 91 - 99 (chain C) in PDB entry 6H7L


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 ALA 91 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ARG*     4.0    16.6    -      -       +      -
     39C  GLN      3.5    32.3    -      -       -      +
     40C  ALA*     3.5     6.5    -      -       +      +
     41C  PRO*     4.9     2.9    -      -       -      -
     89C  ASP      3.1     9.6    +      -       -      +
     90C  THR*     1.3    77.8    -      -       -      +
     92C  VAL*     1.3    62.2    +      -       -      +
     93C  TYR*     3.4     7.2    -      -       +      -
    115C  GLN*     3.9     9.4    -      -       -      +
    116C  VAL      3.1    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ARG*     3.3     2.8    -      -       -      -
     39C  GLN*     3.0    35.2    +      -       +      +
     91C  ALA*     1.3    72.7    -      -       -      +
     93C  TYR*     1.3    61.4    +      -       -      +
     94C  TYR*     3.5    41.2    -      -       +      +
    112C  GLN      5.0     0.9    -      -       -      +
    113C  GLY*     4.2     2.9    -      -       -      -
    114C  THR      3.7    21.1    -      -       -      +
    115C  GLN*     3.5    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  GLU*     3.9     2.4    -      -       -      +
     20C  LEU*     3.8    28.3    -      -       +      -
     36C  TRP*     4.2     7.2    -      +       +      -
     37C  TYR      3.3     7.6    -      -       -      +
     38C  ARG*     3.0    37.5    +      -       +      -
     48C  VAL*     3.9    18.4    -      -       +      -
     67C  PHE*     3.8     6.1    -      -       -      -
     80C  LEU*     4.4     4.5    -      -       +      -
     82C  MET*     3.9    18.3    -      -       -      -
     89C  ASP*     3.0    35.0    +      -       -      +
     91C  ALA*     3.4    16.2    -      -       +      -
     92C  VAL*     1.3    73.0    -      -       -      +
     94C  TYR*     1.3    59.6    +      -       -      +
    113C  GLY*     3.3     1.6    -      -       -      -
    114C  THR*     2.9    39.9    +      -       +      +
    116C  VAL*     3.5    27.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  GLU*     3.5     2.9    -      -       -      +
     36C  TRP*     3.4     7.9    -      -       -      -
     37C  TYR*     2.7    43.7    +      -       -      +
     38C  ARG*     4.7     3.4    -      -       -      -
     39C  GLN*     4.1    24.9    +      -       +      +
     45C  ARG*     4.2    27.8    -      -       -      -
     92C  VAL*     3.5    40.2    -      -       +      +
     93C  TYR*     1.3    73.2    -      -       -      +
     95C  CYS*     1.3    59.9    +      -       -      +
     96C  ASN      3.9     0.3    +      -       -      -
    110C  TRP*     4.0    21.1    -      +       +      -
    111C  GLY      3.4    19.5    -      -       -      +
    112C  GLN      3.3    19.3    -      -       -      -
    113C  GLY*     3.7     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  LEU*     3.5    14.8    -      -       +      +
      6C  GLU*     2.8    23.1    +      -       +      +
     22C  CYS*     2.0    53.2    -      -       +      -
     34C  MET*     5.1     0.2    -      -       -      -
     35C  GLY      3.4    10.5    -      -       -      -
     36C  TRP*     4.0     5.8    -      -       +      -
     78C  VAL*     4.4     7.4    -      -       -      -
     94C  TYR*     1.3    72.2    -      -       -      +
     96C  ASN*     1.3    65.4    +      -       -      +
     97C  VAL*     4.8     3.4    -      -       -      -
    110C  TRP*     3.6     3.9    -      -       -      -
    111C  GLY      2.8    25.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  ILE*     3.7     1.0    -      -       -      +
     34C  MET*     3.4     4.9    -      -       -      +
     35C  GLY*     2.9    33.5    +      -       -      +
     37C  TYR*     3.4    33.0    +      -       +      -
     94C  TYR      3.9     0.2    +      -       -      -
     95C  CYS*     1.3    75.4    -      -       -      +
     97C  VAL*     1.3    74.3    +      -       -      +
     98C  LYS*     3.0    31.0    +      -       -      +
    108C  ASP*     4.1     4.9    +      -       -      -
    109C  TYR      2.8    26.9    +      -       -      +
    110C  TRP*     3.4    30.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  LEU*     3.7    28.5    -      -       +      -
     24C  ALA*     4.6     2.5    -      -       +      -
     28C  ILE*     4.1    30.7    -      -       +      -
     32C  ASN*     4.8     3.1    -      -       +      -
     33C  ILE      3.3     6.7    -      -       -      +
     34C  MET*     4.0    26.9    -      -       +      -
     95C  CYS*     4.8     1.6    -      -       -      -
     96C  ASN*     1.3    81.6    +      -       -      +
     98C  LYS*     1.3    68.7    +      -       -      +
     99C  ASP*     4.4     0.7    -      -       -      +
    107C  TYR      3.7     1.7    -      -       -      +
    108C  ASP*     3.5     3.8    -      -       -      -
    109C  TYR*     2.9    50.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  ASN*     3.2     9.4    -      -       -      +
     33C  ILE*     2.8    59.0    +      -       +      +
     37C  TYR*     3.7    17.4    +      -       -      -
     96C  ASN*     3.0    23.0    +      -       -      +
     97C  VAL*     1.3    72.9    -      -       -      +
     99C  ASP*     1.3    60.2    +      -       -      +
    100C  PHE*     3.8    12.6    +      -       +      -
    106C  ASP*     4.0    19.1    -      -       +      +
    107C  TYR      3.7     4.5    -      -       -      +
    108C  ASP*     3.3    28.4    +      -       -      +
    110C  TRP*     5.0     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  LYS*     2.7    36.0    +      -       -      +
    287A  LYS*     5.9     0.2    -      -       -      -
     28C  ILE*     3.7     8.6    -      -       +      +
     29C  PHE*     3.2    27.0    +      -       -      +
     32C  ASN*     4.4     5.4    -      -       -      -
     97C  VAL*     3.9     1.5    +      -       +      -
     98C  LYS*     1.3    72.5    -      -       -      +
    100C  PHE*     1.3    59.1    +      -       -      +
    101C  GLY*     2.7    34.1    +      -       -      -
    102C  ALA      5.0     0.2    +      -       -      -
    105C  TYR      4.3     0.3    -      -       -      +
    106C  ASP*     3.4     4.2    -      -       -      -
    107C  TYR*     2.9    42.2    +      -       +      +
    109C  TYR*     4.0    15.4    -      -       +      -
----------------------------------------------------------
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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