Contacts of the strand formed by residues 97 - 107 (chain B) in PDB entry 3I8E


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 SER 97 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LYS      4.2     0.2    -      -       -      +
     93B  GLN*     3.7     0.3    -      -       -      -
     94B  SER*     2.7    43.2    +      -       -      -
     96B  GLU*     1.3    96.9    +      -       -      +
     98B  ILE*     1.3    63.6    +      -       -      +
     99B  ASP*     4.2     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  VAL      4.8     6.1    -      -       -      +
     53B  LYS*     3.5    48.7    +      -       +      +
     91B  TYR*     3.2    32.1    -      -       +      +
     92B  LYS      3.9     3.1    -      -       -      -
     93B  GLN*     3.5    25.4    -      -       +      +
     96B  GLU      4.2     7.6    -      -       -      +
     97B  SER*     1.3    77.7    +      -       -      +
     99B  ASP*     1.3    73.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LYS*     5.3     1.3    -      -       -      +
     90B  GLU      3.6     1.2    -      -       -      +
     91B  TYR*     3.6     4.2    -      -       -      -
     92B  LYS*     2.7    57.2    +      -       +      +
     94B  SER*     3.7    15.9    +      -       -      -
     97B  SER*     4.2     7.4    +      -       -      +
     98B  ILE*     1.3    90.0    -      -       -      +
    100B  ILE*     1.3    63.2    +      -       -      +
    101B  ILE*     3.6    10.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  PHE*     5.0     7.2    -      -       +      -
     39B  LEU*     4.1     4.3    -      -       +      -
     41B  ILE*     3.8    25.4    -      -       +      -
     53B  LYS*     4.0    18.1    -      -       +      +
     55B  VAL*     3.6    41.3    -      -       +      -
     89B  LEU*     4.0    35.7    -      -       +      -
     90B  GLU      3.6     5.4    -      -       -      +
     91B  TYR*     4.3    11.7    -      -       +      -
     99B  ASP*     1.3    70.8    -      -       -      +
    101B  ILE*     1.3    60.7    +      -       -      +
    102B  THR*     4.8     0.2    +      -       -      -
   1065B  VAL*     4.4    23.1    -      -       +      +
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Residues in contact with ILE 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  LEU*     3.2    11.9    -      -       -      +
     90B  GLU*     2.8    58.6    +      -       +      +
     92B  LYS*     4.8    26.0    -      -       +      +
     99B  ASP*     3.6    12.5    +      -       +      +
    100B  ILE*     1.3    74.4    -      -       -      +
    102B  THR*     1.3    68.5    +      -       -      +
    103B  ARG*     4.4     9.6    -      -       +      -
   1067B  LYS*     6.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  CYS*     3.9     8.3    -      -       +      -
     88B  ILE      3.5     1.3    -      -       -      +
     89B  LEU*     4.1     3.1    -      -       +      -
    100B  ILE      4.8     0.2    +      -       -      -
    101B  ILE*     1.3    81.5    -      -       -      +
    103B  ARG*     1.3    64.4    +      -       -      +
    104B  ALA*     3.2    21.5    +      -       -      +
    105B  HIS*     4.0     4.3    -      -       +      +
   1064B  SER      4.4     0.5    +      -       -      -
   1065B  VAL      2.8    19.9    +      -       -      +
   1066B  GLY*     3.5    29.8    -      -       -      +
   1067B  LYS*     3.4    36.7    +      -       +      +
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Residues in contact with ARG 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  GLU*     2.8    32.3    +      -       -      +
     76B  LEU*     4.4    16.5    -      -       +      +
     88B  ILE*     2.6    26.9    +      -       +      +
     90B  GLU*     3.4    41.0    +      -       +      +
    101B  ILE*     3.8     6.0    +      -       +      -
    102B  THR*     1.3    73.0    -      -       -      +
    104B  ALA*     1.3    61.0    +      -       -      +
    150B  LYS*     3.4    29.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  CYS*     3.2     1.7    -      -       -      +
     88B  ILE*     2.7    39.6    +      -       +      +
    102B  THR*     3.2     5.5    -      -       -      +
    103B  ARG*     1.3    80.9    -      -       -      +
    105B  HIS*     1.3    61.5    +      -       -      +
    149B  ASN      4.2     3.4    -      -       -      +
    150B  LYS*     3.4    31.0    -      -       +      +
    152B  LEU*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  ALA      3.3    13.9    -      -       -      +
     87B  CYS*     3.8     1.1    -      -       +      +
    102B  THR*     4.0     5.1    -      -       +      +
    104B  ALA*     1.3    76.6    -      -       -      +
    106B  GLY*     1.3    70.9    +      -       -      +
    150B  LYS      3.1    11.6    +      -       -      +
    151B  GLU*     3.0    27.6    -      -       -      -
    152B  LEU*     3.4     6.5    +      -       -      -
   1066B  GLY      3.2    20.6    -      -       -      +
   1067B  LYS*     3.5    41.4    +      -       +      +
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Residues in contact with GLY 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ASN*     5.1     0.9    -      -       -      -
     86B  ALA*     3.0    28.8    +      -       -      +
    105B  HIS*     1.3    90.6    -      -       -      +
    107B  ASN*     1.3    64.5    +      -       -      -
    108B  VAL*     3.6     6.3    +      -       -      +
    151B  GLU*     3.7    13.5    -      -       -      -
    152B  LEU*     4.6     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  LYS      3.1    26.7    +      -       -      -
     84B  TYR*     3.3    17.7    +      -       -      +
     85B  ASN*     3.9    19.6    -      -       -      +
    106B  GLY*     1.3    71.9    -      -       -      -
    108B  VAL*     1.3    60.6    +      -       -      +
    109B  GLN*     3.1    32.3    +      -       -      +
   1072B  PHE*     4.2     8.6    -      -       +      -
----------------------------------------------------------
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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