Contacts of the strand formed by residues 94 - 102 (chain G) in PDB entry 3CHB


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 ARG 94 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16G  GLN*     4.8     6.6    +      -       -      +
     18G  HIS*     4.8     3.6    -      -       +      +
     47G  THR      4.1     5.7    +      -       -      +
     48G  PHE*     3.3    31.0    -      -       +      +
     49G  GLN      2.9    23.9    +      -       -      -
     87G  VAL*     3.9    16.6    -      -       +      -
     88G  TRP      3.6     5.4    -      -       -      +
     89G  ASN*     3.9    20.8    +      -       -      +
     91G  LYS      2.9    21.1    +      -       -      -
     92G  THR*     3.2    10.3    +      -       -      +
     93G  PRO*     1.3    72.0    -      -       -      +
     95G  ALA*     1.3    58.9    +      -       -      +
   6001G  MES      2.9    46.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 95 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49G  GLN*     3.5     8.5    -      -       +      +
     51G  GLU*     3.6    39.7    -      -       +      +
     87G  VAL*     3.1     3.4    -      -       -      -
     88G  TRP*     2.8    48.6    +      -       +      -
     91G  LYS*     4.2    13.7    -      -       +      -
     93G  PRO      3.3     0.2    +      -       -      -
     94G  ARG*     1.3    71.8    -      -       -      +
     96G  ILE*     1.3    64.5    +      -       -      +
     97G  ALA      3.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40G  ILE*     4.0    13.2    -      -       +      -
     48G  PHE*     3.8    28.9    -      -       +      -
     49G  GLN      2.8    22.4    +      -       -      +
     50G  VAL*     4.3     8.5    -      -       +      +
     51G  GLU      5.7     0.7    +      -       -      -
     68G  MET*     4.0    24.7    -      -       +      -
     72G  LEU*     3.7    30.5    -      -       +      -
     85G  LEU*     4.4    13.9    -      -       +      -
     86G  CYS      3.8     3.8    -      -       -      +
     87G  VAL*     4.3     2.9    -      -       +      -
     88G  TRP*     3.5     4.7    -      -       -      -
     95G  ALA*     1.3    70.4    -      -       -      +
     97G  ALA*     1.3    60.4    +      -       -      +
     98G  ALA      3.7    21.8    -      -       -      +
     31H  LEU*     3.4    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  LEU*     5.7     0.4    -      -       +      -
     12G  TYR*     6.3     0.7    -      -       +      -
     15G  THR*     5.3     0.9    -      -       +      -
     86G  CYS*     2.8    32.3    +      -       -      +
     87G  VAL*     4.7     0.4    -      -       -      +
     88G  TRP*     3.5    38.1    -      -       +      -
     95G  ALA      3.4     1.2    +      -       -      -
     96G  ILE*     1.3    75.2    -      -       -      +
     98G  ALA*     1.3    60.0    +      -       +      +
     30H  SER*     3.5     1.4    +      -       -      -
     31H  LEU*     2.8    31.1    +      -       -      +
     32H  ALA*     3.6    10.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ILE*     3.7    21.8    -      -       +      -
      8G  LEU*     4.3     9.4    -      -       +      -
     68G  MET*     4.0     2.9    -      -       -      -
     85G  LEU*     3.5     8.0    -      -       -      +
     86G  CYS*     2.9    33.3    +      -       +      +
     96G  ILE*     3.7     5.3    -      -       -      +
     97G  ALA*     1.3    80.4    -      -       -      +
     99G  ILE*     1.3    62.2    +      -       -      +
     28H  THR*     5.1     1.6    -      -       +      -
     29H  GLU      3.2    14.8    -      -       -      +
     30H  SER*     3.8    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 99 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ILE*     3.6     4.0    -      -       -      -
     24G  ILE*     5.4     0.7    -      -       +      -
     40G  ILE*     6.0     0.2    -      -       +      -
     68G  MET*     3.7    22.9    -      -       +      -
     71G  THR*     4.3    15.0    -      -       +      -
     72G  LEU*     3.7    26.0    -      -       +      -
     75G  ALA*     5.5     1.6    -      -       +      -
     82G  VAL*     4.0    21.8    -      -       +      -
     84G  LYS      3.5     4.7    -      -       -      +
     85G  LEU*     3.7    18.4    -      -       +      -
     98G  ALA*     1.3    76.3    -      -       -      +
    100G  SER*     1.3    73.2    +      -       -      +
    101G  MET*     4.5    13.7    -      -       +      -
     27H  TYR*     5.7     1.3    -      -       +      +
     28H  THR*     3.2     5.4    -      -       -      +
     29H  GLU*     2.9    45.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 100 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ILE*     3.6    12.5    -      -       -      +
     82G  VAL*     3.7     6.1    -      -       -      +
     83G  GLU*     2.6    53.9    +      -       -      -
     84G  LYS*     2.9    31.8    +      -       -      +
     99G  ILE*     1.3    74.8    -      -       -      +
    101G  MET*     1.3    58.2    +      -       -      +
     26H  SER*     5.9     2.0    -      -       -      -
     27H  TYR      3.4     4.9    -      -       -      -
     28H  THR*     3.4    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 101 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71G  THR*     4.2    18.8    -      -       +      -
     75G  ALA*     4.0    26.2    -      -       +      -
     80G  ALA*     4.1    15.9    -      -       -      +
     81G  LYS      3.5    15.7    -      -       -      +
     82G  VAL*     4.5     3.1    -      -       -      -
     83G  GLU*     4.0     0.9    -      -       -      +
     99G  ILE*     4.5    14.6    -      -       +      -
    100G  SER*     1.3    77.6    -      -       -      +
    102G  ALA*     1.3    60.0    +      -       -      +
     26H  SER*     3.1     8.2    -      -       -      -
     27H  TYR*     2.8    58.5    +      -       +      +
     73H  ARG*     4.8     4.7    -      -       +      -
     76H  TYR*     3.3    26.6    +      -       +      -
     77H  LEU*     4.3    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21G  ASN*     5.2     0.7    -      -       -      +
     81G  LYS*     3.3    24.8    +      -       -      +
     83G  GLU*     4.1    26.8    -      -       +      +
    101G  MET*     1.3    75.5    -      -       -      +
    103G  ASN*     1.3    71.4    +      -       -      +
     25H  PHE*     3.8    24.5    -      -       +      +
     26H  SER*     3.9    10.1    -      -       -      -
     76H  TYR*     3.1     8.8    +      -       -      -
----------------------------------------------------------
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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