Contacts of the strand formed by residues 37 - 41 (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 MET 37 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  THR*     3.5    23.6    -      -       +      -
      2F  PRO*     4.3     3.4    -      -       -      +
      8F  LEU*     4.3    17.7    -      -       +      -
     29G  GLU*     3.3     4.6    -      -       -      +
     30G  SER*     3.0    29.0    +      -       -      +
     35G  ARG*     3.0    32.9    +      -       -      +
     36G  GLU*     1.3    75.8    -      -       -      +
     38G  ALA*     1.3    62.2    +      -       -      +
     39G  ILE*     3.9    27.1    -      -       +      -
     49G  GLN*     3.5    31.4    -      -       +      +
     50G  VAL      3.4    12.8    -      -       -      +
     51G  GLU      5.2     0.2    -      -       -      -
     52G  VAL*     4.0    13.5    -      -       +      +
     69G  LYS*     4.6     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 38 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  TYR*     4.1    22.2    -      -       +      +
     28G  THR      3.2    11.4    -      -       -      +
     29G  GLU*     4.4     1.6    -      -       +      -
     37G  MET*     1.3    75.8    -      -       -      +
     39G  ILE*     1.3    66.6    +      -       -      +
     40G  ILE*     5.8     0.2    -      -       -      -
     49G  GLN*     3.2     6.1    -      -       -      +
     50G  VAL*     2.9    36.2    +      -       +      +
     69G  LYS*     3.9    26.0    -      -       +      +
     72G  LEU*     5.0     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 39 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2F  PRO*     3.6    26.9    -      -       +      +
      3F  GLN      3.7    28.9    -      -       -      +
      4F  ASN*     3.8    12.3    -      -       -      +
      8F  LEU*     5.0     4.9    -      -       +      -
     26G  SER*     4.0     0.9    +      -       -      +
     27G  TYR*     3.7     0.7    -      -       -      -
     28G  THR*     2.8    50.7    +      -       +      +
     37G  MET*     3.9    22.4    -      -       +      -
     38G  ALA*     1.3    78.7    -      -       -      +
     40G  ILE*     1.3    69.5    +      -       -      +
     41G  THR*     4.9     3.6    -      -       +      -
     47G  THR*     3.7    14.8    -      -       +      -
     48G  PHE      3.3    13.2    -      -       -      +
     49G  GLN*     4.6     2.7    -      -       +      -
     93G  PRO*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 40 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  ILE*     4.0    16.4    -      -       +      -
     26G  SER*     3.2    13.0    -      -       -      +
     27G  TYR*     3.9    21.8    -      -       +      -
     39G  ILE*     1.3    78.5    -      -       -      +
     41G  THR*     1.3    66.7    -      -       -      +
     42G  PHE*     3.7    29.8    -      -       +      -
     46G  ALA      4.1     0.2    -      -       -      +
     47G  THR*     3.4     3.8    -      -       -      +
     48G  PHE*     2.9    46.8    +      -       +      +
     72G  LEU*     4.1    28.7    -      -       +      +
     85G  LEU*     4.3     6.7    -      -       +      -
     96G  ILE*     4.0    21.8    -      -       +      -
     99G  ILE*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 41 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  GLN      5.3     2.2    -      -       -      +
     24G  ILE*     3.6     5.4    -      -       -      +
     25G  PHE*     2.8    45.9    +      -       -      -
     26G  SER*     3.1    28.2    +      -       -      +
     39G  ILE*     4.9     4.3    -      -       +      -
     40G  ILE*     1.3    80.6    -      -       -      +
     42G  PHE*     1.3    63.1    +      -       -      +
     45G  GLY*     4.7     2.9    -      -       -      -
     46G  ALA      3.3     9.2    -      -       -      -
     47G  THR*     3.6    23.3    -      -       +      +
----------------------------------------------------------
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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