Contacts of the strand formed by residues 308 - 312 (chain B) in PDB entry 5C5B


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 ASN 308 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  PHE      3.9     0.2    -      -       -      +
    304B  THR*     3.3     6.3    -      -       -      -
    305B  GLN*     3.0    35.9    +      -       -      +
    306B  GLY      3.4     1.0    +      -       -      -
    307B  GLY*     1.3    88.6    +      -       -      +
    309B  LEU*     1.3    60.5    +      -       -      +
    310B  MET*     3.8    16.6    +      -       +      +
    321B  LEU*     3.4    37.1    -      -       +      +
    323B  GLN      3.9     2.5    -      -       -      -
    324B  ASP*     3.6    18.9    -      -       -      +
    325B  LEU*     4.3     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284B  LEU*     6.1     0.2    -      -       +      -
    302B  PHE*     4.4    11.7    -      -       +      -
    303B  PHE      4.0     4.9    -      -       -      +
    304B  THR*     4.0    11.9    -      -       +      -
    308B  ASN*     1.3    71.1    -      -       -      +
    310B  MET*     1.3    62.7    +      -       -      +
    321B  LEU*     3.2     3.7    -      -       -      +
    322B  ILE*     2.9    42.2    +      -       +      +
    323B  GLN*     2.9    22.9    +      -       +      +
    325B  LEU*     3.6    18.6    -      -       +      +
    344B  ILE*     3.6    30.1    -      -       +      -
    353B  ILE*     4.6     1.6    -      -       +      -
    355B  LEU*     4.3    15.3    -      -       +      -
    366B  TRP*     3.8    32.1    -      -       +      -
    370B  ILE*     4.8     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302B  PHE*     3.2     8.3    -      -       -      +
    303B  PHE*     2.9    72.0    +      -       +      +
    305B  GLN*     3.8    30.7    -      -       +      +
    308B  ASN*     3.8    33.0    -      -       +      +
    309B  LEU*     1.3    74.6    -      -       -      +
    311B  CYS*     1.3    61.1    +      -       -      +
    312B  GLN      4.3     0.2    -      -       -      -
    319B  GLY      5.0     3.6    -      -       -      +
    320B  GLY*     3.2    10.5    -      -       -      +
    321B  LEU*     3.5    32.3    -      -       +      -
    322B  ILE*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  LEU*     4.9     3.8    -      -       -      -
    300B  LEU*     3.5    37.0    -      -       -      -
    301B  TYR      3.3     3.1    -      -       -      -
    302B  PHE*     3.5    26.9    -      -       +      -
    310B  MET*     1.3    73.6    -      -       -      +
    312B  GLN*     1.3    64.1    +      -       -      +
    313B  PRO*     3.9     8.0    -      -       -      +
    319B  GLY*     4.2     0.7    -      -       -      -
    320B  GLY*     2.7    32.2    +      -       -      +
    322B  ILE*     3.8    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  SER*     5.3     0.5    +      -       -      -
     17A  PRO*     3.6    27.1    +      -       +      +
     18A  GLN*     4.5     8.8    +      -       -      +
     21A  SER*     4.7     1.0    +      -       -      -
    301B  TYR*     2.9    45.7    +      -       +      +
    303B  PHE*     4.2    19.5    -      -       +      -
    310B  MET      4.3     0.4    -      -       -      -
    311B  CYS*     1.3    73.3    -      -       -      +
    313B  PRO*     1.3    76.1    -      -       -      +
    316B  ALA      2.6    26.7    +      -       -      +
    317B  VAL      3.5    16.6    +      -       -      -
    318B  ALA      4.0     3.1    -      -       -      +
    319B  GLY*     3.5    22.9    +      -       -      +
----------------------------------------------------------
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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