Contacts of the strand formed by residues 327 - 331 (chain B) in PDB entry 6CMO


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 VAL 327 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  MET*     4.6     9.0    -      -       +      -
     63B  TRP*     4.9     0.2    -      -       -      -
    277B  SER*     5.6     0.7    -      -       -      +
    279B  SER*     5.7     0.7    -      -       -      +
    286B  LEU*     4.7    24.0    -      -       +      -
    318B  LEU*     3.8    22.7    -      -       +      -
    319B  GLY      3.3    16.4    -      -       -      +
    320B  VAL*     4.0    16.4    -      -       +      -
    326B  ALA*     1.3    79.4    -      -       -      +
    328B  ALA*     1.3    59.8    +      -       -      +
    329B  THR*     4.2     4.7    +      -       +      -
    338B  ILE*     3.5     3.7    -      -       -      +
    339B  TRP*     2.8    50.6    +      -       +      +
     50G  LEU*     4.3    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  MET*     3.7    17.9    -      -       +      +
     63B  TRP*     3.6    30.2    -      -       +      -
     70B  LEU*     4.5     9.2    -      -       +      -
    318B  LEU*     3.8     1.4    -      -       -      +
    319B  GLY      3.1    31.4    +      -       -      +
    327B  VAL*     1.3    73.0    -      -       -      +
    329B  THR*     1.3    68.0    +      -       -      +
    336B  LEU*     6.1     0.7    -      -       +      -
    338B  ILE*     3.8    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  MET*     5.0     4.9    -      -       -      +
    294B  CYS*     5.5     8.5    -      -       -      -
    311B  HIS*     3.2    24.8    +      -       +      +
    315B  VAL*     4.9     8.1    -      -       +      -
    317B  CYS      3.5     8.3    -      -       -      +
    318B  LEU*     3.7    20.9    -      -       +      -
    327B  VAL*     4.6     2.5    -      -       +      -
    328B  ALA*     1.3    80.6    -      -       -      +
    330B  GLY*     1.3    59.4    -      -       -      +
    336B  LEU*     3.9    14.0    -      -       -      +
    337B  LYS      2.5    39.3    +      -       -      -
    338B  ILE*     5.7     0.3    -      -       -      +
    339B  TRP*     4.0    21.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ILE*     4.6    13.9    -      -       -      -
     61B  MET*     6.1     1.8    -      -       -      -
    311B  HIS*     5.4     1.6    -      -       -      -
    315B  VAL*     3.3     8.1    -      -       -      +
    316B  SER*     2.9    25.6    +      -       -      -
    317B  CYS*     3.0    20.0    +      -       -      +
    329B  THR*     1.3    76.8    -      -       -      +
    331B  SER*     1.3    61.8    +      -       -      -
    335B  PHE      4.8     2.5    -      -       -      -
    336B  LEU*     4.6     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ILE*     3.3    29.5    +      -       -      +
    311B  HIS*     4.1    24.2    -      -       -      -
    313B  ASN      3.0    18.3    +      -       -      -
    314B  ARG      2.5    23.9    +      -       -      -
    315B  VAL*     3.9     5.6    -      -       -      -
    316B  SER*     3.9     3.6    +      -       -      +
    330B  GLY*     1.3    75.8    -      -       -      -
    332B  TRP*     1.3    68.0    +      -       -      +
    333B  ASP*     3.1    15.5    +      -       -      +
    334B  SER      3.8     2.6    +      -       -      -
    335B  PHE      4.3     6.9    +      -       -      +
----------------------------------------------------------
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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