Contacts of the strand formed by residues 244 - 249 (chain B) in PDB entry 2COJ


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 GLN 244 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  TYR*     4.7     9.9    +      -       -      -
    194B  PHE*     3.4    31.2    -      -       +      -
    202B  VAL*     5.0     2.5    -      -       +      -
    203B  SER      3.7     2.5    +      -       -      +
    204B  LEU*     3.3    26.1    -      -       +      -
    205B  TRP      3.0    22.0    +      -       -      -
    234B  GLN*     3.1    24.2    +      -       -      +
    237B  ALA*     4.0     4.8    -      -       -      +
    242B  CYS*     3.6     3.9    -      -       -      +
    243B  GLN*     1.3    88.7    -      -       +      +
    245B  VAL*     1.3    68.9    +      -       -      +
    258B  VAL*     5.0     0.9    -      -       +      -
    259B  GLY*     3.4    28.5    -      -       -      +
    260B  THR*     3.7    12.7    +      -       -      +
    261B  MET*     4.5     8.5    -      -       +      +
    420B  GBN      4.9     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  LEU*     4.6     2.2    -      -       -      +
    205B  TRP*     3.6    15.0    -      -       +      +
    207B  ASN      5.8     2.2    -      -       -      +
    210B  TYR*     6.3     0.2    -      -       +      -
    233B  ALA*     3.6    31.2    -      -       +      +
    234B  GLN*     3.7    19.5    -      -       +      +
    237B  ALA*     4.1     5.2    -      -       +      -
    244B  GLN*     1.3    82.1    +      -       -      +
    246B  LEU*     1.3    68.6    +      -       -      +
    247B  TRP*     3.6    46.9    +      -       +      +
    258B  VAL*     4.1     0.7    -      -       -      -
    259B  GLY*     2.7    30.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  LEU*     3.9    28.0    -      -       +      -
    205B  TRP      3.1    10.4    +      -       -      +
    206B  ALA*     3.9    21.9    -      -       +      -
    207B  ASN      4.6     2.3    +      -       -      +
    244B  GLN      4.1     0.6    +      -       -      -
    245B  VAL*     1.3    78.7    -      -       -      +
    247B  TRP*     1.3    60.4    +      -       -      +
    248B  LEU*     3.4    18.8    +      -       +      +
    255B  ILE*     3.4    30.5    -      -       +      -
    257B  GLU      3.8    14.6    -      -       -      +
    258B  VAL*     4.9     3.1    -      -       +      -
    263B  LEU*     5.2     1.1    -      -       +      -
    313B  MET*     3.9    23.1    -      -       -      -
    328B  MET*     5.7     1.3    -      -       -      -
    343B  ILE*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  TYR*     4.0    31.0    -      -       +      -
    211B  VAL      4.1     1.8    -      -       -      -
    212B  ARG*     3.6    52.7    -      -       +      +
    229B  SER      5.5     0.4    -      -       -      -
    230B  SER*     3.6    33.7    -      -       -      -
    233B  ALA*     3.7    21.3    -      -       +      -
    234B  GLN*     6.2     0.2    -      -       +      -
    245B  VAL*     3.7    34.3    -      -       +      +
    246B  LEU*     1.3    70.4    -      -       -      +
    248B  LEU*     1.3    63.9    +      -       -      +
    254B  GLN      3.6     0.7    -      -       -      +
    255B  ILE*     3.8     0.3    -      -       -      -
    256B  THR*     2.9    46.0    +      -       -      +
    257B  GLU*     3.2    15.0    +      -       +      +
    259B  GLY*     3.1    33.4    +      -       -      -
    260B  THR*     5.2     2.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  ALA*     3.9    12.6    -      -       +      -
    207B  ASN      4.3     1.9    +      -       -      +
    208B  PRO*     4.1    34.6    -      -       +      +
    210B  TYR      4.0    15.3    +      -       -      +
    211B  VAL*     4.4    10.7    -      -       -      +
    212B  ARG      5.3     0.7    +      -       -      -
    246B  LEU*     3.4    26.6    +      -       +      +
    247B  TRP*     1.3    82.7    -      -       -      +
    249B  TYR*     1.3    61.7    +      -       -      +
    253B  HIS*     4.1    15.0    -      -       +      +
    254B  GLN      3.0    13.5    -      -       -      +
    255B  ILE*     4.0    14.6    -      -       +      -
    313B  MET*     4.1     8.3    -      -       +      -
    345B  TYR*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  TRP*     3.3    34.9    -      +       -      -
    211B  VAL*     3.8    14.6    -      -       +      -
    213B  ALA      3.5    25.6    -      -       -      +
    214B  TRP*     3.7    10.1    -      -       +      -
    215B  LYS*     3.1    45.0    +      -       +      +
    248B  LEU*     1.3    75.9    -      -       -      +
    250B  GLY*     1.3    73.9    +      -       -      +
    253B  HIS*     4.4     0.2    -      -       -      -
    254B  GLN*     2.7    53.0    +      -       +      +
    256B  THR*     3.9    18.8    -      -       +      -
    284B  ILE*     3.5    22.0    -      -       +      -
----------------------------------------------------------
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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