Contacts of the strand formed by residues 218 - 224 (chain B) in PDB entry 6GR2


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 LEU 218 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  LEU*     3.6    27.8    -      -       +      -
    215B  ASP*     2.8    30.2    +      -       +      +
    216B  PRO*     4.3     3.1    -      -       -      +
    217B  LYS*     1.3    79.8    -      -       -      +
    219B  ALA*     1.3    63.8    +      -       -      +
    220B  VAL*     5.5     2.5    -      -       +      -
    295B  LEU*     5.1     0.4    -      -       +      -
    300B  TYR*     3.4    40.4    -      -       +      +
    339B  TYR*     3.7    12.8    -      -       +      -
    355B  LEU*     3.1    37.9    -      -       +      -
    356B  LEU      3.5    14.1    -      -       -      +
    358B  ALA*     4.4     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  LEU*     1.3    78.0    -      -       -      +
    220B  VAL*     1.3    66.6    +      -       -      +
    355B  LEU*     3.6     3.6    -      -       -      -
    356B  LEU*     2.9    51.7    +      -       +      +
    358B  ALA*     3.8    21.3    -      -       +      +
    361B  ALA*     5.0     1.6    -      -       +      -
    380B  LEU*     4.8    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  VAL*     4.8     0.9    -      -       +      -
     40B  LEU*     4.5    10.5    -      -       +      -
     55B  MET*     3.7    31.6    -      -       +      -
    213B  LEU*     4.9    10.5    -      -       +      -
    218B  LEU*     5.5     4.0    -      -       +      -
    219B  ALA*     1.3    76.5    -      -       -      +
    221B  LEU*     1.3    60.6    +      -       -      +
    222B  ILE*     3.9     9.4    +      -       +      +
    353B  VAL*     3.9    26.2    -      -       +      -
    354B  THR      3.5     3.8    -      -       -      +
    355B  LEU*     4.9    14.6    -      -       +      -
    356B  LEU*     4.5     0.2    -      -       -      -
    379B  TYR      3.7     0.9    -      -       -      +
    380B  LEU*     3.9     5.1    -      -       -      +
    381B  SER      3.4    38.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  VAL*     1.3    72.7    -      -       -      +
    222B  ILE*     1.3    64.3    +      -       -      +
    223B  THR*     3.9    17.2    +      -       -      +
    352B  THR      3.5     2.4    -      -       -      +
    353B  VAL*     3.6     0.5    -      -       -      -
    354B  THR*     2.7    49.8    +      -       +      +
    356B  LEU*     3.8    19.2    -      -       +      +
    361B  ALA*     5.5     0.9    -      -       +      -
    364B  ALA*     4.5    13.7    -      -       +      -
    365B  MET*     3.7    31.0    -      -       +      -
    368B  ILE*     4.2    19.3    -      -       +      -
    378B  PHE*     4.2    11.7    -      -       +      -
    379B  TYR      3.8     3.8    -      -       -      +
    380B  LEU*     3.3    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  VAL*     3.9    18.8    -      -       +      -
     57B  LEU*     3.1    47.8    -      -       +      -
    139B  LEU*     4.1    12.1    -      -       +      -
    220B  VAL*     4.6    11.2    -      -       +      +
    221B  LEU*     1.3    75.7    -      -       -      +
    223B  THR*     1.3    63.0    +      -       -      +
    351B  CYS*     3.8    30.5    -      -       +      -
    352B  THR      3.3     5.6    -      -       -      +
    353B  VAL*     5.0     0.9    -      -       +      -
    377B  THR      3.7     0.2    -      -       -      +
    378B  PHE*     3.2     6.8    -      -       -      +
    379B  TYR*     2.8    58.1    +      -       +      +
    381B  SER*     4.6     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  LEU*     3.9    12.3    +      -       -      +
    222B  ILE*     1.3    72.6    -      -       -      +
    224B  ASN*     1.3    61.9    -      -       -      +
    225B  SER      3.6     1.0    +      -       -      -
    328B  LEU*     3.7    34.0    -      -       +      +
    351B  CYS*     3.1     5.2    -      -       -      -
    352B  THR*     2.7    49.5    +      -       -      -
    354B  THR*     5.0     2.3    +      -       -      -
    368B  ILE*     4.2     8.1    -      -       +      +
    376B  ALA*     4.1     8.1    -      -       +      -
    377B  THR      3.3     4.7    -      -       -      +
    378B  PHE*     3.3    34.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  PRO*     4.1    29.1    -      -       -      +
    137B  GLY*     4.3     9.0    -      -       -      -
    222B  ILE      4.1     0.8    +      -       -      -
    223B  THR*     1.3    72.1    -      -       -      +
    225B  SER*     1.3    63.6    +      -       -      +
    226B  ASN*     2.6    47.0    +      -       -      +
    227B  VAL      4.4     1.6    +      -       -      +
    350B  GLY*     3.6     9.2    -      -       -      +
    351B  CYS*     3.4    20.5    -      -       -      -
    376B  ALA*     3.3     7.3    -      -       -      +
    377B  THR*     2.6    44.5    +      -       -      +
    379B  TYR*     4.3     8.9    +      -       +      -
----------------------------------------------------------
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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