Contacts of the strand formed by residues 205 - 210 (chain R) in PDB entry 5G04


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 SER 205 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200R  VAL      3.9     0.3    -      -       -      +
    201R  ALA*     3.6     2.6    -      -       -      -
    202R  LEU*     2.8    40.2    +      -       -      +
    203R  ASP      3.4     0.6    -      -       -      -
    204R  ASN*     1.3    79.5    +      -       -      +
    206R  VAL*     1.3    57.7    +      -       -      +
    207R  TYR*     4.0    17.3    -      -       -      -
    218R  GLN*     3.0    25.4    +      -       -      -
    220R  LEU      3.4     9.6    -      -       -      -
    221R  GLN*     3.4    21.7    +      -       -      +
    229R  ILE*     3.6     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 206 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199R  ALA*     4.5     4.7    -      -       +      -
    200R  VAL      3.6     6.5    -      -       -      +
    201R  ALA*     4.5     2.0    -      -       -      -
    205R  SER*     1.3    72.9    -      -       -      +
    207R  TYR*     1.3    65.4    +      -       -      +
    208R  LEU*     4.0    13.9    -      -       +      -
    218R  GLN*     3.7     4.5    -      -       -      +
    219R  LEU*     3.0    31.2    +      -       +      -
    220R  LEU*     3.4    29.2    +      -       +      -
    229R  ILE*     3.7    22.8    -      -       +      +
    232R  VAL*     4.1    22.0    -      -       +      -
    241R  LEU*     3.7    26.5    -      -       +      -
    243R  VAL*     4.1     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 207 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198R  LEU      3.5     0.9    -      -       -      +
    199R  ALA*     3.5     3.6    -      -       -      -
    200R  VAL*     2.9    38.1    +      -       +      +
    202R  LEU*     3.5    31.6    -      -       +      -
    205R  SER*     4.0    18.3    -      -       -      -
    206R  VAL*     1.3    75.8    -      -       -      +
    208R  LEU*     1.3    61.8    +      -       -      +
    209R  TRP      4.2     0.2    -      -       -      -
    216R  ILE*     3.7    21.3    -      -       +      -
    217R  LEU      3.4     8.5    -      -       -      -
    218R  GLN*     3.7    35.0    +      -       +      -
    830S  ALA*     3.7    20.2    -      -       +      -
    831S  LEU*     3.9    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197R  VAL*     3.9    11.2    -      -       +      -
    198R  LEU      3.2     3.6    -      -       -      -
    199R  ALA*     3.8    27.8    -      -       +      -
    206R  VAL*     4.0    11.9    -      -       +      -
    207R  TYR*     1.3    75.6    -      -       -      +
    209R  TRP*     1.3    61.2    +      -       -      +
    210R  SER      4.1     0.2    -      -       -      -
    215R  ASP      3.6     1.6    -      -       -      +
    216R  ILE*     3.4     5.1    -      -       -      -
    217R  LEU*     2.7    58.6    +      -       +      +
    219R  LEU*     3.9    26.7    -      -       +      -
    234R  TRP*     3.8    15.0    -      -       +      -
    241R  LEU*     4.2     5.4    -      -       +      -
    255R  VAL*     3.8    33.7    -      -       +      -
    831S  LEU*     4.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 209 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174R  ARG*     3.5    35.7    -      -       -      -
    176R  LEU*     3.6    26.3    -      -       +      +
    192R  TRP*     4.7     0.9    -      +       -      -
    197R  VAL*     3.5     5.2    -      -       -      +
    198R  LEU*     2.8    66.2    +      -       +      +
    208R  LEU*     1.3    72.4    -      -       -      +
    210R  SER*     1.3    68.8    +      -       -      +
    211R  ALA*     3.5    30.5    +      -       +      -
    214R  GLY*     3.6    18.2    +      -       -      -
    215R  ASP      3.5     7.2    -      -       -      -
    216R  ILE*     3.6    25.4    -      -       +      -
    469R  LEU*     3.8    26.2    -      -       +      -
    831S  LEU*     3.7    29.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 210 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196R  ASN      4.2     6.1    +      -       -      -
    197R  VAL*     4.7     9.8    -      -       -      +
    208R  LEU      4.1     0.4    -      -       -      -
    209R  TRP*     1.3    74.7    -      -       -      +
    211R  ALA*     1.3    59.9    +      -       -      +
    212R  SER*     3.7     7.4    +      -       -      -
    213R  SER*     3.1    29.8    +      -       -      -
    214R  GLY*     2.9    30.3    +      -       -      -
    215R  ASP*     3.1    14.4    +      -       -      -
----------------------------------------------------------
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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