Contacts of the strand formed by residues 210 - 217 (chain B) in PDB entry 3V4R


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 HIS 210 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  PHE*     3.9     5.6    -      -       -      -
    204B  PRO*     3.2    23.4    -      -       +      +
    208B  ASP*     3.6    35.8    +      -       +      +
    209B  GLU*     1.3    77.6    -      -       -      +
    211B  CYS*     1.3    67.1    +      -       -      +
    226B  GLU*     4.3    12.1    -      -       +      +
    227B  VAL      3.2    12.3    +      -       -      -
    228B  ASP*     4.9     8.4    +      -       +      +
    235B  LEU*     3.7    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  THR*     5.2     2.0    -      -       -      -
    188B  PHE*     4.4    15.3    -      -       +      -
    201B  GLU*     5.3     6.7    -      -       +      +
    202B  ILE      3.6     9.6    -      -       -      +
    203B  PHE*     4.0    23.3    -      -       -      -
    204B  PRO*     4.1     0.7    -      -       -      -
    210B  HIS*     1.3    80.7    -      -       -      +
    212B  VAL*     1.3    66.4    +      -       -      +
    213B  ARG*     3.9     0.7    -      -       +      -
    225B  ARG      3.6     0.7    -      -       -      +
    226B  GLU*     3.2     7.4    -      -       -      +
    227B  VAL*     2.6    53.0    +      -       +      +
    229B  ALA*     3.9    24.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  VAL      3.8     2.3    -      -       -      +
    201B  GLU*     3.4     2.8    -      -       -      +
    202B  ILE*     2.8    38.3    +      -       +      +
    204B  PRO*     4.1    13.9    -      -       +      -
    211B  CYS*     1.3    75.0    -      -       -      +
    213B  ARG*     1.3    59.8    +      -       -      +
    214B  VAL*     3.9    21.5    -      -       +      -
    224B  ILE*     5.2     4.9    -      -       +      -
    225B  ARG      4.0     5.8    -      -       -      +
    226B  GLU*     4.8     4.0    -      -       +      +
    241B  VAL*     3.9    33.7    -      -       +      -
    243B  ILE*     3.8    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  VAL*     5.3     4.7    -      -       +      -
    200B  VAL      3.8     3.8    -      -       -      -
    201B  GLU*     4.3    18.6    -      -       +      -
    211B  CYS*     3.8     0.6    +      -       +      -
    212B  VAL*     1.3    71.9    -      -       -      +
    214B  VAL*     1.3    60.9    +      -       -      +
    215B  GLU*     4.0     0.6    +      -       -      -
    223B  ARG      3.6     2.3    -      -       -      +
    224B  ILE*     3.4     4.2    -      -       -      -
    225B  ARG*     3.0    44.8    +      -       +      +
    227B  VAL*     4.1    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     4.0    15.5    -      -       +      -
    172B  LEU*     5.1     9.4    -      -       +      -
    199B  VAL*     3.3     6.5    -      -       -      +
    200B  VAL*     2.8    48.8    +      -       +      +
    202B  ILE*     3.9    25.1    -      -       +      -
    212B  VAL*     3.9    11.9    -      -       +      -
    213B  ARG*     1.3    74.6    -      -       -      +
    215B  GLU*     1.3    62.6    +      -       -      +
    216B  PHE*     4.0     5.8    +      -       +      +
    221B  ILE*     3.8    35.7    -      -       +      -
    223B  ARG      3.6     2.9    -      -       -      -
    224B  ILE*     4.8     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  ASP      3.7     4.9    -      -       -      +
    199B  VAL*     3.7    15.0    -      -       +      -
    213B  ARG      4.0     1.0    +      -       -      +
    214B  VAL*     1.3    72.5    -      -       -      +
    216B  PHE*     1.3    54.2    +      -       -      +
    221B  ILE*     3.6     4.3    -      -       -      +
    222B  GLU*     2.8    34.2    +      -       +      -
    223B  ARG*     2.8    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ILE      6.0     1.1    -      -       -      +
    169B  ARG*     5.1    17.0    -      -       +      -
    198B  ASP*     2.7    41.9    +      -       -      +
    200B  VAL*     6.2     3.6    -      -       +      -
    214B  VAL*     4.0     8.0    +      -       +      +
    215B  GLU*     1.3    73.3    -      -       -      +
    217B  PHE*     1.4    58.1    +      -       -      +
    218B  GLY      3.3     8.9    +      -       -      +
    219B  ASP*     5.3     4.0    -      -       -      +
    220B  GLU      3.2    14.8    -      -       -      +
    221B  ILE*     4.9     4.3    -      -       +      -
    222B  GLU*     4.6     1.1    -      -       -      -
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Residues in contact with PHE 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  PHE*     1.4    65.5    -      -       -      +
    218B  GLY*     1.3    56.3    +      -       -      +
    219B  ASP      3.0     9.8    +      -       -      -
    220B  GLU*     2.9    39.7    +      -       +      +
    222B  GLU*     3.9    17.1    -      -       +      +
----------------------------------------------------------
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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