Contacts of the strand formed by residues 209 - 214 (chain B) in PDB entry 3VZC


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 ARG 209 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  GLY*     1.3    70.8    -      -       -      -
    210B  LEU*     1.3    67.1    +      -       -      +
    211B  ALA*     5.5     2.2    -      -       +      +
    251B  VAL*     3.9    23.8    -      -       +      +
    252B  VAL      5.5     0.9    -      -       -      +
    254B  ASP      5.3     0.4    -      -       -      -
    255B  GLU*     3.1    35.9    +      -       -      +
    328B  ARG*     3.5     2.4    -      -       -      +
    329B  LEU*     3.4     7.3    -      -       -      +
    330B  GLU*     2.8    61.9    +      -       +      +
    332B  LYS*     4.8    11.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  GLY      4.2     1.8    +      -       -      -
    209B  ARG*     1.3    73.3    -      -       -      +
    211B  ALA*     1.3    86.8    +      -       -      +
    212B  TYR*     4.6     1.8    -      -       +      -
    251B  VAL*     3.8     5.4    -      -       -      +
    252B  VAL*     3.0    44.5    +      -       +      +
    254B  ASP      5.1     1.4    +      -       -      -
    257B  PHE*     3.9    17.4    -      -       +      -
    260B  VAL*     3.9    35.9    -      -       +      -
    287B  LEU*     4.3    19.1    -      -       +      -
    289B  TYR*     3.6    34.1    -      -       +      -
    327B  PHE*     4.9     6.7    -      -       +      -
    328B  ARG      3.5     8.7    -      -       -      +
    329B  LEU*     4.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  ARG*     5.5     2.7    -      -       +      +
    210B  LEU*     1.3    80.4    -      -       -      +
    212B  TYR*     1.3    61.0    +      -       -      +
    245B  VAL*     4.2    21.1    -      -       +      -
    249B  TRP*     3.9    16.4    -      -       +      -
    250B  THR      3.4    13.7    -      -       -      +
    251B  VAL*     4.3     8.5    -      -       +      -
    252B  VAL      4.7     0.2    -      -       -      +
    327B  PHE*     3.3     3.5    -      -       -      +
    328B  ARG*     2.7    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  LEU*     4.6     2.0    -      -       +      -
    211B  ALA*     1.3    75.7    -      -       -      +
    213B  LEU*     1.3    58.8    +      -       -      +
    214B  PRO*     3.5    15.8    -      -       +      +
    249B  TRP*     3.7     8.5    -      -       -      +
    250B  THR*     3.0    65.0    +      -       +      +
    252B  VAL*     3.9    26.6    -      -       +      +
    287B  LEU*     3.7    22.2    -      -       +      -
    289B  TYR*     4.5    11.0    +      +       -      -
    320B  VAL*     5.8     0.2    -      -       -      +
    322B  VAL*     3.8    36.2    -      -       +      +
    324B  VAL*     3.8    20.4    -      -       +      -
    326B  ALA      3.5    12.1    -      -       -      +
    327B  PHE*     3.9     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     1.3    71.0    -      -       -      +
    214B  PRO*     1.4    76.8    -      -       +      +
    216B  GLY      4.4     0.9    -      -       -      +
    217B  ARG*     3.9    28.9    -      -       +      +
    218B  VAL      5.3     2.2    -      -       -      +
    237B  HIS*     3.7    31.4    -      -       +      +
    248B  HIS*     4.3    16.4    -      -       +      +
    249B  TRP*     3.8    34.0    -      -       +      +
    324B  VAL*     3.4     4.0    -      -       -      +
    325B  VAL*     2.9    51.8    +      -       +      +
    326B  ALA*     2.9    14.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  TYR*     3.5    28.6    -      -       +      +
    213B  LEU*     1.4    94.6    -      -       +      +
    215B  VAL*     1.3    57.9    +      -       -      +
    216B  GLY      2.7    28.3    -      -       -      +
    217B  ARG*     3.4    42.6    -      -       -      +
    250B  THR*     4.3     0.4    -      -       -      +
    322B  VAL*     4.2     6.7    -      -       +      -
    323B  PRO      3.5    12.8    -      -       -      +
    324B  VAL*     4.1     3.1    -      -       +      -
    325B  VAL*     4.6     1.8    -      -       -      +
     98D  GLU*     4.8     4.0    -      -       -      +
----------------------------------------------------------
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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