Contacts of the strand formed by residues 355 - 360 (chain B) in PDB entry 2VGZ


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 PHE 355 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLY      3.8    11.4    -      -       -      -
     39A  GLY*     3.9    19.5    -      -       -      -
    200B  GLY      5.6     0.7    -      -       -      -
    201B  ASN      5.1     2.7    -      -       -      +
    202B  ASN*     3.3    45.1    -      -       +      -
    203B  PRO      3.8    18.4    -      -       -      +
    204B  THR      4.9     0.2    -      -       -      +
    205B  GLY*     4.2    11.1    -      -       -      +
    233B  TYR*     3.6    16.4    -      +       -      -
    350B  PRO*     3.4    22.7    -      -       -      +
    352B  ALA      5.1     0.4    +      -       -      -
    353B  GLY      3.8     0.4    -      -       -      -
    354B  MET*     1.3    99.9    -      -       +      +
    356B  LEU*     1.3    59.6    +      -       -      +
    357B  TRP      4.3     0.3    +      -       -      -
    399B  ARG*     3.3    46.2    -      -       +      -
    400B  ALA      3.5     0.9    -      -       -      -
    401B  SER*     3.9    13.7    -      -       -      -
    402B  PHE*     3.4     7.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  PRO      4.6     1.6    -      -       -      -
    333B  ILE*     4.1    40.6    -      -       +      +
    334B  LEU*     4.2    11.2    -      -       +      -
    337B  ALA*     4.4    10.1    -      -       +      -
    347B  TRP*     3.8    28.9    -      -       +      -
    348B  HIS      3.8    15.7    -      -       -      +
    350B  PRO*     4.3     7.2    -      -       +      -
    355B  PHE*     1.3    72.9    -      -       -      +
    357B  TRP*     1.3    64.7    +      -       -      +
    358B  ILE*     3.8    26.4    +      -       +      +
    398B  LEU      3.5     1.9    -      -       -      +
    399B  ARG*     3.4     3.8    -      -       -      -
    400B  ALA*     2.7    48.0    +      -       +      +
    402B  PHE*     4.1     1.7    -      -       +      -
    414B  PHE*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  PRO*     3.7    17.9    -      -       +      +
    203B  PRO*     3.5    38.8    -      -       +      +
    204B  THR*     3.5    41.7    +      -       +      +
    206B  ASN*     5.8     1.3    -      -       -      -
    346B  GLU      4.0     0.2    -      -       -      +
    347B  TRP*     3.5    21.8    -      -       -      +
    348B  HIS*     4.5     4.0    +      -       -      +
    355B  PHE      4.2     0.8    +      -       -      -
    356B  LEU*     1.3    75.3    -      -       -      +
    358B  ILE*     1.3    61.2    +      -       -      +
    359B  LYS      4.0     0.5    +      -       -      -
    384B  GLY*     3.6    30.3    -      -       -      -
    387B  PHE*     4.1     4.0    -      +       -      -
    388B  TYR*     3.5    16.6    -      -       -      -
    397B  TYR*     3.1    55.8    -      +       +      -
    398B  LEU      3.6    13.0    -      -       -      -
    399B  ARG*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337B  ALA*     5.7     0.2    -      -       +      -
    341B  LEU*     4.3    15.7    -      -       +      -
    345B  ALA*     3.7    27.8    -      -       +      -
    346B  GLU      3.6     5.2    -      -       -      +
    347B  TRP*     4.4     7.4    -      -       +      -
    356B  LEU*     3.8    32.5    -      -       +      +
    357B  TRP*     1.3    76.7    -      -       -      +
    359B  LYS*     1.3    62.8    +      -       -      +
    360B  VAL*     3.7     6.4    +      -       +      +
    396B  PRO      3.7     0.2    -      -       -      +
    397B  TYR*     3.1     6.7    -      -       -      -
    398B  LEU*     2.8    68.0    +      -       +      +
    400B  ALA*     4.1     7.9    -      -       +      -
    414B  PHE*     4.0    20.2    -      -       +      -
    417B  LEU*     4.8     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 359 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345B  ALA*     3.2     4.9    -      -       -      -
    346B  GLU*     2.8    68.6    +      -       +      +
    357B  TRP      4.0     0.6    +      -       -      -
    358B  ILE*     1.3    70.7    -      -       -      +
    360B  VAL*     1.3    66.6    -      -       -      +
    361B  LYS*     3.7     2.6    +      -       +      +
    396B  PRO*     3.9    16.0    -      -       +      +
    397B  TYR*     3.3    51.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 360 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344B  LEU      4.1     2.7    -      -       -      -
    345B  ALA*     4.2     0.4    -      -       -      -
    358B  ILE*     4.6     7.2    -      -       +      -
    359B  LYS*     1.3    76.9    -      -       -      +
    361B  LYS*     1.3    65.4    +      -       -      +
    362B  GLY      3.8     1.2    +      -       -      -
    363B  ILE*     3.4    38.8    -      -       +      +
    366B  VAL*     4.0    10.8    -      -       +      -
    369B  LEU*     5.0     1.3    -      -       +      -
    396B  PRO*     2.9    35.5    +      -       -      +
    398B  LEU*     3.9    28.5    -      -       +      -
    417B  LEU*     4.8     1.6    -      -       +      -
    421B  ILE*     3.8    33.7    -      -       +      -
----------------------------------------------------------
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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