Contacts of the strand formed by residues 394 - 403 (chain B) in PDB entry 6VSB


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 ASN 394 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357B  ARG*     3.9    19.8    -      -       +      +
    358B  ILE      3.5    13.5    -      -       -      +
    359B  SER*     4.6     4.0    -      -       -      -
    392B  PHE*     3.5     5.2    -      -       -      +
    393B  THR*     1.3    90.9    +      -       -      +
    395B  VAL*     1.3    68.6    +      -       -      +
    396B  TYR*     2.4    35.6    +      -       -      -
    514B  SER      4.4     0.2    -      -       -      +
    515B  PHE*     4.3     0.2    -      -       -      -
    516B  GLU*     3.1    31.9    +      -       -      +
    524B  VAL*     4.3     3.8    -      -       -      -
    200C  TYR*     4.4     4.2    +      -       -      -
    228C  ASP*     5.6     1.6    +      -       -      -
    230C  PRO*     5.0     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 395 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338B  PHE*     5.9     1.1    -      -       +      -
    357B  ARG*     3.6     1.0    -      -       -      -
    358B  ILE*     2.6    59.7    +      -       +      +
    365B  TYR*     3.8    19.1    -      -       +      +
    392B  PHE*     4.6     1.1    -      -       +      -
    394B  ASN*     1.3    79.4    -      -       -      +
    396B  TYR*     1.3    66.2    +      -       -      +
    513B  LEU*     4.3    23.1    -      -       +      -
    514B  SER      3.6    11.4    -      -       -      +
    515B  PHE*     4.2    27.6    -      -       +      -
    524B  VAL*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355B  ARG*     3.8    35.9    -      -       +      +
    356B  LYS      3.7     2.7    -      -       -      -
    357B  ARG*     3.6    23.8    -      -       +      -
    394B  ASN*     2.4    41.8    +      -       -      -
    395B  VAL*     1.3    73.5    -      -       -      +
    397B  ALA*     1.3    59.3    +      -       -      +
    398B  ASP*     3.7     1.4    +      -       -      +
    512B  VAL      3.2     2.8    -      -       -      +
    513B  LEU*     3.4     1.8    -      -       -      -
    514B  SER*     2.7    57.9    +      -       -      +
    515B  PHE      5.6     0.2    -      -       -      -
    516B  GLU*     4.5     3.4    -      -       +      -
    200C  TYR*     3.1    28.4    -      +       -      -
    230C  PRO*     3.1    42.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  VAL*     3.9    24.2    -      -       +      +
    355B  ARG*     3.5     1.6    -      -       -      -
    356B  LYS*     3.2    36.4    +      -       +      +
    358B  ILE*     4.3    15.3    -      -       +      -
    395B  VAL      4.0     1.6    +      -       -      -
    396B  TYR*     1.3    69.6    -      -       -      +
    398B  ASP*     1.3    62.4    +      -       -      +
    399B  SER*     3.4     6.7    +      -       -      -
    511B  VAL*     4.6     2.9    -      -       +      -
    512B  VAL      3.3     6.5    -      -       -      -
    513B  LEU*     3.7    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 398 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  TRP*     3.6    31.2    -      -       +      -
    354B  ASN      3.5     5.2    -      -       -      -
    355B  ARG*     4.1    12.8    -      -       -      +
    396B  TYR      3.7     1.2    +      -       -      +
    397B  ALA*     1.3    69.8    -      -       -      +
    399B  SER*     1.3    59.2    +      -       -      +
    400B  PHE*     3.9     6.0    -      -       +      -
    423B  TYR*     3.7    19.7    -      -       +      +
    510B  VAL      3.8     1.2    -      -       -      +
    511B  VAL*     3.5     3.5    -      -       -      -
    512B  VAL*     2.6    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 399 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  VAL*     5.0     7.4    -      -       -      -
    347B  PHE*     4.0    34.7    -      -       -      -
    348B  ALA      5.0     2.8    +      -       -      +
    353B  TRP*     3.5     1.0    -      -       -      -
    354B  ASN*     2.7    49.9    +      -       -      +
    356B  LYS*     4.8     9.3    +      -       -      -
    397B  ALA      3.4     5.4    +      -       -      -
    398B  ASP*     1.3    74.0    -      -       -      +
    400B  PHE*     1.3    64.1    +      -       -      +
    510B  VAL      3.8     4.3    -      -       -      -
    511B  VAL*     4.6     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 400 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347B  PHE*     4.5    11.4    -      -       -      -
    348B  ALA      3.9     7.6    -      -       -      -
    349B  SER      4.1     0.9    -      -       -      +
    350B  VAL*     3.9    19.7    -      -       +      -
    353B  TRP*     3.5    26.9    -      +       +      -
    398B  ASP      3.9     8.1    -      -       -      -
    399B  SER*     1.3    78.5    -      -       -      +
    401B  VAL*     1.3    59.0    +      -       -      +
    402B  ILE*     3.5    30.5    -      -       +      -
    410B  ILE*     4.2    11.2    -      -       +      -
    423B  TYR*     3.8    39.0    -      +       -      -
    509B  ARG*     3.9     1.4    -      -       -      -
    510B  VAL*     2.8    61.2    +      -       +      +
    512B  VAL*     3.9    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 401 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347B  PHE*     4.8     8.7    -      -       +      +
    348B  ALA      3.5    17.7    +      -       -      +
    349B  SER*     4.5     2.5    -      -       -      -
    350B  VAL*     3.5    15.9    +      -       -      +
    400B  PHE*     1.3    73.1    -      -       -      +
    402B  ILE*     1.3    76.7    +      -       -      +
    442B  ASP*     4.4     6.5    -      -       -      +
    451B  TYR*     3.5    63.0    -      -       +      -
    452B  LEU      5.1     0.2    -      -       -      +
    495B  TYR*     4.9     3.4    -      -       -      -
    507B  PRO*     4.3     4.5    -      -       +      -
    508B  TYR      3.1    22.0    -      -       -      +
    509B  ARG*     4.5     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 402 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350B  VAL*     3.6    21.1    -      -       +      -
    400B  PHE*     3.5    19.9    +      -       +      -
    401B  VAL*     1.3    82.5    -      -       -      +
    403B  ARG*     1.3    64.0    -      -       -      +
    406B  GLU*     3.4    34.1    -      -       +      +
    407B  VAL*     3.8     9.6    -      -       +      -
    410B  ILE*     3.9    16.6    -      -       +      -
    418B  ILE*     5.0     7.4    -      -       +      -
    495B  TYR*     4.8    15.3    -      -       -      +
    507B  PRO*     3.4     4.3    -      -       -      +
    508B  TYR*     2.5    40.8    +      -       +      +
    510B  VAL*     3.5    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 403 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402B  ILE*     1.3    98.0    -      -       -      +
    404B  GLY*     1.3    64.9    +      -       -      +
    405B  ASP*     4.4     2.9    -      -       +      +
    406B  GLU*     4.3    12.4    +      -       +      +
    407B  VAL*     4.3     1.0    +      -       -      +
    495B  TYR*     4.3    25.7    +      -       +      -
    504B  GLY      3.8    13.5    -      -       -      +
    505B  TYR*     4.6     7.4    -      -       -      +
    506B  GLN      3.4    10.1    -      -       -      +
    507B  PRO*     4.2     2.7    -      -       -      -
    508B  TYR*     3.6     7.0    -      -       -      +
----------------------------------------------------------
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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