Contacts of the strand formed by residues 243 - 253 (chain B) in PDB entry 3V56


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 243 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  ILE      3.6     2.7    -      -       -      -
    234A  GLN*     3.4     4.2    -      -       -      +
    235A  ASN*     2.8    40.0    +      -       -      +
    499A  SO4      3.0    21.8    +      -       -      -
    200B  LEU*     3.6     4.2    -      -       -      +
    201B  TYR*     2.8    39.9    +      -       -      +
    234B  GLN*     3.9    17.0    -      -       +      +
    235B  ASN      2.9    28.3    +      -       -      -
    236B  MET*     3.6    20.0    -      -       -      +
    237B  PRO*     4.2     1.0    -      -       -      +
    242B  ASN*     1.3    70.9    -      -       -      +
    244B  SER*     1.3    59.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  ARG      4.6     1.3    -      -       -      -
    232A  CYS*     3.4    16.7    -      -       -      -
    233A  ILE      2.9    33.7    +      -       -      -
    234A  GLN*     3.4    14.9    -      -       -      +
    245A  CYS*     3.9     2.9    -      -       -      -
    198B  GLN*     4.0    21.7    +      -       -      -
    199B  VAL      3.3    10.3    -      -       -      -
    200B  LEU*     3.8    14.5    -      -       -      +
    234B  GLN*     4.1     4.6    +      -       -      +
    243B  ASN*     1.3    74.5    -      -       -      +
    245B  CYS*     1.3    63.2    +      -       -      +
    276B  VAL*     5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  GLN*     3.2    23.4    -      -       -      +
    199B  VAL      2.9     8.8    +      -       -      -
    201B  TYR*     4.2    15.0    -      -       +      -
    210B  HIS*     3.2    10.6    -      -       +      -
    232B  CYS*     2.0    48.5    -      -       +      -
    233B  ILE      4.0     2.7    -      -       -      -
    234B  GLN*     3.7    28.5    -      -       +      -
    243B  ASN      4.1     0.2    +      -       -      -
    244B  SER*     1.3    75.1    -      -       -      +
    246B  TYR*     1.3    60.1    +      -       -      +
    244C  SER*     3.9    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  PHE*     4.4     1.4    -      -       -      -
    246A  TYR*     3.5    34.1    -      +       +      +
    248A  ALA*     3.4    39.3    +      -       -      +
    194B  PHE*     4.0     9.9    -      -       -      -
    196B  TYR*     3.4    27.5    -      -       +      +
    197B  GLY      3.4    13.0    -      -       -      -
    198B  GLN*     3.7    22.7    -      -       +      +
    232B  CYS*     3.5     9.7    -      -       -      -
    244B  SER      4.2     0.4    -      -       -      -
    245B  CYS*     1.3    75.3    -      -       -      +
    247B  SER*     1.3    61.2    +      -       -      +
    248B  ALA*     3.6    20.8    -      -       +      +
    278B  PHE*     4.3     3.4    -      +       -      -
    198C  GLN*     4.0     0.5    -      -       -      +
    246C  TYR*     3.4    53.4    +      +       +      +
----------------------------------------------------------
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Residues in contact with SER 247 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  TYR*     3.6     0.7    -      -       -      -
    197B  GLY      3.1    31.3    +      -       -      +
    210B  HIS*     5.0     4.7    -      -       -      -
    212B  ILE*     3.8     8.6    -      -       -      +
    230B  PHE*     3.9    14.0    -      -       -      +
    231B  ARG      4.2     2.8    +      -       -      -
    232B  CYS*     3.9    16.5    -      -       -      -
    246B  TYR*     1.3    79.4    -      -       -      +
    248B  ALA*     1.3    62.4    +      -       -      +
    198C  GLN*     2.6    33.4    +      -       -      -
    246C  TYR*     4.4     1.6    -      -       -      -
    278C  PHE*     3.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  PHE*     3.6    24.7    -      -       +      -
    195B  ILE      3.1    15.5    -      -       -      +
    196B  TYR*     3.7     3.6    -      -       +      -
    230B  PHE*     4.4     7.4    -      -       -      -
    246B  TYR*     3.6    18.6    -      -       +      +
    247B  SER*     1.3    78.3    +      -       -      +
    249B  GLY*     1.3    58.5    +      -       -      +
    196C  TYR*     4.4     0.3    -      -       -      -
    246C  TYR*     3.1    18.8    -      -       -      +
    278C  PHE*     3.1    26.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  PHE      3.6     0.2    -      -       -      +
    194B  PHE*     3.5     7.9    -      -       -      -
    195B  ILE      2.9    31.0    +      -       -      +
    230B  PHE*     3.5    21.4    -      -       -      -
    248B  ALA*     1.3    75.7    -      -       -      +
    250B  ILE*     1.3    66.0    +      -       -      -
    148C  GLN*     4.0     4.0    -      -       -      -
    196C  TYR*     4.1    12.8    -      -       -      -
    278C  PHE*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  TYR*     4.3     7.6    -      -       +      -
    193B  PHE      3.2    14.8    -      -       -      +
    194B  PHE*     4.3    11.0    -      -       +      -
    230B  PHE*     3.7     3.7    -      -       -      -
    249B  GLY*     1.3    77.7    -      -       -      +
    251B  ALA*     1.3    65.8    +      -       -      +
    284B  LEU*     3.9    24.2    -      -       +      -
    146C  CYS*     4.0    23.1    -      -       +      -
    148C  GLN*     3.0    28.4    +      -       -      +
    172C  PHE*     3.5    24.8    -      -       +      -
    196C  TYR*     3.4    34.8    -      -       +      +
    281C  ALA      4.6     0.7    -      -       -      +
    282C  LEU*     4.1    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  TYR*     4.6     1.3    -      -       -      -
    193B  PHE      2.9    28.7    +      -       -      +
    195B  ILE*     3.8    20.2    -      -       +      -
    229B  LEU*     4.0    23.3    -      -       +      -
    230B  PHE*     4.4     3.4    -      -       +      -
    250B  ILE*     1.3    78.9    -      -       -      +
    252B  LYS*     1.4    62.9    +      -       -      +
    253B  LEU*     3.4    18.7    +      -       +      +
    172C  PHE*     4.2     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLY      3.4    10.5    -      -       -      +
    192B  TYR*     3.9    34.5    -      -       +      +
    214B  ARG*     3.9    17.3    +      -       -      -
    251B  ALA*     1.4    68.9    -      -       -      +
    253B  LEU*     1.3    64.8    +      -       -      +
    172C  PHE*     4.1    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  LEU*     5.7     0.2    -      -       +      -
    187B  VAL*     3.8    25.8    -      -       +      -
    190B  THR*     3.4     6.0    -      -       -      +
    191B  GLY      2.9    31.5    +      -       -      +
    193B  PHE*     3.7    28.3    -      -       +      -
    195B  ILE*     3.9     9.0    -      -       +      -
    214B  ARG*     3.7    31.9    -      -       +      -
    229B  LEU*     4.3     1.3    -      -       +      -
    251B  ALA*     3.4    25.5    +      -       +      +
    252B  LYS*     1.3    77.5    -      -       -      +
    254B  GLU*     1.4    62.1    +      -       -      +
    257B  ASP*     3.7     6.7    -      -       +      +
    259B  LEU*     3.8    29.6    -      -       +      -
----------------------------------------------------------
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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