Contacts of the strand formed by residues 243 - 253 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200D  LEU*     3.6     4.4    -      -       -      +
    201D  TYR*     2.8    39.4    +      -       -      +
    234D  GLN*     4.0    18.2    -      -       +      +
    235D  ASN      2.9    27.9    +      -       -      -
    236D  MET*     3.5    20.8    -      -       -      +
    237D  PRO*     4.2     1.8    -      -       -      +
    242D  ASN*     1.4    71.5    -      -       -      +
    244D  SER*     1.3    60.6    +      -       -      +
    499D  SO4      3.1    15.4    +      -       -      -
    233F  ILE      3.5     2.0    -      -       -      -
    234F  GLN*     3.4     7.0    -      -       -      +
    235F  ASN*     2.8    41.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 244 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198D  GLN*     3.9    21.9    +      -       -      -
    199D  VAL      3.3    10.8    -      -       -      -
    200D  LEU*     3.7    15.1    -      -       -      +
    234D  GLN*     4.1     4.6    +      -       -      +
    243D  ASN*     1.3    73.9    -      -       -      +
    245D  CYS*     1.3    62.1    +      -       -      +
    276D  VAL*     5.0     0.7    -      -       -      -
    231F  ARG      4.6     1.3    -      -       -      -
    232F  CYS*     3.4    17.4    -      -       -      -
    233F  ILE      2.9    33.4    +      -       -      -
    234F  GLN*     3.4    15.1    -      -       -      +
    245F  CYS*     4.8     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 245 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198D  GLN*     3.2    23.5    -      -       -      -
    199D  VAL      2.9     8.8    +      -       -      -
    201D  TYR*     4.2    15.0    -      -       +      -
    210D  HIS*     3.2    10.6    -      -       +      -
    232D  CYS*     2.0    48.7    -      -       +      -
    233D  ILE      4.0     2.9    -      -       -      -
    234D  GLN*     3.7    28.0    -      -       +      -
    243D  ASN      4.1     0.4    +      -       -      -
    244D  SER*     1.3    75.0    -      -       -      +
    246D  TYR*     1.3    61.3    +      -       -      +
    244E  SER*     3.9    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 246 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  PHE*     4.0     9.9    -      -       -      -
    196D  TYR*     3.4    26.6    -      -       +      +
    197D  GLY      3.4    11.7    -      -       -      -
    198D  GLN*     3.7    22.2    -      -       +      +
    232D  CYS*     3.4    11.3    -      -       -      -
    244D  SER      4.2     0.4    -      -       -      -
    245D  CYS*     1.3    75.5    -      -       -      +
    247D  SER*     1.3    60.4    +      -       -      +
    248D  ALA*     3.6    19.8    -      -       +      +
    278D  PHE*     4.3     3.4    -      +       -      -
    198E  GLN*     4.0     0.3    -      -       -      +
    246E  TYR*     3.4    57.8    +      +       +      +
    194F  PHE*     4.5     1.6    -      -       -      -
    246F  TYR*     3.5    35.0    -      +       +      +
    248F  ALA*     3.3    41.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 247 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196D  TYR*     3.6     0.5    -      -       -      -
    197D  GLY      3.1    31.7    +      -       -      +
    210D  HIS*     4.9     5.2    -      -       -      -
    212D  ILE*     3.9     7.3    -      -       -      +
    230D  PHE*     3.9    15.0    -      -       -      +
    231D  ARG      4.2     2.3    +      -       -      -
    232D  CYS*     3.9    16.6    -      -       -      -
    246D  TYR*     1.3    79.6    -      -       -      +
    248D  ALA*     1.3    62.9    +      -       -      +
    198E  GLN*     2.7    32.2    +      -       -      -
    246E  TYR*     4.4     1.8    -      -       -      -
    278E  PHE*     3.8     7.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 248 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  PHE*     3.6    25.8    -      -       +      -
    195D  ILE      3.1    15.9    -      -       -      +
    196D  TYR*     3.7     2.9    -      -       +      -
    230D  PHE*     4.5     6.5    -      -       -      +
    246D  TYR*     3.6    14.8    -      -       +      +
    247D  SER*     1.3    78.9    +      -       -      +
    249D  GLY*     1.3    58.5    +      -       -      +
    196E  TYR*     4.4     0.2    -      -       -      -
    246E  TYR*     3.2    22.4    -      -       -      +
    278E  PHE*     3.1    26.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 249 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  PHE*     3.4     8.9    -      -       -      -
    195D  ILE*     2.9    31.4    +      -       -      +
    230D  PHE*     3.4    22.6    -      -       -      -
    248D  ALA*     1.3    74.6    -      -       -      +
    250D  ILE*     1.3    63.7    +      -       -      -
    148E  GLN*     4.0     4.0    -      -       -      -
    196E  TYR*     4.1    11.4    -      -       -      -
    278E  PHE*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 250 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192D  TYR*     4.5     3.1    -      -       +      -
    193D  PHE      3.3    11.2    -      -       -      +
    194D  PHE*     4.4    10.8    -      -       +      -
    230D  PHE*     3.7     5.2    -      -       -      -
    249D  GLY*     1.3    77.7    -      -       -      +
    251D  ALA*     1.3    66.2    +      -       -      +
    284D  LEU*     3.8    24.7    -      -       +      -
    146E  CYS*     3.9    17.7    -      -       +      -
    147E  LEU      5.5     0.7    -      -       -      +
    148E  GLN*     2.9    19.8    +      -       -      +
    172E  PHE*     3.3    36.4    -      -       +      -
    196E  TYR*     3.2    35.4    +      -       +      +
    281E  ALA      4.4     1.3    -      -       -      +
    282E  LEU*     3.9    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 251 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192D  TYR*     4.4     1.8    -      -       -      -
    193D  PHE*     2.7    38.8    +      -       -      -
    195D  ILE*     3.3    26.0    -      -       +      -
    229D  LEU*     4.0    20.4    -      -       +      -
    230D  PHE*     4.6     2.5    -      -       +      -
    250D  ILE*     1.3    76.4    -      -       -      +
    252D  LYS*     1.3    61.7    +      -       -      +
    253D  LEU*     3.4    17.7    +      -       +      +
    172E  PHE*     4.3     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 252 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  GLY      3.6     7.2    -      -       -      +
    192D  TYR*     3.1    48.4    +      -       +      +
    214D  ARG*     3.8    17.5    +      -       -      -
    229D  LEU*     5.8     0.7    -      -       -      +
    251D  ALA*     1.3    71.2    -      -       -      +
    253D  LEU*     1.4    66.2    +      -       -      +
    172E  PHE*     4.1    32.6    -      -       +      -
    173E  LYS      5.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 253 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178D  LEU*     5.7     0.2    -      -       +      -
    187D  VAL*     3.9    18.8    -      -       +      -
    190D  THR*     3.4     5.1    -      -       -      +
    191D  GLY      2.8    34.4    +      -       -      +
    193D  PHE*     3.6    33.8    -      -       +      -
    195D  ILE*     3.8     7.2    -      -       +      -
    214D  ARG*     3.7    30.1    -      -       +      +
    229D  LEU*     4.2     1.6    -      -       +      -
    251D  ALA*     3.4    18.4    +      -       +      +
    252D  LYS*     1.4    82.1    -      -       -      +
    254D  GLU*     1.3    62.9    +      -       -      +
    257D  ASP*     3.8     6.3    -      -       +      +
    259D  LEU*     3.8    35.2    -      -       +      -
----------------------------------------------------------
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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