Contacts of the strand formed by residues 258 - 263 (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 GLU 258 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  LYS*     5.5     6.6    -      -       +      +
    184B  LYS*     3.4    31.4    -      -       +      +
    185B  ILE      3.2     9.2    -      -       -      +
    186B  LEU*     3.8    24.3    -      -       +      +
    213B  GLN      3.8     0.2    -      -       -      +
    214B  ARG*     3.4     4.5    -      -       -      +
    215B  LYS*     2.7    52.4    +      -       +      +
    256B  GLY      4.3     4.5    -      -       -      +
    257B  ASP*     1.3    79.0    -      -       -      +
    259B  LEU*     1.3    63.6    +      -       -      +
    260B  GLN*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  LEU*     5.4     0.4    -      -       +      -
    184B  LYS*     3.4     9.8    -      -       -      +
    185B  ILE*     2.7    49.8    +      -       +      +
    187B  VAL*     4.8     4.5    -      -       +      -
    195B  ILE*     3.8    26.7    -      -       +      -
    212B  ILE*     5.0     3.6    -      -       +      -
    213B  GLN      3.3    11.7    -      -       -      +
    214B  ARG*     4.2     5.4    -      -       +      -
    229B  LEU*     4.0    24.5    -      -       +      -
    253B  LEU*     3.8    32.5    -      -       +      -
    257B  ASP*     6.0     0.2    -      -       +      -
    258B  GLU*     1.3    78.6    -      -       -      +
    260B  GLN*     1.3    60.8    +      -       -      +
    279B  PHE*     3.8    15.9    -      -       +      -
    281B  ALA*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  PHE*     4.0    28.4    -      -       +      -
    183B  ASN      5.2     2.7    -      -       -      +
    184B  LYS*     4.2    23.1    -      -       +      +
    211B  LEU      3.3     1.6    -      -       -      +
    212B  ILE*     3.5     2.3    -      -       -      -
    213B  GLN*     2.7    74.7    +      -       +      +
    215B  LYS*     6.0     2.2    -      -       +      +
    226B  LEU*     4.1    20.9    -      -       +      +
    258B  GLU      5.7     0.4    -      -       -      +
    259B  LEU*     1.3    75.8    -      -       -      +
    261B  LEU*     1.3    60.1    +      -       -      +
    262B  ALA*     4.3     0.2    -      -       -      +
    279B  PHE*     3.8    10.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  PHE*     3.4    22.3    -      -       -      +
    166B  VAL*     4.4    18.0    +      -       +      -
    168B  TRP*     4.1    27.6    +      -       +      +
    183B  ASN      5.8     0.4    +      -       -      -
    197B  GLY*     4.3    10.5    -      -       -      -
    199B  VAL*     3.6    28.3    -      -       +      -
    210B  HIS*     3.7    39.9    -      -       +      +
    211B  LEU      3.3     4.7    -      -       -      +
    212B  ILE*     4.6     2.7    -      -       +      +
    260B  GLN*     1.3    72.4    -      -       -      +
    262B  ALA*     1.3    60.1    +      -       -      +
    263B  ILE*     4.4     4.9    -      -       +      -
    278B  PHE      4.4     2.0    -      -       -      +
    279B  PHE*     3.9    29.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  TYR*     4.0    15.5    -      -       +      -
    164B  THR      4.1     0.7    -      -       -      -
    165B  PHE*     3.5    27.6    -      -       +      -
    210B  HIS*     3.4     2.2    -      -       -      -
    211B  LEU*     2.8    38.3    +      -       +      +
    213B  GLN*     3.6    24.2    -      -       -      +
    260B  GLN*     4.0     0.9    -      -       -      +
    261B  LEU*     1.3    74.0    -      -       -      +
    263B  ILE*     1.3    61.4    +      -       -      +
    264B  PRO*     3.5     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  TYR*     3.3     3.9    -      -       -      -
    164B  THR*     2.9    49.6    +      -       +      +
    166B  VAL*     4.1    23.8    -      -       +      -
    199B  VAL*     4.1     9.2    -      -       +      -
    201B  TYR*     4.0    14.6    -      -       +      +
    208B  MET*     4.1     6.7    -      -       +      -
    209B  GLY      3.5    12.8    -      -       -      +
    210B  HIS*     4.0     6.7    -      -       +      -
    261B  LEU*     4.4     3.1    -      -       +      -
    262B  ALA*     1.3    73.6    -      -       -      +
    264B  PRO*     1.4    54.2    -      -       -      +
    265B  ARG*     2.7    29.0    +      -       +      -
    268B  ALA*     3.7    24.2    -      -       +      -
    270B  ILE*     4.0    26.9    -      -       +      -
----------------------------------------------------------
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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