Contacts of the strand formed by residues 252 - 260 (chain A) in PDB entry 5V8V


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 TYR 252 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  SER*     3.7    19.7    +      -       -      -
    248A  ASP      3.1    31.9    -      -       -      -
    249A  PRO*     3.0    39.2    +      -       +      +
    250A  GLN      3.7     0.6    -      -       -      -
    251A  HIS*     1.3    79.7    -      -       -      +
    253A  GLU*     1.3    58.9    +      -       -      +
    254A  GLY      3.5    22.6    -      -       -      +
    255A  ASN*     5.2     3.1    -      -       -      -
    256A  PHE*     3.7    24.3    -      +       -      -
    390A  TYR*     3.8    28.3    -      +       +      -
    403A  ALA*     3.8    16.8    -      -       +      -
    404A  LEU      3.2    12.6    -      -       -      +
    406A  ARG*     3.3     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  TYR*     1.3    73.3    -      -       -      +
    254A  GLY*     1.3    67.3    +      -       -      +
    255A  ASN      4.8     0.5    -      -       -      +
    403A  ALA*     4.0     3.6    -      -       -      +
    404A  LEU*     3.1    54.5    +      -       +      +
    405A  ALA      5.0     0.3    -      -       -      +
    406A  ARG*     3.6    29.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  TYR*     3.5    20.6    -      -       -      +
    253A  GLU*     1.3    79.9    -      -       -      +
    255A  ASN*     1.3    67.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  TYR*     5.2     2.7    -      -       -      -
    253A  GLU      4.8     0.3    -      -       -      +
    254A  GLY*     1.3    80.1    +      -       -      -
    256A  PHE*     1.3    69.4    +      -       -      +
    257A  HIS*     3.6     2.1    +      -       -      +
    402A  PHE      3.9     5.2    -      -       -      +
    403A  ALA*     3.9     8.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  SER*     3.4    21.1    -      -       -      -
    252A  TYR*     3.7    28.9    -      +       -      -
    255A  ASN*     1.3    79.6    -      -       -      +
    257A  HIS*     1.3    58.0    +      -       -      +
    258A  TYR*     3.3    49.3    -      +       +      -
    390A  TYR*     3.6    34.8    -      +       -      -
    392A  GLU*     3.2    25.6    -      -       +      -
    401A  GLY*     3.8     4.0    -      -       -      -
    402A  PHE      3.3    23.3    -      -       -      -
    403A  ALA*     3.6    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  ASN      3.6     1.7    +      -       -      +
    256A  PHE*     1.3    71.0    -      -       -      +
    258A  TYR*     1.3    74.5    +      -       -      +
    259A  ILE*     3.8    10.7    -      -       +      +
    338A  LEU      3.6    15.0    -      -       -      -
    339A  GLY*     3.1    35.5    +      -       -      -
    341A  LYS*     3.5    40.1    -      -       +      +
    343A  TYR*     2.7    26.1    +      -       -      +
    400A  ILE      3.7     1.7    -      -       -      +
    401A  GLY*     3.5     0.7    -      -       -      -
    402A  PHE*     2.8    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  PHE*     3.3    39.5    -      -       +      -
    257A  HIS*     1.3    85.5    +      -       -      +
    259A  ILE*     1.3    63.2    +      -       -      +
    260A  ASN*     5.8     1.1    -      -       -      -
    392A  GLU*     2.8    31.1    +      -       +      -
    394A  ASP*     5.2     0.7    -      -       +      -
    399A  ARG*     3.5    60.6    +      -       +      +
    400A  ILE      3.4     0.7    -      -       -      -
    401A  GLY*     3.4    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  HIS*     3.8    25.8    -      -       +      +
    258A  TYR*     1.3    79.2    -      -       -      +
    260A  ASN*     1.3    73.1    +      -       -      +
    269A  ILE*     3.8    27.3    -      -       +      +
    270A  GLN*     4.8     6.7    -      -       +      +
    338A  LEU*     3.9    21.3    -      -       +      +
    339A  GLY*     4.1    14.8    -      -       -      +
    343A  TYR*     4.5     0.4    -      -       -      +
    399A  ARG*     3.9     3.1    -      -       -      -
    400A  ILE*     2.8    37.0    +      -       -      +
    402A  PHE*     3.6    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258A  TYR*     5.8     0.7    -      -       -      +
    259A  ILE*     1.3    81.8    -      -       -      +
    261A  LEU*     1.3    70.6    +      -       -      +
    262A  ILE*     3.7     0.9    +      -       -      +
    269A  ILE*     3.5    12.8    -      -       -      +
    270A  GLN*     4.8     2.1    +      -       -      +
    397A  ASN      4.2     6.1    -      -       -      +
    398A  ASN      3.7     7.2    -      -       -      +
    399A  ARG*     3.8    16.5    -      -       -      +
----------------------------------------------------------
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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