Contacts of the strand formed by residues 254 - 258 (chain A) in PDB entry 6N8P


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 254 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  VAL*     3.9    12.3    -      -       +      -
    247A  SER      3.1    14.4    -      -       -      +
    248A  CYS*     4.0     5.2    -      -       +      -
    249A  HIS*     4.5     1.6    -      -       -      -
    253A  SER*     1.3    76.2    -      -       -      +
    255A  CYS*     1.3    65.4    +      -       -      +
    256A  GLN*     4.8    15.0    -      -       +      -
    270A  ARG      5.8     0.4    -      -       -      -
    271A  SER*     4.7     1.1    -      -       -      -
    272A  LEU*     3.1    56.9    +      -       +      +
    274A  PRO*     3.5    33.7    -      -       +      -
    283A  ILE*     4.3     6.5    -      -       +      -
    286A  ILE*     3.5    28.0    -      -       +      -
    288A  TRP*     5.5     1.5    -      +       -      -
    298A  THR*     3.8    29.8    +      -       +      +
    300A  PHE*     4.5     6.1    -      +       -      -
    318A  ILE*     4.2     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  VAL*     3.4     4.8    -      -       -      +
    247A  SER*     3.0    32.3    +      -       -      +
    249A  HIS*     3.5    22.0    -      -       -      -
    254A  TYR*     1.3    74.8    -      -       -      +
    256A  GLN*     1.3    62.6    +      -       -      +
    257A  TRP*     2.9    44.6    -      -       -      -
    268A  PRO*     4.5     9.0    -      -       +      -
    270A  ARG      3.1    15.5    -      -       -      +
    271A  SER*     3.7    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  LEU*     3.9    20.5    -      -       +      +
    245A  LEU      3.2     4.3    -      -       -      +
    246A  VAL*     4.1    16.4    -      -       +      -
    254A  TYR*     4.8    11.7    -      -       +      -
    255A  CYS*     1.3    79.0    -      -       -      +
    257A  TRP*     1.3    61.8    +      -       -      +
    268A  PRO*     3.8     1.6    -      -       -      +
    269A  LEU*     2.8    55.8    +      -       +      +
    270A  ARG*     3.1    29.6    +      -       -      +
    288A  TRP*     3.5    36.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  TYR*     3.6    15.5    -      -       -      +
    227A  PHE*     3.3    57.4    -      +       +      -
    228A  LEU      3.8    13.9    -      -       -      -
    229A  SER*     4.4    11.0    -      -       -      -
    230A  SER      5.6     1.3    -      -       -      -
    244A  LEU*     3.2     6.9    -      -       -      +
    245A  LEU*     2.6    55.7    +      -       +      +
    247A  SER*     2.9    27.9    +      -       -      -
    255A  CYS*     2.9    27.1    -      -       -      -
    256A  GLN*     1.3    76.9    -      -       -      +
    258A  PRO*     1.3    65.9    -      -       +      +
    266A  PRO*     4.1     4.5    -      -       +      -
    267A  GLU*     3.8     9.9    -      -       -      -
    268A  PRO*     3.4    44.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  TYR*     2.8    23.2    +      -       -      -
    243A  ARG      3.9     8.3    -      -       -      +
    244A  LEU*     4.2     3.8    -      -       +      -
    257A  TRP*     1.3    84.9    -      -       +      +
    259A  VAL*     1.3    60.7    +      -       -      +
    260A  SER*     4.0     3.7    +      -       -      -
    263A  ALA      5.1     0.5    -      -       -      +
    266A  PRO*     3.7    17.9    -      -       +      +
    267A  GLU      4.1    13.5    -      -       -      +
    269A  LEU*     4.1    30.7    -      -       +      -
----------------------------------------------------------
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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