Contacts of the strand formed by residues 261 - 267 (chain C) in PDB entry 1YPO


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 PHE 261 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  SER*     3.0    22.2    -      -       -      +
    160C  SER      3.3    26.5    -      -       -      -
    161C  GLY*     3.2    17.7    -      -       -      -
    162C  SER*     4.0    17.7    -      -       -      -
    200C  PHE*     3.6    42.6    -      +       +      -
    201C  PRO      3.0    14.6    +      -       -      +
    202C  PHE*     3.3    16.0    -      -       +      -
    203C  TRP*     2.7    28.8    +      -       -      +
    260C  ALA*     1.3    78.8    -      -       -      +
    262C  SER*     1.3    56.4    +      -       -      +
    196D  SER*     3.9    14.6    -      -       -      -
    197D  TYR*     3.9    25.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with SER 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  SER*     3.0    36.9    +      -       -      -
    163C  PHE*     6.2     0.3    -      -       -      -
    168C  SER*     3.5    21.0    +      -       -      -
    171C  LYS*     6.0     1.2    -      -       -      +
    172C  CYS*     5.1     2.6    -      -       -      -
    179C  LEU*     3.7    21.1    -      -       -      +
    202C  PHE*     3.1    12.1    -      -       -      -
    203C  TRP*     3.6    18.8    -      -       -      +
    261C  PHE*     1.3    79.1    -      -       -      +
    263C  ILE*     1.3    66.4    +      -       -      +
    264C  CYS*     5.1     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156C  TYR*     4.2    15.5    -      -       +      -
    157C  LEU      3.2    21.5    -      -       -      +
    158C  PHE*     3.7    29.8    -      -       +      -
    159C  SER      4.7     0.2    -      -       -      +
    179C  LEU*     3.4     9.7    -      -       -      +
    180C  LEU*     3.0    51.8    +      -       +      +
    191C  ILE*     3.9    16.2    -      -       +      -
    195C  ILE*     4.8     0.4    -      -       +      -
    202C  PHE*     3.4    27.8    -      -       +      -
    203C  TRP      3.8     7.0    +      -       -      +
    246C  ILE*     4.8     1.3    -      -       +      -
    262C  SER*     1.3    82.5    -      -       -      +
    264C  CYS*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 264 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148C  TRP*     3.9    13.1    -      -       +      -
    155C  CYS      3.5     0.2    -      -       -      +
    156C  TYR*     3.2     8.1    -      -       -      +
    157C  LEU*     3.0    34.7    +      -       +      +
    159C  SER*     5.9     5.2    -      -       -      -
    171C  LYS*     4.6     4.3    -      -       -      -
    172C  CYS*     2.0    55.2    -      -       +      -
    175C  LEU*     4.8     8.5    -      -       -      -
    177C  ALA*     4.0    10.8    -      -       +      -
    178C  LYS      3.2     5.2    -      -       -      +
    180C  LEU*     4.8     0.7    -      -       -      -
    262C  SER*     5.1     4.3    -      -       -      -
    263C  ILE*     1.3    76.9    -      -       -      +
    265C  GLN*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 265 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148C  TRP*     4.6     0.2    -      -       -      -
    154C  ASN*     3.8    24.2    +      -       +      +
    155C  CYS      2.9    10.5    -      -       -      +
    156C  TYR*     3.4    31.3    +      -       +      -
    177C  ALA*     3.2     4.7    -      -       -      +
    178C  LYS*     2.7    73.7    +      -       +      +
    180C  LEU*     3.6     6.9    -      -       -      +
    181C  LYS*     3.2    32.4    +      -       -      +
    183C  ASN*     5.7     1.8    +      -       -      -
    264C  CYS*     1.3    76.6    -      -       -      +
    266C  LYS*     1.3    62.5    +      -       -      +
    267C  LYS*     4.8     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 266 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145C  PRO*     3.9    31.3    -      -       -      +
    148C  TRP*     3.7    32.2    -      -       +      -
    154C  ASN*     3.3     6.2    -      -       -      -
    155C  CYS*     2.6    35.8    +      -       +      +
    175C  LEU      3.2    19.5    +      -       -      +
    176C  ASP*     3.2    25.9    -      -       +      +
    177C  ALA*     3.8     1.6    -      -       +      -
    178C  LYS*     6.0     1.1    -      -       -      +
    265C  GLN*     1.3    78.1    -      -       -      +
    267C  LYS*     1.3    87.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 267 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153C  GLU*     3.2    14.1    -      -       +      +
    154C  ASN*     3.5     7.7    +      -       -      +
    155C  CYS*     4.3     1.1    -      -       -      -
    176C  ASP      4.2     6.8    +      -       -      -
    177C  ALA*     5.3     1.4    -      -       -      +
    266C  LYS*     1.3   105.4    -      -       -      +
    268C  ALA*     1.3    67.7    +      -       -      +
----------------------------------------------------------
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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