Contacts of the strand formed by residues 261 - 267 (chain C) in PDB entry 3U8Z


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 ILE 261 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  TRP*     5.0     6.4    +      -       +      -
    241C  LEU*     4.1    13.2    -      -       +      -
    256C  PHE*     3.4    41.7    -      -       +      +
    257C  PRO      3.4     9.2    +      -       -      +
    258C  TRP*     3.4    44.1    +      -       +      +
    259C  ASN      3.5     1.8    -      -       -      +
    260C  GLU*     1.4    77.7    -      -       -      +
    262C  ARG*     1.4    61.4    +      -       -      +
    263C  ASN*     3.5    31.9    -      -       -      +
    264C  ILE*     3.9    13.7    -      -       +      -
    273C  ILE*     4.0     9.2    -      -       +      -
    274C  LYS      3.9     4.5    -      -       -      +
    275C  PRO*     4.5     0.4    -      -       +      -
    276C  LEU*     4.3     5.6    -      -       -      +
    304C  HIS*     5.4     4.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 262 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  TRP*     4.2     3.7    +      -       -      -
    185A  GLU*     4.2    11.3    -      -       -      +
    261C  ILE*     1.4    73.2    -      -       -      +
    263C  ASN*     1.3    78.2    +      -       -      +
    274C  LYS*     2.8    26.1    +      -       -      +
    275C  PRO      3.6    15.9    -      -       -      +
    276C  LEU*     3.6    26.3    -      -       +      +
    278C  LYS*     4.4    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 263 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  PRO*     3.8    29.6    -      -       +      +
    184A  TRP*     3.6    21.3    -      -       +      +
    185A  GLU*     4.7     4.3    -      -       -      +
    261C  ILE*     3.5     7.6    -      -       -      +
    262C  ARG*     1.3   102.9    -      -       -      +
    264C  ILE*     1.3    66.9    +      -       -      +
    265C  SER*     4.2     1.0    +      -       -      -
    274C  LYS*     2.9    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 264 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  MET*     3.1    26.2    -      -       +      +
    181A  PRO*     4.2     4.3    -      -       -      +
    184A  TRP*     3.3    51.6    -      -       +      +
    241C  LEU*     3.7    30.7    -      -       +      -
    258C  TRP*     3.7    12.1    -      -       +      -
    261C  ILE*     3.9    15.0    -      -       +      -
    263C  ASN*     1.3    80.1    -      -       -      +
    265C  SER*     1.3    69.3    +      -       -      +
    271C  PHE*     4.7     9.0    -      -       +      -
    272C  THR      3.4    10.8    -      -       -      +
    273C  ILE*     4.5     6.5    -      -       +      -
    297C  LEU*     4.2    12.8    -      -       +      -
    300C  CYS*     4.6     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 265 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  MET*     3.4    15.0    -      -       -      -
    180A  THR*     4.7     0.4    -      -       -      -
    181A  PRO*     3.9    22.9    -      -       -      -
    263C  ASN*     4.2     5.9    +      -       -      -
    264C  ILE*     1.3    76.4    -      -       -      +
    266C  TYR*     1.3    61.2    +      -       -      +
    271C  PHE*     3.4     4.7    -      -       -      +
    272C  THR*     2.9    52.9    +      -       -      +
    274C  LYS*     4.4     6.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 266 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  GLN*     3.7    20.5    -      -       -      +
    179A  MET*     2.7    42.6    +      -       +      +
    265C  SER*     1.3    74.8    -      -       -      +
    267C  SER*     1.3    61.6    +      -       -      +
    268C  ASP*     4.0     8.8    -      -       -      -
    269C  LYS*     3.0    34.9    +      -       -      -
    270C  GLU      3.4    14.1    -      -       -      -
    271C  PHE*     3.6    27.1    -      +       +      -
    290C  LEU*     3.6    15.5    -      -       +      +
    293C  ASN*     2.8    40.8    +      -       +      +
    294C  LYS      6.0     0.2    -      -       -      -
    297C  LEU*     3.9    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 267 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  GLN*     4.9    16.0    +      -       -      +
    266C  TYR*     1.3    76.9    -      -       -      +
    268C  ASP*     1.4    73.8    +      -       -      +
    269C  LYS      3.7     0.9    -      -       -      -
    270C  GLU*     3.2    20.9    +      -       -      +
----------------------------------------------------------
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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