Contacts of the strand formed by residues 201 - 208 (chain B) in PDB entry 3OFN


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 LEU 201 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  VAL*     4.2    22.2    -      -       +      -
    163B  ARG*     3.4    29.2    -      -       -      +
    188B  GLN*     3.3    34.4    +      -       +      +
    191B  TRP*     5.5     0.6    -      -       -      +
    192B  ASN*     3.1    23.9    +      -       -      -
    199B  LYS      3.8     0.8    +      -       -      -
    200B  LYS*     1.3    69.2    -      -       -      +
    202B  TYR*     1.3    66.2    +      -       -      +
    203B  CYS*     3.6     9.7    -      -       -      -
    265B  HIS*     3.8    11.9    -      -       +      -
    266B  ALA      3.5    35.2    -      -       -      +
    267B  LEU*     3.9    22.7    -      -       +      -
    324B  THR*     4.6     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  LEU*     3.9    31.0    -      -       +      -
    192B  ASN*     5.8     1.1    -      -       -      -
    197B  GLU*     2.7    34.2    +      -       -      -
    200B  LYS*     3.5    33.1    +      -       +      +
    201B  LEU*     1.3    75.3    -      -       -      +
    203B  CYS*     1.3    59.5    +      -       -      +
    204B  VAL*     5.7     0.2    -      -       -      -
    230B  TYR*     3.5    21.8    -      -       +      +
    259B  PHE*     3.4    40.8    -      +       +      -
    264B  LYS*     4.2    14.6    +      -       +      -
    265B  HIS      3.4    19.0    +      -       -      +
    266B  ALA*     3.2     4.8    -      -       +      -
    267B  LEU      2.9    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  LEU*     5.8     0.4    -      -       -      +
    185B  ILE*     3.7    44.4    -      -       +      -
    188B  GLN*     4.2     8.3    -      -       -      -
    201B  LEU      3.6    15.9    -      -       -      -
    202B  TYR*     1.3    75.3    -      -       -      +
    204B  VAL*     1.3    58.9    +      -       -      +
    230B  TYR*     2.9    19.5    +      -       -      -
    231B  SER*     3.0    22.7    -      -       -      -
    232B  ILE*     2.7    33.4    +      -       -      +
    267B  LEU*     3.4    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  ILE*     5.5     0.2    -      -       -      -
    202B  TYR*     6.4     0.4    -      -       +      -
    203B  CYS*     1.3    77.4    -      -       -      +
    205B  TYR*     1.3    56.8    +      -       -      +
    232B  ILE*     3.4    13.7    -      -       +      +
    234B  VAL*     4.2    20.6    -      -       +      -
    252B  ALA*     4.2     9.2    -      -       +      +
    255B  ILE*     4.0    15.5    -      -       +      -
    256B  GLY*     3.9    29.4    -      -       -      +
    259B  PHE*     5.7     3.8    -      -       +      -
    266B  ALA*     5.2     4.7    -      -       +      -
    267B  LEU      2.6    14.9    +      -       -      +
    268B  ILE*     3.1    27.1    -      -       +      +
    269B  VAL*     2.7    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  THR*     3.7    14.9    -      -       +      +
    181B  ALA*     5.0     2.2    -      -       +      -
    182B  LEU*     6.4     1.1    -      -       +      -
    185B  ILE*     4.2    22.0    -      -       +      -
    203B  CYS      4.1     0.6    -      -       -      -
    204B  VAL*     1.3    75.0    -      -       -      +
    206B  VAL*     1.3    56.9    +      -       -      +
    207B  ALA*     4.1    20.0    -      -       +      -
    210B  GLN*     3.0    18.7    +      -       -      -
    215B  VAL*     5.3     3.1    -      -       +      -
    218B  LEU*     3.4    32.4    -      -       +      +
    222B  LEU*     5.6     0.7    -      -       +      -
    231B  SER*     5.8     1.3    -      -       -      -
    232B  ILE      2.9     9.7    +      -       -      -
    233B  ILE*     3.4    30.1    -      -       +      -
    234B  VAL      2.8    31.4    +      -       -      +
    269B  VAL*     3.7    23.1    -      -       +      -
    271B  ASP*     2.6    39.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  VAL*     4.7     0.9    -      -       +      -
    205B  TYR*     1.3    77.3    -      -       -      +
    207B  ALA*     1.3    60.0    +      -       -      +
    208B  VAL*     3.6    22.6    +      -       +      -
    234B  VAL*     3.3     7.9    -      -       +      +
    248B  ALA*     4.1     9.2    -      -       +      +
    249B  PRO*     3.9    22.2    -      -       +      -
    252B  ALA*     3.7    23.1    -      -       +      -
    268B  ILE*     3.9    11.7    -      -       +      -
    269B  VAL      2.7    21.0    +      -       -      +
    270B  TYR*     3.7    20.9    -      -       +      -
    271B  ASP*     2.9    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  TYR*     3.9    10.9    +      -       +      -
    206B  VAL*     1.3    70.0    -      -       -      +
    208B  VAL*     1.3    62.1    +      -       -      +
    209B  GLY      3.9     0.4    -      -       -      -
    210B  GLN*     3.7    13.0    -      -       +      +
    215B  VAL*     3.6    34.1    -      -       +      -
    233B  ILE*     5.3     0.2    -      -       +      -
    234B  VAL      2.6    14.8    +      -       -      +
    235B  ALA*     3.5     8.4    -      -       +      +
    236B  ALA      3.1    29.6    +      -       -      +
    237B  THR*     4.7     0.8    -      -       +      -
    248B  ALA*     5.3     0.2    -      -       -      +
    271B  ASP      3.6     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  VAL*     3.7    19.3    -      -       +      +
    207B  ALA*     1.3    71.4    -      -       -      +
    209B  GLY*     1.3    65.0    +      -       -      +
    210B  GLN*     3.3     1.9    +      -       -      +
    236B  ALA      3.5     2.0    -      -       -      -
    245B  GLN*     3.4    36.8    -      -       +      +
    248B  ALA*     4.3     4.0    -      -       +      -
    249B  PRO*     3.6    30.3    -      -       +      -
    270B  TYR*     5.9     0.9    -      -       +      -
    271B  ASP      2.9    17.6    +      -       -      +
    272B  ASP      3.8    14.4    +      -       -      +
    273B  LEU*     6.0     0.2    -      -       +      -
    275B  LYS*     3.5    17.9    -      -       -      +
    276B  GLN*     3.8    22.7    -      -       -      +
----------------------------------------------------------
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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