Contacts of the strand formed by residues 417 - 425 (chain B) in PDB entry 1B0P


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 THR 417 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  THR*     3.9    14.3    +      -       -      +
    414B  PRO*     3.0    34.8    +      -       +      +
    415B  LYS      4.5     0.2    +      -       -      -
    416B  GLY*     1.3    78.9    +      -       -      +
    418B  ILE*     1.3    72.0    +      -       -      +
    419B  GLN*     3.8    16.7    +      -       +      -
    469B  ARG*     4.1    22.9    -      -       +      -
    470B  PHE      3.3    11.9    -      -       -      +
    471B  GLY*     4.3     6.8    -      -       -      +
    473B  LYS      5.1     2.8    +      -       -      -
    475B  ILE*     5.0     6.8    -      -       +      +
    485B  ASP*     3.4    11.4    -      -       -      +
    505B  LYS*     5.6     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 418 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  GLY      5.0     5.2    -      -       -      +
    417B  THR*     1.3    76.9    -      -       -      +
    419B  GLN*     1.3    63.5    +      -       -      +
    420B  CYS*     3.6    23.1    -      -       -      -
    447B  LEU*     6.2     1.6    -      -       +      -
    468B  LEU      3.7     0.7    -      -       -      +
    469B  ARG*     3.1     7.4    -      -       -      +
    470B  PHE*     2.9    41.5    +      -       +      +
    485B  ASP*     3.5    17.0    -      -       +      +
    486B  TYR*     5.3     0.4    -      -       +      -
    571B  ALA*     3.6    23.3    -      -       -      +
    572B  GLY      4.2    14.6    -      -       -      +
    573B  VAL*     3.8    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 419 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411B  ASP*     3.0    38.0    +      -       -      +
    413B  THR*     3.5    11.7    +      -       -      +
    417B  THR*     4.2    11.2    +      -       +      +
    418B  ILE*     1.3    78.1    -      -       -      +
    420B  CYS*     1.3    61.6    +      -       -      +
    468B  LEU      3.5     4.0    -      -       -      -
    469B  ARG*     2.4    42.1    +      -       +      +
    479B  TYR*     5.6     0.9    -      -       -      -
    481B  VAL*     3.7    25.8    -      -       +      +
    482B  ASN*     4.5     2.8    +      -       -      +
    483B  ARG      3.9    14.9    +      -       -      +
    484B  ALA*     3.6     1.9    -      -       -      -
    485B  ASP*     2.8    40.6    +      -       -      +
    486B  TYR      3.3     3.6    +      -       -      -
    505B  LYS*     3.9     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 420 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418B  ILE*     3.6    24.0    -      -       -      -
    419B  GLN*     1.3    76.7    -      -       -      +
    421B  GLN*     1.3    65.3    +      -       -      +
    422B  PHE*     3.7    19.3    -      -       +      -
    466B  SER      3.8     0.3    -      -       -      +
    467B  HIS*     3.6     5.0    -      -       -      -
    468B  LEU*     2.9    37.8    +      -       +      +
    470B  PHE*     4.6     8.5    -      -       -      -
    481B  VAL*     4.2     2.2    -      -       -      +
    486B  TYR*     3.0    26.2    -      -       +      +
    567B  PHE*     4.0    21.8    -      -       -      -
    571B  ALA*     4.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 421 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420B  CYS*     1.3    77.4    -      -       -      +
    422B  PHE*     1.3    61.3    +      -       -      +
    423B  TRP*     4.7     4.6    -      -       -      +
    465B  ILE*     4.0    13.4    -      -       +      +
    466B  SER      3.4     3.4    -      -       -      -
    467B  HIS*     4.2    13.5    +      -       +      -
    481B  VAL*     2.9    43.6    -      -       +      +
    482B  ASN*     4.5     2.3    +      -       -      -
    484B  ALA*     3.3    20.3    -      -       +      +
    486B  TYR*     2.7    10.9    +      -       -      +
    487B  VAL*     3.2    22.4    -      -       +      +
    488B  ALA*     2.7    31.5    +      -       -      +
    500B  ILE      4.8     3.6    +      -       -      -
    502B  GLU      4.3    13.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 422 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420B  CYS*     3.7    19.1    -      -       +      -
    421B  GLN*     1.3    77.0    -      -       -      +
    423B  TRP*     1.3    63.7    +      -       -      +
    424B  GLY      4.0     0.4    +      -       -      -
    430B  THR*     3.9    19.0    -      -       +      +
    434B  ASN*     3.5    33.9    -      -       -      +
    464B  THR      3.8     0.2    -      -       -      +
    465B  ILE*     3.2     6.2    -      -       -      +
    466B  SER*     2.8    37.3    +      -       -      -
    468B  LEU*     3.9    17.3    -      -       +      -
    486B  TYR*     3.6    21.3    -      +       -      -
    488B  ALA*     3.2    21.3    -      -       +      +
    490B  HIS*     3.9    15.5    -      +       +      -
    563B  MET      5.5     1.1    -      -       -      -
    567B  PHE*     3.5    39.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 423 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421B  GLN*     4.7     5.8    -      -       -      +
    422B  PHE*     1.3    78.9    -      -       -      +
    424B  GLY*     1.3    59.5    +      -       -      +
    463B  ILE*     3.6    35.7    -      -       +      -
    464B  THR      3.5     4.7    -      -       -      -
    465B  ILE*     3.7    26.4    -      -       +      +
    487B  VAL*     4.4     8.1    -      -       +      +
    488B  ALA      2.7    18.5    +      -       -      +
    489B  CYS*     4.1     6.5    -      -       -      -
    490B  HIS*     2.8    32.8    +      -       -      +
    494B  TYR*     3.8    20.0    -      +       +      -
    498B  TYR*     3.6    31.4    -      +       +      -
    499B  ASP      4.2     8.3    -      -       -      -
    500B  ILE*     3.9    48.1    +      -       +      -
    649B  GLN*     4.6    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 424 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  PHE      4.0     1.2    -      -       -      -
    423B  TRP*     1.3    75.3    -      -       -      +
    425B  LEU*     1.3    62.0    +      -       -      -
    428B  ASP*     3.7     8.1    -      -       -      -
    430B  THR*     3.7    14.8    -      -       -      +
    464B  THR*     2.8    39.7    +      -       -      +
    490B  HIS*     4.3     2.0    -      -       -      -
    494B  TYR*     2.8    18.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 425 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1216A  ARG*     3.8    25.8    -      -       -      +
    424B  GLY*     1.3    75.5    -      -       -      -
    426B  GLY*     1.3    78.6    +      -       -      +
    427B  ALA      3.3     0.3    +      -       -      -
    428B  ASP*     2.7    43.4    +      -       +      +
    461B  GLY*     3.5    32.8    -      -       -      +
    462B  GLY      3.7     1.1    -      -       -      +
    464B  THR*     5.1     3.5    -      -       -      +
    491B  ASN*     3.9    27.0    -      -       +      +
    494B  TYR*     3.3    12.5    -      -       +      +
    677B  VAL*     5.5     4.0    -      -       +      -
----------------------------------------------------------
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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