Contacts of the strand formed by residues 381 - 388 (chain A) in PDB entry 1RP1


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 381 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  SER*     4.2    19.3    -      -       -      -
    344A  ILE      3.0    13.5    -      -       -      +
    345A  THR*     2.8    28.1    +      -       -      +
    379A  GLY      4.9     1.2    +      -       -      -
    380A  SER*     1.3    74.9    -      -       -      +
    382A  HIS*     1.3    72.7    +      -       -      +
    383A  SER*     4.9     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  SER*     3.5     0.4    -      -       -      -
    344A  ILE*     2.9    35.0    +      -       +      +
    346A  LEU*     3.8    18.3    -      -       +      +
    371A  ILE*     4.0     6.3    -      -       +      +
    372A  PHE*     3.5    69.4    -      +       +      -
    375A  ILE      4.5     4.3    +      -       -      -
    377A  LYS*     5.5     0.9    -      -       +      +
    380A  SER*     3.1    27.4    +      -       -      -
    381A  THR*     1.3    82.0    +      -       -      +
    383A  SER*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASN*     4.5     3.8    +      -       -      -
    342A  VAL      3.1    11.7    -      -       -      -
    343A  SER*     2.9    23.2    +      -       -      -
    371A  ILE*     4.2     7.0    -      -       -      +
    381A  THR*     4.9     2.6    -      -       -      +
    382A  HIS*     1.3    75.3    -      -       -      +
    384A  ASN*     1.3    69.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  GLU      5.7     0.2    -      -       -      +
    294A  ASN*     2.9    25.2    +      -       -      +
    341A  GLY*     3.5     2.1    -      -       -      -
    342A  VAL*     3.0    32.3    +      -       -      +
    370A  ASN      3.5    16.0    +      -       -      -
    371A  ILE*     3.3    37.8    +      -       +      +
    383A  SER*     1.3    79.4    -      -       -      +
    385A  GLU*     1.3    77.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  PHE*     4.2     0.9    -      -       -      +
    294A  ASN*     3.3    41.5    -      -       +      +
    296A  CYS      5.3     0.2    +      -       -      -
    297A  PHE*     3.4    40.2    -      -       +      +
    339A  ARG*     2.6    46.3    +      -       -      +
    340A  TYR      3.1    13.0    -      -       -      +
    341A  GLY*     4.0     9.2    -      -       -      -
    384A  ASN*     1.3    95.0    +      -       -      +
    386A  PHE*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 386 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  TRP      3.8     0.3    -      -       -      +
    339A  ARG*     3.3     4.5    -      -       -      +
    340A  TYR*     3.0    52.9    +      +       +      -
    342A  VAL*     3.8    26.5    -      -       +      -
    357A  VAL*     3.9    17.7    -      -       +      -
    359A  LEU*     3.3    34.3    -      -       +      -
    369A  PHE*     3.4    50.9    -      +       +      -
    370A  ASN      5.5     3.1    -      -       -      +
    371A  ILE*     3.8    17.9    -      -       +      -
    385A  GLU*     1.3    76.4    -      -       -      +
    387A  ASP*     1.3    64.3    +      -       -      +
    388A  ALA*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 387 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  PHE*     5.0     0.7    -      -       -      -
    328A  ASN*     3.0    39.6    +      -       +      +
    337A  ARG*     3.8    33.2    +      -       +      +
    338A  TRP      3.5     4.4    -      -       -      +
    339A  ARG*     3.0    41.4    +      -       -      +
    369A  PHE*     3.2    17.6    -      -       -      -
    386A  PHE*     1.3    72.9    -      -       -      +
    388A  ALA*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 388 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  ARG*     3.1    12.5    -      -       -      -
    338A  TRP      2.8    29.0    +      -       -      -
    340A  TYR*     3.9    20.2    -      -       +      -
    366A  THR*     3.7    31.0    -      -       +      -
    369A  PHE*     3.6    18.4    -      -       +      -
    386A  PHE*     3.9     2.5    +      -       +      -
    387A  ASP*     1.3    74.0    -      -       -      +
    389A  LYS*     1.3    61.6    +      -       -      +
    390A  LEU      3.4     3.8    -      -       -      +
----------------------------------------------------------
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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