Contacts of the strand formed by residues 448 - 455 (chain H) in PDB entry 1P8J


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 ARG 448 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276E  ARG*     3.8     0.4    -      -       -      -
   4049E  SO4      3.2    37.8    +      -       -      -
    445H  ALA*     5.5     2.6    -      -       -      +
    446H  PRO*     3.3    41.1    +      -       -      +
    447H  GLN*     1.3    81.3    -      -       -      +
    449H  LYS*     1.3    62.2    +      -       -      +
    478H  PRO      3.2    27.3    +      -       -      -
    479H  ASN*     3.7    13.2    -      -       -      +
    480H  HIS      3.8    14.6    -      -       -      +
    481H  ILE*     3.6    16.4    -      -       +      -
    571H  TYR*     3.4     5.2    -      -       -      -
    572H  GLY      2.7    38.9    +      -       -      +
    573H  THR*     4.1     7.0    -      -       -      -
    574H  ALA*     4.7    13.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 449 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269E  LEU*     4.3     6.4    +      -       -      +
    272E  GLU*     2.6    45.2    +      -       -      +
    273E  ALA*     5.0     1.0    -      -       -      +
    276E  ARG*     3.6    37.2    -      -       -      +
    275H  PHE*     6.1     1.2    -      -       -      -
    448H  ARG*     1.3    73.2    -      -       -      +
    450H  CYS*     1.3    61.9    +      -       -      +
    451H  ILE*     3.9    25.8    +      -       +      +
    479H  ASN*     3.0    29.1    +      -       -      +
    569H  VAL*     4.0    18.4    -      -       +      -
    570H  LEU      3.4     3.8    -      -       -      -
    571H  TYR*     3.4    34.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 450 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449H  LYS*     1.3    73.0    -      -       -      +
    451H  ILE*     1.3    64.5    +      -       -      +
    452H  VAL*     4.7     6.7    -      -       -      -
    471H  VAL*     5.8     0.2    -      -       -      -
    473H  ALA*     3.5    10.3    -      -       -      -
    474H  CYS*     2.1    58.1    -      -       -      -
    479H  ASN      3.8    12.1    -      -       -      +
    481H  ILE*     4.0     8.9    -      -       +      +
    568H  LEU      3.6     2.4    -      -       -      +
    569H  VAL*     3.4     2.4    -      -       -      -
    570H  LEU*     2.7    53.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 451 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234E  ALA*     4.0    20.2    -      -       +      -
    237E  ALA*     3.8    31.6    -      -       +      +
    238E  ARG*     3.6    38.8    +      -       +      +
    269E  LEU*     4.1    10.1    -      -       +      -
    449H  LYS*     3.9    33.8    +      -       +      +
    450H  CYS*     1.3    78.2    -      -       -      +
    452H  VAL*     1.3    64.5    +      -       -      +
    453H  GLU      5.1     0.2    -      -       -      +
    474H  CYS*     4.3     3.3    -      -       -      -
    567H  THR*     3.8    22.4    -      -       +      -
    568H  LEU      3.8     2.7    -      -       -      -
    569H  VAL*     4.6     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 452 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178E  GLN*     6.1     0.4    -      -       -      -
    450H  CYS*     4.4    11.0    -      -       -      +
    451H  ILE*     1.3    78.7    -      -       -      +
    453H  GLU*     1.3    66.0    +      -       -      +
    454H  ILE*     3.4    22.1    +      -       +      -
    469H  LYS*     5.3     2.5    -      -       +      -
    471H  VAL*     4.4    22.4    -      -       +      -
    567H  THR*     3.6     3.4    -      -       -      -
    568H  LEU*     2.8    67.7    +      -       +      +
    570H  LEU*     4.7     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 453 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175E  VAL*     4.9     1.9    -      -       -      +
    178E  GLN*     3.8    21.2    +      -       -      +
    232E  THR*     3.0    29.1    +      -       -      +
    234E  ALA*     3.5    30.0    -      -       +      +
    235E  VAL*     3.9    16.2    +      -       -      +
    238E  ARG*     4.6     7.8    +      -       -      +
    451H  ILE*     5.3     0.7    -      -       +      -
    452H  VAL*     1.3    75.4    -      -       -      +
    454H  ILE*     1.3    65.1    +      -       -      +
    455H  LEU      3.7     7.3    -      -       -      +
    456H  VAL*     6.1     0.3    -      -       -      +
    469H  LYS*     5.0     3.5    -      -       -      +
    566H  PHE      4.2     3.6    -      -       -      -
    567H  THR*     4.6     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 454 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452H  VAL*     3.5    30.3    -      -       +      +
    453H  GLU*     1.3    73.5    -      -       -      +
    455H  LEU*     1.3    59.4    +      -       +      +
    456H  VAL*     4.0     4.4    +      -       -      +
    467H  VAL*     3.8    15.6    -      -       +      +
    469H  LYS*     3.6    51.5    +      -       +      +
    471H  VAL*     4.4     6.1    -      -       +      -
    547H  TRP*     5.9     1.8    -      -       +      -
    566H  PHE*     2.9    63.0    +      -       +      +
    568H  LEU*     4.1    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 455 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453H  GLU*     3.7     8.6    -      -       -      +
    454H  ILE*     1.3    78.8    -      -       -      +
    456H  VAL*     1.3    65.1    +      -       -      +
    457H  GLU      3.6    19.3    -      -       -      +
    458H  PRO*     4.8     0.2    -      -       +      -
    459H  LYS*     4.3    19.5    -      -       +      +
    467H  VAL*     4.1    30.1    -      -       +      -
    563H  LEU*     3.7    34.1    -      -       +      +
    564H  THR      3.9     5.8    -      -       -      +
    565H  LYS*     3.8    21.3    -      -       -      +
    566H  PHE*     3.9    19.9    +      -       +      +
----------------------------------------------------------
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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