Contacts of the strand formed by residues 499 - 503 (chain A) in PDB entry 1P0P


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 LYS 499 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  PHE*     4.6     1.0    +      -       -      +
    491A  PRO*     3.8    35.9    -      -       +      +
    492A  VAL      4.4     7.2    -      -       -      +
    493A  PHE*     3.3    30.6    +      -       -      +
    494A  LYS      4.8     0.6    -      -       -      +
    497A  GLU*     4.0    38.1    +      -       +      +
    498A  GLN*     1.3    76.5    -      -       -      +
    500A  TYR*     1.3    58.8    +      -       -      +
    510A  ILE*     4.2    11.0    -      -       +      -
    511A  MET      3.2     9.4    -      -       -      +
    512A  THR*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 500 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403A  LEU*     6.0     0.4    -      -       +      -
    418A  PHE*     3.3    33.7    -      +       +      +
    420A  TYR*     3.7    34.4    -      +       +      -
    490A  TRP*     4.9     2.5    -      -       -      +
    491A  PRO*     5.2     1.8    -      -       -      -
    493A  PHE*     5.0     2.9    -      +       +      -
    498A  GLN      3.9     9.4    -      -       -      +
    499A  LYS*     1.3    74.3    -      -       -      +
    501A  LEU*     1.3    64.6    +      -       -      +
    502A  THR*     3.8    10.1    -      -       +      -
    510A  ILE*     3.6     8.2    -      -       -      +
    511A  MET*     2.9    75.4    +      -       +      +
    512A  THR      3.5     4.9    +      -       -      -
    514A  LEU*     3.5    50.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 501 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  PHE      2.8     8.9    +      -       -      -
    419A  TYR*     3.1     6.5    -      -       +      +
    420A  TYR      2.8    25.0    +      -       -      -
    470A  ARG*     4.0    22.7    -      -       -      +
    488A  THR*     4.1     4.9    -      -       +      -
    489A  SER      5.0     0.2    -      -       -      +
    490A  TRP*     3.5    54.0    -      -       +      +
    500A  TYR*     1.3    74.7    -      -       -      +
    502A  THR*     1.3    70.0    +      -       -      +
    503A  LEU*     4.1    11.4    -      -       +      -
    508A  THR*     3.7    22.2    -      -       -      +
    509A  ARG      3.2    16.2    -      -       -      +
    510A  ILE*     3.6    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 502 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  TYR*     3.4     8.1    -      -       +      -
    422A  GLU*     3.8    28.6    +      -       -      +
    500A  TYR*     3.8    15.9    -      -       +      +
    501A  LEU*     1.3    77.5    -      -       -      +
    503A  LEU*     1.3    61.6    +      -       -      +
    504A  ASN*     3.5     9.2    +      -       -      -
    508A  THR*     3.5    23.7    -      -       -      -
    509A  ARG*     2.9    32.0    +      -       +      +
    511A  MET*     3.7    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 503 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419A  TYR*     3.8    38.6    -      -       +      -
    420A  TYR      3.0     9.1    +      -       -      +
    421A  PHE*     4.0    18.2    -      -       +      -
    422A  GLU*     3.0    24.6    +      -       -      +
    423A  HIS*     3.9     2.9    +      -       -      +
    463A  LEU*     4.6    11.7    -      -       +      -
    466A  SER*     6.0     1.1    -      -       -      +
    467A  ILE*     4.3    22.2    -      -       +      -
    470A  ARG*     4.7    13.2    -      -       -      +
    471A  TRP*     4.2    17.7    -      -       +      -
    490A  TRP*     5.1     0.7    -      -       +      -
    501A  LEU*     4.1    21.1    -      -       +      +
    502A  THR*     1.3    77.4    -      -       -      +
    504A  ASN*     1.3    63.0    +      -       -      +
    508A  THR*     5.3     5.8    -      -       +      -
----------------------------------------------------------
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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