Contacts of the strand formed by residues 412 - 416 (chain B) in PDB entry 2PY5


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 412 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ALA*     4.1    24.2    -      -       +      +
     71B  ILE*     3.9    16.4    -      -       +      -
     72B  ASN*     4.2    11.5    -      -       -      +
    100B  TRP*     4.1     7.6    -      -       +      -
    404B  PRO*     3.7    21.8    -      -       +      -
    405B  TYR      3.5    17.9    -      -       -      +
    406B  LEU*     4.1     7.5    -      -       +      +
    407B  LYS*     4.3     6.0    +      -       -      -
    410B  GLY      4.2     0.2    +      -       -      -
    411B  ALA*     1.3    74.9    -      -       -      +
    413B  GLY*     1.3    65.6    +      -       -      +
    414B  PHE*     3.5    27.8    -      -       +      -
    560B  GLN*     3.5    49.3    +      -       -      +
    561B  VAL      4.6     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 413 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404B  PRO*     3.4     2.3    -      -       -      +
    405B  TYR*     2.9    44.0    +      -       -      +
    407B  LYS*     3.7    22.4    -      -       -      +
    411B  ALA      3.5     2.4    +      -       -      -
    412B  LEU*     1.3    74.1    -      -       -      +
    414B  PHE*     1.3    72.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 414 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419A  GLU*     3.8    13.5    -      -       -      +
     94B  ILE*     3.9    23.6    -      -       +      -
    100B  TRP*     3.6    16.8    -      +       -      -
    402B  LYS*     3.8    49.4    -      -       +      +
    403B  VAL      3.3     4.3    -      -       -      -
    404B  PRO*     3.8    22.0    -      -       +      -
    405B  TYR*     3.5     2.0    -      -       -      -
    407B  LYS*     5.3     0.4    -      -       -      +
    412B  LEU*     3.5    36.1    -      -       +      -
    413B  GLY*     1.3    79.2    -      -       -      -
    415B  ARG*     1.3    63.3    +      -       -      +
    560B  GLN*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 415 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  THR*     4.0     0.6    -      -       -      +
    416A  LEU*     3.3    45.4    +      -       -      +
    417A  GLY      2.8    29.6    +      -       -      -
    419A  GLU*     2.8    54.9    +      -       -      +
    402B  LYS*     3.2     7.7    -      -       -      +
    403B  VAL*     2.7    50.4    +      -       +      +
    405B  TYR*     3.5    43.5    -      -       +      +
    414B  PHE*     1.3    74.8    -      -       -      +
    416B  LEU*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 416 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  LYS*     3.2    31.2    -      -       -      +
    419A  GLU*     5.0     3.0    +      -       -      -
     96B  ARG*     3.9    39.7    -      -       +      +
    400B  THR*     3.9     9.2    -      -       +      -
    401B  GLY      3.7    15.9    -      -       -      +
    402B  LYS*     4.6     2.9    -      -       +      +
    403B  VAL*     4.8     1.3    -      -       -      +
    415B  ARG*     1.3    79.9    -      -       -      +
    417B  GLY*     1.3    71.0    +      -       -      +
----------------------------------------------------------
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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