Contacts of the strand formed by residues 504 - 510 (chain B) in PDB entry 1DY7


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 504 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459B  THR*     3.4    31.4    -      -       +      +
    460B  LEU*     3.7    22.9    -      -       -      +
    461B  ASN      5.8     0.7    -      -       -      -
    467B  SER*     4.0    10.8    -      -       -      +
    502B  GLN*     3.9    11.9    +      -       +      +
    503B  PRO*     1.3    78.9    -      -       -      +
    505B  VAL*     1.3    65.6    +      -       -      +
    506B  VAL*     3.6     1.7    +      -       -      +
    521B  VAL*     4.7     0.2    -      -       -      -
    522B  TRP*     2.9    88.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 505 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457B  ASP*     4.2     5.1    -      -       +      +
    459B  THR*     2.7    32.4    +      -       -      -
    467B  SER      2.9    15.5    +      -       -      +
    468B  GLY*     3.5    31.0    -      -       -      +
    469B  SER      4.5     2.2    -      -       -      +
    470B  VAL*     3.8    28.9    -      -       +      -
    492B  ILE*     3.8    17.5    -      -       +      -
    493B  ALA*     3.9    10.1    -      -       +      +
    504B  ARG*     1.3    72.1    -      -       -      +
    506B  VAL*     1.3    56.3    +      -       -      +
    519B  PHE*     4.0    18.6    -      -       +      -
    520B  SER      3.1    11.4    -      -       -      +
    521B  VAL*     4.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 506 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443B  LEU*     4.2     5.6    -      -       +      -
    444B  PHE*     3.6    26.0    -      -       +      -
    457B  ASP*     3.7     1.6    -      -       -      -
    459B  THR*     3.5    24.7    -      -       +      +
    504B  ARG      4.3     2.2    -      -       -      +
    505B  VAL*     1.3    77.3    -      -       -      +
    507B  GLN*     1.3    72.7    +      -       +      +
    519B  PHE*     4.6     4.0    -      -       -      -
    520B  SER*     2.9    35.9    +      -       -      +
    522B  TRP*     4.1    22.0    -      -       +      -
    554B  THR*     4.5    13.9    -      -       -      +
    556B  LYS*     3.1    13.2    +      -       -      -
    602B  DHE      4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 507 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391B  ARG*     4.6     2.2    -      -       -      +
    444B  PHE*     3.5    34.8    -      -       +      -
    446B  LYS*     6.1     0.4    -      -       +      -
    457B  ASP*     2.8    19.4    +      -       -      +
    506B  VAL*     1.3    75.6    -      -       +      +
    508B  GLY*     1.3    72.0    +      -       -      +
    509B  GLU*     4.6     1.6    -      -       -      +
    518B  TRP      3.3     1.6    -      -       -      +
    519B  PHE*     3.9     3.1    -      -       -      -
    554B  THR      5.1     1.1    -      -       -      +
    555B  GLY*     3.4     6.5    -      -       -      -
    556B  LYS*     2.6    88.1    +      -       -      +
    557B  PHE*     3.6    10.7    -      -       -      -
    602B  DHE      3.2    28.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 508 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  PHE*     4.7     6.3    +      -       -      +
    446B  LYS*     3.4    35.1    -      -       -      +
    457B  ASP*     4.8     0.6    +      -       -      +
    507B  GLN*     1.3    83.0    +      -       -      +
    509B  GLU*     1.3    60.1    +      -       -      +
    517B  VAL*     4.0     4.3    -      -       -      -
    518B  TRP      3.2     8.7    -      -       -      -
    519B  PHE*     3.4    25.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 509 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  PHE*     3.7    14.5    -      -       +      -
    391B  ARG*     4.0     9.2    +      -       -      -
    446B  LYS*     3.4    26.6    +      -       -      +
    507B  GLN*     4.6     1.9    +      -       -      +
    508B  GLY*     1.3    74.9    -      -       -      +
    510B  PHE*     1.3    64.6    +      -       -      +
    517B  VAL*     3.7     4.3    -      -       -      +
    518B  TRP*     2.8    33.1    +      -       -      +
    556B  LYS*     3.4    38.9    -      -       +      +
    557B  PHE*     3.5     3.0    -      -       -      -
    558B  ASN*     2.7    37.1    +      -       -      +
    561B  ASN*     4.1     9.1    -      -       -      +
    562B  THR*     3.8     8.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 510 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  PHE*     3.5     3.7    -      -       -      -
    446B  LYS*     3.9    21.0    -      -       +      +
    447B  THR*     3.4    37.7    -      -       -      -
    448B  HIS*     3.7    26.0    -      +       +      -
    451B  SER*     3.9    11.2    -      -       -      -
    455B  TYR*     3.7    24.0    -      +       -      -
    509B  GLU*     1.3    78.7    +      -       -      +
    511B  ASN*     1.4    66.5    +      -       -      +
    514B  GLY*     3.8    11.9    -      -       -      -
    516B  GLU      3.3    18.8    -      -       -      -
    517B  VAL*     4.0    17.5    -      -       +      -
    536B  ASP*     3.7    20.6    -      -       +      -
    558B  ASN*     3.2    17.5    -      -       -      +
    561B  ASN*     3.0    22.4    +      -       -      +
----------------------------------------------------------
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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