Contacts of the strand formed by residues 455 - 461 (chain D) in PDB entry 1RQQ


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 455 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1162A  PTR      3.3    38.5    +      -       +      +
   1164A  ARG*     5.1     2.0    -      -       -      +
    424D  LEU*     3.7     2.7    -      -       -      -
    451D  ASN*     3.5     1.2    -      -       -      -
    452D  PHE*     2.7    46.6    +      -       +      +
    453D  GLN*     4.2    18.6    -      -       +      +
    454D  GLY*     1.3    80.5    -      -       -      +
    456D  ALA*     1.3    61.9    +      -       -      +
    457D  LYS*     3.8    16.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 456 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1159A  GLU      4.1     4.7    -      -       -      +
   1160A  THR*     4.6     7.6    -      -       -      +
    420D  ALA*     3.8    26.2    -      -       +      -
    423D  VAL*     4.4     2.9    -      -       +      -
    424D  LEU*     3.6    29.4    -      -       +      +
    449D  THR*     5.1     0.4    -      -       +      -
    450D  PHE      3.4     6.5    -      -       -      +
    455D  LYS*     1.3    73.0    -      -       -      +
    457D  LYS*     1.3    69.4    +      -       -      +
    458D  HIS*     4.6    10.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 457 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1159A  GLU      3.4     3.6    -      -       -      -
   1160A  THR*     3.8    23.3    -      -       +      +
   1162A  PTR      3.3    36.8    +      -       -      -
    471C  VAL*     3.9     8.5    -      -       +      -
    474C  LEU*     4.2    18.9    -      -       +      +
    448D  LEU      3.6     0.7    -      -       -      +
    449D  THR*     3.2     5.4    -      -       -      +
    450D  PHE*     2.8    73.9    +      -       +      +
    452D  PHE*     4.1    15.5    -      -       +      -
    455D  LYS*     4.0    30.4    -      -       -      +
    456D  ALA*     1.3    79.3    +      -       -      +
    458D  HIS*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 458 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1158A  PTR      3.7    15.9    -      -       +      +
   1159A  GLU*     3.0    42.3    +      -       -      +
   1160A  THR*     5.4     1.1    -      -       -      -
   1161A  ASP*     5.1     2.2    -      -       -      -
    471C  VAL*     5.0     0.7    -      -       -      -
    416D  ARG*     3.5    52.4    +      -       -      +
    420D  ALA*     4.3    12.2    -      -       +      +
    437D  ARG*     3.1    13.5    +      -       -      -
    447D  VAL*     4.0    10.3    -      -       +      -
    448D  LEU      3.5     3.1    -      -       -      -
    449D  THR*     2.9    38.7    +      -       +      +
    456D  ALA*     4.6     9.0    +      -       +      +
    457D  LYS*     1.3    77.3    -      -       -      +
    459D  LEU*     1.3    63.6    +      -       -      +
    460D  ARG      4.1     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 459 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1159A  GLU*     3.7    18.6    -      -       -      +
    468C  GLN      6.0     0.9    -      -       -      +
    471C  VAL*     3.6    26.9    -      -       +      +
    472C  GLN*     3.7    40.8    -      -       +      +
    475C  TRP*     4.0    20.2    -      -       +      -
    447D  VAL*     3.3     5.0    -      -       -      +
    448D  LEU*     2.7    59.2    +      -       +      +
    450D  PHE*     4.3     4.7    -      -       +      -
    457D  LYS      4.2     0.2    -      -       -      -
    458D  HIS*     1.3    72.5    -      -       -      +
    460D  ARG*     1.3    68.8    +      -       -      +
    461D  LEU*     3.5     8.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 460 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1156A  ASP*     2.7    30.9    +      -       -      -
   1158A  PTR      3.6    54.7    -      -       +      +
   1159A  GLU*     3.6    26.3    +      -       -      +
    439D  SER*     6.1     0.2    -      -       -      -
    441D  THR*     5.7     0.9    -      -       -      -
    442D  ARG*     5.8     5.4    -      -       -      -
    445D  GLU*     4.4    15.9    -      -       -      +
    446D  CYS      3.9     5.6    -      -       -      +
    447D  VAL*     4.5     5.4    -      -       +      +
    458D  HIS      4.1     0.6    +      -       -      +
    459D  LEU*     1.3    78.0    -      -       -      +
    461D  LEU*     1.3    63.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 461 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    436D  ILE*     3.8    31.6    -      -       +      -
    445D  GLU*     3.5    18.0    -      -       -      +
    446D  CYS*     2.9    33.8    +      -       +      +
    447D  VAL      4.1     4.0    -      -       -      -
    448D  LEU*     3.9    22.9    -      -       +      +
    459D  LEU*     3.7    15.7    -      -       +      +
    460D  ARG*     1.3    77.3    -      -       -      +
    462D  SER*     1.3    66.8    +      -       -      +
    463D  LEU*     3.5    12.1    +      -       +      -
    472D  GLN*     4.7     7.4    -      -       -      +
    476D  PHE*     4.3    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