Contacts of the strand formed by residues 743 - 749 (chain B) in PDB entry 1RL3


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 743 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673B  GLN*     3.2     2.9    -      -       -      +
    674B  PHE*     2.6    45.7    +      -       +      +
    680B  ILE*     4.3    11.0    -      -       +      -
    693B  ILE*     3.4    36.3    -      -       +      -
    695B  GLU      3.5     8.5    -      -       -      +
    696B  GLY      3.6    15.5    -      -       -      +
    697B  SER      4.0     4.5    -      -       -      +
    698B  ALA*     3.4    28.9    -      -       +      -
    722B  PHE*     5.5     3.4    -      -       +      -
    739B  ALA*     3.5    25.6    -      -       +      -
    741B  GLY      3.2     1.9    +      -       -      +
    742B  PRO*     1.3    73.2    -      -       -      +
    744B  LYS*     1.3    61.5    +      -       -      +
    745B  CYS*     3.7    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 744 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    672B  VAL      3.8     3.4    -      -       -      -
    673B  GLN*     2.9    38.6    +      -       +      +
    693B  ILE*     3.7     2.6    -      -       -      +
    694B  LEU*     2.9    34.6    +      -       +      -
    695B  GLU*     3.0    50.1    +      -       +      +
    742B  PRO*     5.6     3.6    -      -       +      -
    743B  LEU*     1.3    75.2    -      -       -      +
    745B  CYS*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 745 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    671B  PRO*     3.5     1.4    -      -       -      +
    672B  VAL*     2.7    51.7    +      -       +      +
    674B  PHE*     4.1    17.3    -      -       +      -
    691B  PHE*     4.7    12.1    -      -       +      -
    692B  ILE      3.2    16.6    -      -       -      +
    693B  ILE*     4.4     8.3    -      -       -      -
    694B  LEU*     3.5     9.8    -      -       -      +
    722B  PHE*     5.1     5.4    -      -       -      -
    743B  LEU*     3.7    27.1    -      -       -      -
    744B  LYS*     1.3    81.1    -      -       -      +
    746B  VAL*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 746 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644B  TYR*     3.2    35.4    -      -       +      +
    647B  PHE*     4.8     2.2    -      -       +      -
    669B  LEU*     3.7    32.1    -      -       +      +
    670B  GLU      3.1     6.7    -      -       -      +
    671B  PRO*     4.1     9.6    -      -       +      -
    690B  PHE      4.0     1.4    -      -       -      +
    691B  PHE      4.1     0.2    -      -       -      -
    692B  ILE*     3.1    42.4    +      -       +      +
    694B  LEU*     3.5    22.2    -      -       +      -
    745B  CYS*     1.3    80.6    -      -       -      +
    747B  LYS*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 747 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    670B  GLU*     2.9    64.6    +      -       -      +
    672B  VAL*     3.8    25.1    -      -       +      +
    674B  PHE*     6.3     0.2    -      -       +      -
    689B  GLU*     2.8    40.5    +      -       +      +
    690B  PHE      3.2    11.7    -      -       -      +
    691B  PHE*     4.1    22.4    -      -       +      +
    746B  VAL*     1.3    73.3    -      -       -      +
    748B  LEU*     1.3    81.9    +      -       -      +
    752B  ARG*     3.4     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 748 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    665B  VAL*     4.9     2.2    -      -       +      +
    668B  ALA*     3.9    15.5    -      -       +      +
    669B  LEU*     3.6    23.6    -      -       +      -
    689B  GLU*     3.1    11.4    -      -       -      +
    690B  PHE*     2.9    41.5    +      -       +      +
    692B  ILE*     6.2     0.9    -      -       +      -
    747B  LYS*     1.3    98.6    -      -       -      +
    749B  ASP*     1.3    60.7    +      -       -      +
    752B  ARG*     3.8    10.8    -      -       +      +
    753B  PHE*     3.8    18.8    -      -       +      +
    756B  VAL*     3.5    23.3    -      -       +      -
    757B  LEU*     3.4    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 749 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532B  LYS*     5.6     1.2    -      -       -      +
    688B  ASP*     3.8     9.9    -      -       -      +
    689B  GLU*     4.5     7.9    -      -       +      +
    727B  LEU*     4.8     0.9    -      -       -      -
    748B  LEU*     1.3    75.6    -      -       -      +
    750B  ARG*     1.3    67.0    +      -       -      +
    751B  PRO*     3.2    20.0    -      -       +      +
    752B  ARG*     3.0    50.6    +      -       -      +
    753B  PHE*     2.8    19.8    +      -       -      +
----------------------------------------------------------
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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