Contacts of the strand formed by residues 712 - 719 (chain A) in PDB entry 3RLN


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 GLY 712 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675A  ILE*     3.6     9.7    -      -       -      +
    676A  ASN*     5.2     0.7    -      -       -      -
    708A  GLN*     3.4     2.5    -      -       -      +
    709A  ASP*     3.0    35.2    +      -       -      +
    710A  ALA      3.4     1.0    +      -       -      -
    711A  THR*     1.3    79.9    -      -       -      +
    713A  LYS*     1.3    61.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 713 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675A  ILE*     3.5     8.3    -      -       -      +
    679A  CYS*     4.4     8.5    -      -       -      +
    694A  HIS*     5.2    10.2    +      -       +      +
    695A  LYS*     5.9     1.8    -      -       -      +
    706A  GLU*     3.5    38.2    +      -       +      +
    707A  ILE      3.1    16.6    -      -       -      +
    708A  GLN*     4.2     7.9    -      -       +      -
    712A  GLY*     1.3    74.5    -      -       -      +
    714A  MET*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 714 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675A  ILE*     3.5    22.7    -      -       +      +
    678A  LEU*     3.7    38.1    -      -       +      -
    679A  CYS*     4.1     8.1    -      -       +      -
    706A  GLU*     3.3     8.5    -      -       -      +
    707A  ILE*     2.9    46.8    +      -       +      -
    713A  LYS*     1.3    75.3    -      -       -      +
    715A  GLU*     1.3    67.5    +      -       -      +
    740A  LEU*     4.4     2.5    -      -       +      -
    748A  GLY      3.4    27.4    -      -       -      +
    749A  GLU*     3.8     2.7    -      -       -      -
    750A  LEU*     3.7    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 715 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    697A  ASN*     5.9     0.9    -      -       -      +
    699A  ARG*     4.4     7.6    +      -       -      -
    704A  TYR*     3.5    41.6    -      -       +      +
    705A  TYR      3.2     9.4    -      -       -      +
    706A  GLU*     4.3    18.4    +      -       +      +
    714A  MET*     1.3    85.3    -      -       -      +
    716A  VAL*     1.3    63.6    +      -       -      +
    717A  VAL*     4.1     0.7    -      -       +      -
    743A  LYS*     5.4     3.6    +      -       -      -
    748A  GLY      4.7     2.4    +      -       -      -
    749A  GLU*     3.3    20.6    -      -       +      +
    750A  LEU      3.0    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 716 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703A  THR      3.5     4.2    -      -       -      +
    704A  TYR*     3.5     2.0    -      -       -      -
    705A  TYR*     2.8    43.0    +      -       +      +
    707A  ILE*     3.7    37.7    -      -       +      -
    715A  GLU*     1.3    77.0    -      -       -      +
    717A  VAL*     1.3    61.5    +      -       -      +
    718A  VAL*     4.0     9.6    +      -       +      -
    733A  LEU*     4.6    11.2    -      -       +      -
    735A  LEU*     4.3    13.2    -      -       +      -
    738A  PHE*     3.7    31.9    -      -       +      -
    750A  LEU*     3.2    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 717 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    702A  PHE*     3.9    23.8    -      -       +      -
    703A  THR      3.6     2.9    -      -       -      +
    704A  TYR*     3.4    45.1    -      -       +      +
    715A  GLU*     4.8     0.9    -      -       +      -
    716A  VAL*     1.3    75.1    -      -       -      +
    718A  VAL*     1.3    65.3    +      -       -      +
    719A  HIS*     5.1     0.7    +      -       -      -
    738A  PHE*     4.4     0.5    -      -       -      -
    749A  GLU*     3.2    36.6    -      -       +      +
    750A  LEU      2.7    13.9    +      -       -      +
    751A  ARG*     3.4     7.4    -      -       +      +
    752A  SER*     2.9    28.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 718 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    701A  GLU      3.9     0.2    -      -       -      +
    702A  PHE*     3.2     9.8    -      -       -      +
    703A  THR*     2.9    39.0    +      -       -      +
    705A  TYR*     4.2    18.6    -      -       +      -
    716A  VAL*     4.4     5.4    -      -       +      -
    717A  VAL*     1.3    77.9    -      -       -      +
    719A  HIS*     1.3    65.1    +      -       -      +
    722A  LEU*     3.2    44.9    -      -       +      +
    723A  THR*     3.6     7.5    -      -       +      +
    738A  PHE*     4.1    14.1    -      -       +      -
    752A  SER*     3.5     3.4    -      -       -      +
    758A  ILE*     4.1    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 719 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    701A  GLU*     3.6     6.3    -      -       +      +
    702A  PHE*     3.7    29.8    -      +       +      -
    717A  VAL      5.1     0.4    +      -       -      -
    718A  VAL*     1.3    77.4    -      -       -      +
    720A  GLY*     1.3    73.3    +      -       -      +
    721A  ARG*     3.7     1.6    +      -       -      +
    722A  LEU*     3.8     8.7    +      -       -      +
    723A  THR*     3.6     8.7    -      -       -      -
    752A  SER*     3.0    50.2    +      -       -      -
    753A  VAL*     4.8     6.9    -      -       -      -
----------------------------------------------------------
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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