Contacts of the strand formed by residues 651 - 660 (chain E) in PDB entry 3HR4


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 SER 651 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618E  LYS      3.9     7.7    +      -       -      -
    619E  PHE      3.4     7.4    +      -       -      -
    620E  ARG*     3.1    38.3    +      -       -      +
    621E  TYR*     3.1    26.8    +      -       -      -
    649E  GLY      4.3     0.2    +      -       -      -
    650E  ALA*     1.3    73.0    -      -       -      +
    652E  GLN*     1.3    60.5    +      -       -      +
    653E  LEU      3.1     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 652 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620E  ARG*     4.7     1.2    +      -       -      -
    621E  TYR*     3.3    29.3    +      -       +      +
    622E  ALA*     5.4     0.2    -      -       -      -
    642E  ASP*     3.6    25.1    -      -       -      +
    646E  SER*     6.0     0.7    -      -       -      +
    650E  ALA      3.9     1.0    +      -       -      -
    651E  SER*     1.3    68.8    -      -       -      +
    653E  LEU*     1.3    68.8    +      -       -      +
    654E  THR*     3.0    22.4    -      -       -      +
    655E  PRO*     3.2    29.2    -      -       -      +
    656E  MET      4.1     3.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 653 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585E  LEU*     4.5    12.8    -      -       +      -
    587E  LEU*     6.1     0.2    -      -       +      -
    620E  ARG*     3.7    29.4    -      -       +      +
    621E  TYR      2.6    23.4    +      -       -      +
    622E  ALA*     4.5     4.3    -      -       +      -
    651E  SER      3.1     4.2    +      -       -      -
    652E  GLN*     1.3    73.3    -      -       -      +
    654E  THR*     1.3    61.0    +      -       +      +
    655E  PRO*     4.8     0.2    -      -       -      +
    676E  THR*     3.8    11.7    -      -       -      +
    679E  ALA*     3.4    39.9    -      -       +      +
    680E  ALA*     4.6     5.8    -      -       +      -
    683E  THR*     3.7    32.3    -      -       +      +
    684E  PHE*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 654 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    621E  TYR      4.0     1.0    +      -       -      -
    622E  ALA*     3.3    21.6    -      -       +      -
    623E  VAL      4.6     0.3    +      -       -      -
    642E  ASP*     5.6     0.2    -      -       -      +
    652E  GLN*     3.0    16.8    -      -       -      +
    653E  LEU*     1.3    86.5    -      -       +      +
    655E  PRO*     1.3    86.1    +      -       -      +
    656E  MET*     4.5     0.5    -      -       -      -
    672E  TRP*     3.7    10.8    +      -       -      +
    675E  GLN*     3.7    22.0    +      -       -      +
    676E  THR*     2.9    39.9    -      -       -      +
    679E  ALA*     5.1     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 655 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    652E  GLN*     3.2    19.0    -      -       -      +
    653E  LEU      4.8     0.4    -      -       -      +
    654E  THR*     1.3    98.1    +      -       -      +
    656E  MET*     1.3    66.5    +      -       -      +
    657E  GLY      3.2     3.8    +      -       -      -
    672E  TRP*     3.3    16.1    +      -       -      -
    675E  GLN*     5.0     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 656 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623E  VAL*     3.4    17.9    -      -       +      +
    625E  GLY      4.6     0.2    -      -       -      +
    635E  CYS*     3.8     4.7    -      -       +      +
    638E  ALA*     3.4    48.9    -      -       +      +
    639E  HIS*     3.2    49.5    -      -       +      +
    642E  ASP*     3.4    25.4    -      -       -      +
    652E  GLN*     4.1     6.1    +      -       -      -
    654E  THR      3.6     1.5    +      -       -      -
    655E  PRO*     1.3    74.5    -      -       -      +
    657E  GLY*     1.3    68.1    +      -       -      +
    658E  GLU*     3.4    26.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 657 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623E  VAL      3.0     9.1    +      -       -      -
    624E  PHE*     3.3    13.5    -      -       -      -
    625E  GLY      3.2    20.4    +      -       -      -
    655E  PRO      3.2     4.6    +      -       -      -
    656E  MET*     1.3    73.4    -      -       -      +
    658E  GLU*     1.3    67.9    +      -       -      +
    672E  TRP*     3.7    21.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 658 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    624E  PHE*     3.8     6.4    -      -       -      -
    625E  GLY      3.5     4.3    -      -       -      -
    634E  PHE*     4.3    20.9    -      -       +      +
    635E  CYS*     4.0    18.1    -      -       -      +
    639E  HIS*     2.6    38.0    +      -       -      -
    656E  MET*     3.4    20.4    -      -       +      +
    657E  GLY*     1.3    81.8    -      -       -      +
    659E  GLY*     1.3    59.4    +      -       -      +
    660E  ASP      4.0     1.8    +      -       -      -
    668E  ALA*     3.7    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 659 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    624E  PHE*     3.6    15.5    -      -       -      -
    625E  GLY      2.7    16.1    +      -       -      +
    626E  LEU*     3.5     0.7    -      -       -      -
    627E  GLY      3.0    26.7    +      -       -      -
    634E  PHE*     4.5     3.1    -      -       -      -
    635E  CYS*     4.3     1.4    -      -       -      -
    658E  GLU*     1.3    72.5    -      -       -      +
    660E  ASP*     1.3    59.2    -      -       -      -
    665E  GLN*     3.3    26.9    +      -       -      -
    668E  ALA*     4.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 660 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    627E  GLY      3.7     1.8    -      -       -      -
    628E  SER*     3.6     0.7    -      -       -      -
    629E  SER*     3.2    37.8    +      -       -      -
    634E  PHE*     3.7    20.8    -      -       +      -
    658E  GLU      4.0     2.2    +      -       -      -
    659E  GLY*     1.3    70.3    -      -       -      -
    661E  GLU*     1.3    72.7    +      -       -      +
    662E  LEU*     2.9    17.4    +      -       -      +
    663E  SER*     2.7    56.4    +      -       -      +
    665E  GLN*     3.3     8.3    -      -       -      +
    668E  ALA*     5.3     1.0    -      -       -      +
----------------------------------------------------------
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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