Contacts of the strand formed by residues 670 - 684 (chain B) in PDB entry 2C11


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 ALA 670 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538B  TRP*     3.3    29.2    +      -       +      +
    568B  LEU*     5.2     2.5    -      -       +      -
    569B  LEU      4.6     1.6    -      -       -      +
    570B  GLU*     4.4    22.2    -      -       +      +
    668B  THR*     3.2    22.6    +      -       -      +
    669B  ILE*     1.3    78.1    -      -       -      +
    671B  GLY*     1.3    60.5    +      -       -      +
    672B  LYS*     3.5     4.9    -      -       -      +
      5H  FUC      5.3     3.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 671 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  GLU*     3.0    24.5    -      -       -      +
    537B  ASN      3.1    13.5    +      -       -      -
    538B  TRP*     3.2    34.7    -      -       -      -
    670B  ALA*     1.3    72.8    -      -       -      +
    672B  LYS*     1.3    67.1    +      -       -      +
      5H  FUC      5.7     2.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 672 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  LEU      3.2     2.6    -      -       -      +
    536B  GLU*     4.0     3.1    -      -       -      -
    537B  ASN      2.9    24.5    +      -       -      -
    636B  GLN*     4.2    21.0    +      -       +      +
    668B  THR*     3.2    48.5    -      -       +      +
    670B  ALA      4.3     4.0    -      -       -      +
    671B  GLY*     1.3    84.4    -      -       -      +
    673B  ASP*     1.3    62.9    +      -       -      +
    674B  LEU*     3.2    22.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 673 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  LYS*     2.9    21.5    +      -       -      +
    535B  LEU*     2.8    43.7    -      -       +      +
    536B  GLU*     5.3     0.8    -      -       -      +
    636B  GLN*     3.5     6.8    -      -       -      +
    637B  ARG*     2.9    40.6    +      -       +      +
    672B  LYS*     1.3    71.4    -      -       -      +
    674B  LEU*     1.3    60.0    +      -       -      +
   1741B   CA      2.3    27.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 674 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    529B  ASP*     3.2     5.2    -      -       -      +
    530B  LEU      3.4     5.1    +      -       -      +
    535B  LEU      4.2     1.2    +      -       -      -
    537B  ASN*     3.0    34.6    +      -       +      +
    538B  TRP      4.1     0.9    -      -       -      +
    539B  VAL*     3.8    28.3    -      -       +      -
    589B  LEU*     4.4    11.9    -      -       +      -
    634B  VAL*     3.9     8.5    -      -       +      -
    635B  THR      3.3    12.3    -      -       -      +
    636B  GLN*     4.6     0.9    -      -       -      -
    637B  ARG*     4.0     0.2    -      -       -      -
    669B  ILE*     3.6    35.2    -      -       +      +
    672B  LYS*     3.2    25.9    +      -       +      +
    673B  ASP*     1.3    76.5    +      -       -      +
    675B  VAL*     1.3    62.3    +      -       -      +
   1741B   CA      2.3    31.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 675 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    527B  LYS*     3.7    31.0    -      -       +      -
    528B  VAL      3.7    12.6    -      -       -      +
    529B  ASP*     4.1     4.5    -      -       -      +
    589B  LEU*     5.2     0.9    -      -       -      -
    634B  VAL*     3.4     4.9    -      -       -      -
    635B  THR*     3.0    45.0    +      -       -      +
    637B  ARG*     3.4    28.7    -      -       +      -
    674B  LEU*     1.3    75.9    -      -       -      +
    676B  ALA*     1.3    71.8    +      -       -      +
    677B  TRP*     3.6    19.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 676 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526B  PHE      3.7     0.5    -      -       -      +
    527B  LYS      3.8     0.2    -      -       -      -
    528B  VAL*     2.8    47.1    +      -       +      +
    530B  LEU*     5.7     0.4    -      -       +      -
    589B  LEU*     4.6     9.2    -      -       +      +
    605B  ILE*     3.7    30.3    -      -       +      -
    632B  LEU*     4.0     9.6    -      -       +      -
    633B  ALA      3.5     3.8    -      -       -      -
    634B  VAL*     4.3     9.0    -      -       +      +
    675B  VAL*     1.3    78.5    -      -       -      +
    677B  TRP*     1.3    60.8    +      -       -      +
    678B  VAL*     4.9     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 677 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366B  GLN*     3.9     7.2    -      -       +      -
    525B  HIS*     3.2    33.7    +      +       -      +
    526B  PHE      3.4     6.1    -      -       -      -
    527B  LYS*     3.6    46.7    -      -       +      -
    630B  TYR*     5.8     0.2    -      -       -      +
    631B  GLN      3.9     0.2    -      -       -      +
    632B  LEU*     3.2    25.7    -      -       -      +
    633B  ALA      2.7    27.5    +      -       -      +
    635B  THR*     3.1    30.9    +      -       +      +
    637B  ARG*     6.1     0.2    -      -       -      -
    641B  GLU*     4.1    17.0    -      -       +      -
    643B  SER      4.5     1.3    -      -       -      -
    644B  SER*     3.8    19.1    -      -       -      -
    660B  PHE*     3.4    25.2    -      +       +      -
    663B  PHE*     3.9    22.6    -      +       -      -
    675B  VAL*     3.6    28.8    -      -       +      +
    676B  ALA*     1.3    74.5    -      -       -      +
    678B  VAL*     1.3    62.4    +      -       -      +
    679B  THR*     4.5     0.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 678 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525B  HIS*     3.2     4.1    -      -       -      -
    526B  PHE*     2.7    41.9    +      -       +      +
    528B  VAL*     3.9    20.2    -      -       +      -
    605B  ILE*     4.5    14.1    -      -       +      -
    607B  MET*     3.9    19.7    -      -       +      -
    631B  GLN      3.7     8.7    -      -       -      +
    632B  LEU*     4.3    12.3    -      -       +      -
    676B  ALA*     4.9     1.6    -      -       +      -
    677B  TRP*     1.3    75.7    -      -       -      +
    679B  THR*     1.3    74.0    +      -       -      +
    680B  ALA*     4.7     1.1    -      -       +      +
    702B  GLY      4.9     1.8    -      -       -      +
    703B  PHE*     3.6    37.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 679 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523B  SER*     4.6     4.9    -      -       -      -
    524B  ALA      3.3     5.4    -      -       -      +
    525B  HIS*     3.4    17.3    +      -       -      -
    579B  VAL*     5.6     1.1    -      -       +      -
    607B  MET*     5.2     1.7    -      -       -      +
    609B  SER*     4.0    11.1    +      -       -      -
    611B  ALA*     5.3     5.5    -      -       +      +
    627B  TRP*     3.4    41.5    +      -       +      +
    628B  GLU*     4.1     8.3    -      -       +      +
    630B  TYR*     3.0    31.3    +      -       -      +
    631B  GLN*     3.1    17.8    +      -       -      +
    677B  TRP      4.5     1.0    +      -       -      -
    678B  VAL*     1.3    78.3    -      -       -      +
    680B  ALA*     1.3    63.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 680 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489B  PHE*     4.3     4.1    -      -       +      -
    523B  SER*     3.3     3.3    -      -       -      -
    524B  ALA      3.0    29.5    +      -       -      +
    526B  PHE*     4.6    13.7    -      -       +      -
    609B  SER*     3.8     9.0    -      -       -      -
    611B  ALA*     4.9     0.9    -      -       -      -
    678B  VAL*     4.1     4.6    -      -       +      -
    679B  THR*     1.3    76.7    -      -       -      +
    681B  GLY*     1.3    58.7    +      -       -      +
    701B  VAL*     4.1    10.5    -      -       +      -
    702B  GLY*     4.0    36.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 681 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489B  PHE*     5.0     1.3    -      -       -      -
    522B  HIS      3.2    14.8    -      -       -      -
    523B  SER*     4.1     2.0    -      -       -      -
    609B  SER*     3.3     6.4    +      -       -      -
    610B  PHE      2.9    10.2    +      -       -      -
    611B  ALA*     2.7    30.7    +      -       -      +
    680B  ALA*     1.3    77.8    -      -       -      +
    682B  PHE*     1.3    68.4    +      -       -      +
    701B  VAL*     4.0     8.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 682 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  TYR*     5.7     1.1    -      -       -      -
    606A  GLN*     6.3     0.2    -      -       -      -
    489B  PHE*     4.6     8.3    -      +       -      -
    491B  ALA*     4.5    11.2    -      -       +      -
    521B  THR*     3.8     1.0    -      -       -      -
    522B  HIS*     3.2    64.2    +      +       +      -
    610B  PHE*     3.5    35.2    -      +       +      -
    611B  ALA*     3.6     2.9    -      -       -      +
    612B  GLY      4.2     5.4    -      -       -      +
    681B  GLY*     1.3    80.2    -      -       -      +
    683B  LEU*     1.3    76.4    +      -       -      +
    684B  HIS*     3.7    11.3    +      +       +      -
    699B  ASN*     4.1    41.3    -      -       +      -
    701B  VAL*     4.0    18.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 683 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543A  ASP*     4.6     1.6    -      -       -      -
    544A  MET*     4.0    39.0    -      -       +      +
    562A  LEU*     5.5     0.2    -      -       +      -
    564A  VAL*     5.9     0.4    -      -       +      -
    585A  ARG*     3.7    33.4    -      -       +      +
    586A  TYR*     3.3    40.7    +      -       +      -
    604A  ARG*     5.3     0.5    +      -       -      -
    519B  VAL*     3.9    26.7    -      -       +      -
    520B  HIS      3.9     6.7    -      -       -      +
    521B  THR*     4.2     8.7    -      -       +      +
    610B  PHE*     4.0     6.1    +      -       -      +
    612B  GLY*     4.2     1.9    -      -       -      +
    682B  PHE*     1.3    85.0    -      -       -      +
    684B  HIS*     1.3    64.3    +      -       -      +
    685B  ILE*     3.8    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 684 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  TYR*     3.8     9.2    -      -       -      -
    491B  ALA*     6.0     0.2    -      -       -      +
    495B  ILE*     3.6    24.5    -      -       +      -
    519B  VAL*     3.7     0.2    -      -       -      -
    520B  HIS*     2.9    45.5    +      +       -      +
    522B  HIS*     3.4    11.7    +      +       +      -
    682B  PHE*     3.7     9.4    +      +       +      -
    683B  LEU*     1.3    75.8    -      -       -      +
    685B  ILE*     1.3    70.7    +      -       -      +
    686B  PRO*     3.2    14.7    -      -       +      +
    690B  ASP*     2.8    24.9    +      -       -      -
    694B  THR*     3.8    18.6    -      -       +      -
   1742B   CU      2.0    31.2    -      -       -      -
   1750B   CU      3.9     8.1    -      -       -      -
----------------------------------------------------------
 Back to top of page


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