Contacts of the strand formed by residues 210 - 221 (chain E) in PDB entry 6CU0


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 GLN 210 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  LEU      3.6     1.4    -      -       -      +
    134E  VAL*     3.5     1.8    -      -       -      -
    135E  VAL*     2.9    38.7    +      -       +      +
    167E  LEU*     3.9    37.7    -      -       +      +
    168E  GLN      3.3    19.0    -      -       -      +
    169E  PRO*     3.4    26.1    +      -       -      +
    205E  HIS      4.9     1.6    +      -       -      -
    206E  LEU*     4.4    11.0    -      -       +      +
    207E  SER*     3.2    51.5    +      -       -      +
    208E  ALA      3.3     2.0    -      -       -      -
    209E  GLY*     1.3    76.4    -      -       -      +
    211E  ARG*     1.3    62.5    +      -       -      +
    212E  LEU*     3.9     1.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127E  LYS*     5.8     1.1    -      -       +      +
    132E  GLU*     3.7    30.6    -      -       +      +
    133E  LEU      3.2     8.5    -      -       -      +
    134E  VAL*     4.5    10.5    -      -       +      +
    166E  HIS      3.9     0.3    -      -       -      +
    168E  GLN*     2.9    45.2    +      -       +      +
    209E  GLY      3.7     3.9    +      -       -      +
    210E  GLN*     1.3    72.7    -      -       -      +
    212E  LEU*     1.3    63.0    +      -       -      +
    213E  GLY      3.9     1.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 212 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132E  GLU*     3.3     4.3    -      -       -      -
    133E  LEU*     2.8    55.2    +      -       +      +
    135E  VAL*     5.6     5.8    -      -       +      -
    165E  LEU*     4.0    20.9    -      -       +      -
    166E  HIS      3.7     4.7    -      -       -      -
    167E  LEU*     4.3    15.3    -      -       +      -
    206E  LEU*     6.1     3.1    -      -       +      -
    210E  GLN*     3.9     3.3    +      -       +      -
    211E  ARG*     1.3    72.0    -      -       -      +
    213E  GLY*     1.3    58.7    +      -       -      +
    214E  VAL*     5.7     0.2    -      -       -      -
    235E  LEU*     5.3     3.4    -      -       +      +
    237E  LEU*     5.8     4.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 213 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109E  TRP*     5.9     0.4    -      -       -      -
    131E  LYS      4.2    13.2    -      -       -      -
    132E  GLU*     4.7     7.1    +      -       -      +
    164E  ALA      3.8     0.3    -      -       -      +
    165E  LEU*     3.5     2.8    -      -       -      -
    166E  HIS*     2.8    40.1    +      -       -      +
    211E  ARG      3.9     1.0    +      -       -      -
    212E  LEU*     1.3    74.7    -      -       -      +
    214E  VAL*     1.3    64.5    +      -       -      -
    215E  HIS      4.3     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 214 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  PRO*     3.4     7.9    -      -       -      +
    107E  LEU*     3.0    29.1    +      -       +      +
    109E  TRP*     3.6    38.6    -      -       +      +
    131E  LYS      4.8     2.0    +      -       -      -
    163E  LEU*     4.2    38.4    -      -       +      -
    164E  ALA      3.4     9.9    -      -       -      +
    165E  LEU*     3.7    20.0    -      -       +      -
    213E  GLY*     1.3    77.3    -      -       -      -
    215E  HIS*     1.3    62.1    +      -       -      +
    235E  LEU*     3.8    16.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 215 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105E  GLY*     5.0     1.8    -      -       -      -
    106E  PRO*     4.1    12.3    -      -       +      -
    162E  SER      3.5     1.2    -      -       -      +
    163E  LEU*     3.5     5.3    -      -       -      -
    164E  ALA*     2.8    39.4    +      -       +      +
    166E  HIS*     4.2    20.4    -      -       +      +
    214E  VAL*     1.3    77.0    -      -       -      +
    216E  LEU*     1.3    61.3    +      -       -      +
    217E  HIS*     4.0     0.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 216 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99E  ASN*     5.8     3.4    -      -       +      -
    101E  LEU      4.5     3.8    -      -       -      +
    102E  LEU*     4.1    13.0    -      -       +      -
    103E  ILE      3.8    29.8    -      -       -      +
    104E  ASP*     3.4     3.5    -      -       -      +
    105E  GLY      3.1    37.0    +      -       -      +
    107E  LEU*     5.0     8.0    -      -       +      +
    161E  VAL*     3.5    29.2    -      -       +      -
    162E  SER      3.3     4.3    -      -       -      +
    163E  LEU*     3.5    25.8    -      -       +      -
    214E  VAL      4.3     0.6    +      -       -      -
    215E  HIS*     1.3    73.4    -      -       -      +
    217E  HIS*     1.3    63.6    +      -       -      +
    218E  THR*     4.8     1.6    -      -       +      -
    228E  LEU*     4.7    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 217 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104E  ASP*     3.4    25.6    +      -       -      +
    161E  VAL*     3.5     2.6    -      -       -      +
    162E  SER*     2.7    54.4    +      -       -      +
    215E  HIS      4.0     1.1    +      -       -      +
    216E  LEU*     1.3    74.7    +      -       -      +
    218E  THR*     1.3    83.0    +      -       -      +
    219E  GLU*     4.5     4.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 218 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102E  LEU*     4.1    22.5    -      -       +      +
    103E  ILE      4.4     1.1    -      -       -      +
    104E  ASP*     2.9    25.0    +      -       -      +
    160E  SER      3.4    11.5    +      -       -      -
    161E  VAL*     4.2    13.7    -      -       -      +
    162E  SER*     5.4     0.2    -      -       -      -
    185E  LEU*     5.8     1.0    -      -       -      +
    216E  LEU*     4.8     4.5    -      -       +      -
    217E  HIS*     1.3    87.7    +      -       -      +
    219E  GLU*     1.3    59.8    +      -       -      +
    220E  ALA*     3.2    16.6    +      -       -      +
    223E  ARG*     3.3    42.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 219 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158E  SER      4.0     0.9    -      -       -      +
    159E  GLY*     3.7     8.2    -      -       -      -
    160E  SER*     3.0    41.7    +      -       -      +
    185E  LEU*     5.8     0.5    -      -       -      +
    217E  HIS*     4.5     6.7    -      -       +      +
    218E  THR*     1.3    68.2    +      -       -      +
    220E  ALA*     1.3    62.9    +      -       -      +
    221E  ARG*     3.5     2.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 220 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158E  SER      4.9     0.2    -      -       -      -
    218E  THR*     3.2     8.3    +      -       -      -
    219E  GLU*     1.3    70.9    -      -       -      +
    221E  ARG*     1.3    60.9    +      -       -      +
    222E  ALA      3.8     1.6    -      -       -      +
    223E  ARG*     3.1    57.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 221 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190C  SER*     5.0    18.4    +      -       -      -
    191C  GLU*     5.4     4.2    -      -       -      +
    157E  GLY*     3.5     0.9    -      -       -      -
    158E  SER*     3.1    55.0    +      -       -      +
    159E  GLY*     5.3     1.3    -      -       -      -
    219E  GLU      3.5     1.2    +      -       -      +
    220E  ALA*     1.3    72.6    -      -       -      +
    222E  ALA*     1.3    68.2    +      -       +      +
    223E  ARG      4.2     0.6    -      -       -      +
----------------------------------------------------------
 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