Contacts of the strand formed by residues 236 - 245 (chain E) in PDB entry 6Q2J


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 LYS 236 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301C  GLU*     5.4     5.4    +      -       -      -
    305C  LYS*     5.4    11.9    -      -       -      +
    234E  ARG*     3.5    25.2    +      -       -      +
    235E  GLU*     1.3   103.6    +      -       +      +
    237E  TYR*     1.3    62.2    +      -       -      +
    238E  GLU*     3.5     8.3    +      -       +      +
    260E  VAL      3.6     5.2    -      -       -      +
    261E  THR*     5.0    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 237 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212E  LEU*     3.9    28.3    -      -       +      -
    213E  PRO*     4.3     8.5    -      -       +      +
    214E  PHE*     3.7    32.8    -      +       +      -
    229E  LEU*     3.7    29.6    -      -       +      +
    230E  ASP      4.9     2.6    +      -       -      -
    233E  GLN*     5.6     2.8    +      -       -      +
    234E  ARG*     3.6    58.9    +      -       +      +
    236E  LYS*     1.3    69.9    -      -       -      +
    238E  GLU*     1.3    60.4    +      -       -      +
    239E  LEU*     3.4    10.5    +      -       +      +
    258E  PHE      3.4     1.7    -      -       -      +
    260E  VAL*     2.9    40.3    +      -       +      +
    262E  VAL*     3.9    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 238 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234E  ARG*     5.2     2.9    -      -       -      +
    236E  LYS*     3.5     9.1    +      -       +      +
    237E  TYR*     1.3    69.6    -      -       -      +
    239E  LEU*     1.3    66.5    +      -       -      +
    240E  VAL*     4.9     4.1    -      -       +      +
    257E  PRO*     4.8    12.8    -      -       +      +
    258E  PHE      3.8     7.6    -      -       -      +
    259E  PRO*     4.4    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 239 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206E  LEU*     4.5    13.5    -      -       +      -
    207E  LEU      5.8     4.3    -      -       -      +
    212E  LEU*     3.7    31.6    -      -       +      -
    214E  PHE*     3.6    45.3    -      -       +      -
    237E  TYR*     3.4     9.6    +      -       +      +
    238E  GLU*     1.3    81.0    -      -       -      +
    240E  VAL*     1.3    69.3    +      -       -      +
    257E  PRO*     3.6     0.9    -      -       -      +
    258E  PHE*     2.9    62.9    +      -       +      +
    260E  VAL*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206E  LEU*     4.1     3.9    -      -       -      +
    207E  LEU*     3.1    53.7    +      -       +      +
    238E  GLU*     4.9     4.9    -      -       +      +
    239E  LEU*     1.3    83.9    -      -       -      +
    241E  ALA*     1.3    63.0    +      -       -      +
    242E  VAL*     4.7     0.7    -      -       +      -
    255E  MET*     3.7    32.5    -      -       +      -
    256E  VAL      3.4    14.4    -      -       -      +
    257E  PRO*     4.4    11.2    -      -       +      -
    258E  PHE*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 241 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167E  PHE*     4.1    11.4    -      -       +      -
    188E  PHE*     3.7    34.1    -      -       +      -
    205E  ARG      3.9     4.5    -      -       -      +
    206E  LEU*     4.3     9.9    -      -       +      -
    240E  VAL*     1.3    73.6    -      -       -      +
    242E  VAL*     1.3    63.2    +      -       -      +
    243E  CYS      4.1     0.3    +      -       -      -
    254E  VAL      4.0     0.5    -      -       -      +
    255E  MET*     3.4     1.4    -      -       -      -
    256E  VAL*     2.9    37.0    +      -       +      +
    258E  PHE*     4.5    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 242 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167E  PHE*     5.2     0.2    -      -       -      -
    203E  ALA      3.9     0.3    -      -       -      +
    204E  TYR*     3.4     7.9    -      -       -      +
    205E  ARG*     2.9    50.8    +      -       +      +
    206E  LEU      5.3     0.2    -      -       -      -
    207E  LEU*     4.8    18.6    -      -       +      +
    240E  VAL*     4.7     5.6    -      -       +      -
    241E  ALA*     1.3    76.7    -      -       -      +
    243E  CYS*     1.3    64.0    +      -       -      +
    244E  THR*     4.5     4.4    +      -       -      +
    253E  VAL*     3.7    25.8    -      -       +      -
    254E  VAL      3.3    10.1    -      -       -      +
    255E  MET*     4.0    20.2    -      -       +      -
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Residues in contact with CYS 243 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166E  CYS*     2.0    54.7    -      -       +      -
    167E  PHE*     3.9     7.8    -      -       +      -
    202E  VAL*     3.6    14.6    -      -       -      -
    203E  ALA      3.6     4.7    -      -       -      -
    204E  TYR*     3.6    22.4    -      -       +      -
    241E  ALA      4.1     1.2    +      -       -      -
    242E  VAL*     1.3    73.4    -      -       -      +
    244E  THR*     1.3    80.2    +      -       -      +
    252E  GLU      4.0     0.7    -      -       -      -
    253E  VAL*     3.3     1.0    -      -       -      -
    254E  VAL*     2.8    35.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 244 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201E  SER      4.1     0.5    -      -       -      +
    202E  VAL*     3.2     6.8    -      -       -      -
    203E  ALA*     2.9    49.4    +      -       +      +
    205E  ARG*     5.1     9.0    +      -       -      -
    242E  VAL*     4.5     4.5    +      -       -      +
    243E  CYS*     1.3    80.0    +      -       -      +
    245E  VAL*     1.3    74.9    +      -       -      +
    246E  HIS      4.9     6.1    -      -       -      -
    252E  GLU*     3.4     6.3    -      -       -      +
    253E  VAL*     3.6    28.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 245 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162E  PRO*     3.8    29.8    -      -       +      -
    165E  LEU*     4.3    23.8    -      -       +      -
    166E  CYS*     3.8    21.8    -      -       -      -
    200E  ILE*     3.9    20.4    -      -       +      -
    202E  VAL*     4.2     9.9    -      -       +      -
    243E  CYS*     4.4     0.7    -      -       -      -
    244E  THR*     1.3    79.5    -      -       -      +
    246E  HIS*     1.3    90.3    +      -       +      +
    252E  GLU      3.0    28.6    +      -       -      +
----------------------------------------------------------
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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