Contacts of the strand formed by residues 271 - 276 (chain A) in PDB entry 6E7P


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 ILE 271 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ALA*     3.3     3.1    -      -       -      -
    119A  ALA*     3.0    38.6    +      -       +      +
    125A  LEU*     3.7    22.9    -      -       +      -
    225A  PHE*     5.8     0.2    -      -       +      -
    228A  LEU*     5.1     6.1    -      -       +      -
    262A  PHE*     3.8    26.5    -      -       +      +
    263A  ASP      3.3    15.3    -      -       -      +
    264A  ASN*     4.0    24.7    -      -       +      +
    270A  ARG*     1.3    75.1    -      -       -      +
    272A  PRO*     1.3    72.5    -      -       -      +
    273A  ILE*     4.2     2.0    -      -       +      +
    144B  LEU*     3.7    38.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ASP      5.8     3.4    -      -       -      +
    117A  PHE      3.8     9.9    -      -       -      +
    118A  ALA*     4.3     2.5    -      -       +      -
    261A  THR      3.6     0.7    -      -       -      +
    262A  PHE*     3.7     0.2    -      -       -      -
    263A  ASP*     3.2    46.6    +      -       +      +
    270A  ARG*     3.3    33.2    -      -       -      +
    271A  ILE*     1.3    92.2    -      -       -      +
    273A  ILE*     1.3    63.4    +      -       -      +
    274A  SER*     5.0     5.6    -      -       -      +
     96B  GLU*     5.1     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     3.7    31.3    -      -       +      +
    114A  ASP      4.5    10.2    -      -       -      +
    117A  PHE*     3.3    46.5    +      -       +      +
    118A  ALA      4.5     3.6    -      -       -      +
    119A  ALA*     4.2    20.2    -      -       +      -
    128A  ALA*     4.4     9.9    -      -       +      -
    260A  ILE*     4.8     1.8    -      -       +      -
    261A  THR      3.5     4.9    -      -       -      +
    262A  PHE*     3.7    36.3    -      -       +      -
    271A  ILE*     4.2     5.6    -      -       +      +
    272A  PRO*     1.3    80.0    -      -       -      +
    274A  SER*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     4.6     4.6    -      -       -      +
    260A  ILE*     3.6    11.4    -      -       -      +
    261A  THR*     3.2    41.0    +      -       -      +
    263A  ASP*     6.0     1.4    -      -       -      +
    272A  PRO*     5.0     5.9    -      -       -      +
    273A  ILE*     1.3    80.7    +      -       -      +
    275A  LEU*     1.3    66.6    +      -       -      +
    276A  GLU*     5.0     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  THR*     4.7     7.2    -      -       -      +
    101A  PHE*     4.3    30.5    -      -       +      +
    102A  ARG*     3.9    54.6    +      -       +      +
    105A  PHE*     4.6     2.0    -      -       +      -
    106A  LEU*     4.6    11.0    -      -       +      -
    258A  VAL*     4.3    14.6    -      -       +      -
    259A  LEU      3.4     5.8    -      -       -      -
    260A  ILE*     4.1    21.3    -      -       +      -
    274A  SER*     1.3    77.9    -      -       -      +
    276A  GLU*     1.3    88.4    +      -       -      +
    277A  THR*     4.4    11.4    -      -       +      -
    486D  ARG*     4.2     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  SER      3.3     4.2    -      -       -      +
    258A  VAL*     3.3     2.3    -      -       -      -
    259A  LEU*     3.2    48.3    +      -       +      +
    261A  THR*     5.5     2.5    -      -       -      +
    274A  SER*     5.0     7.4    -      -       -      -
    275A  LEU*     1.3    84.4    +      -       -      +
    277A  THR*     1.3    71.2    +      -       -      +
    278A  GLN*     4.4    13.7    +      -       -      +
    486D  ARG*     2.5    48.2    +      -       -      +
----------------------------------------------------------
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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