Contacts of the strand formed by residues 215 - 220 (chain E) in PDB entry 5A0Q


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 215 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50E  VAL      3.5    17.7    -      -       -      +
     52E  LYS*     3.8     7.4    +      -       -      +
    199E  LEU*     3.7    27.4    -      -       +      -
    202E  LEU*     3.4    27.6    -      -       +      -
    210E  LEU*     4.2    15.7    -      -       +      -
    211E  ASN      3.7    11.9    -      -       -      +
    212E  ALA*     3.0    30.2    -      -       -      +
    213E  THR      3.5     0.4    -      -       -      -
    214E  ASN*     1.4    76.8    -      -       -      +
    216E  GLU*     1.3    78.9    +      -       -      +
    217E  LEU*     4.0    17.7    -      -       +      -
    228E  MET*     5.6     0.5    -      -       -      +
    231E  LYS*     4.9     0.7    -      -       -      -
    234E  LEU*     3.8    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 216 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49E  ALA*     4.3     0.3    -      -       -      -
     50E  VAL*     3.2    38.3    +      -       +      +
     52E  LYS*     3.2    35.7    +      -       +      +
     62E  SER*     5.2     2.6    -      -       -      -
     64E  ILE      2.9    22.9    -      -       -      +
     65E  GLU*     3.5    40.3    -      -       -      +
     66E  LYS*     3.7    15.5    +      -       +      +
     67E  ILE*     4.3     5.1    -      -       +      +
    215E  ILE*     1.3    81.3    -      -       -      +
    217E  LEU*     1.3    61.0    +      -       -      +
    218E  ALA      4.2     0.7    +      -       -      -
    228E  MET*     4.4    20.9    -      -       +      +
    231E  LYS*     5.6     0.2    -      -       -      -
    234E  LEU*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 217 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47E  CYS*     3.8     5.2    -      -       -      -
     48E  LEU      3.8     5.4    -      -       -      +
     49E  ALA*     3.4    30.1    -      -       +      +
     67E  ILE*     5.1     0.2    -      -       -      -
    195E  ILE*     3.8    21.8    -      -       +      -
    198E  SER*     3.8    14.1    -      -       -      +
    199E  LEU*     4.7     2.5    -      -       +      -
    215E  ILE*     4.0    16.0    -      -       +      +
    216E  GLU*     1.3    73.4    -      -       -      +
    218E  ALA*     1.4    62.6    +      -       -      +
    219E  THR*     3.7    23.8    -      -       +      -
    228E  MET*     3.3    10.3    -      -       -      +
    229E  PHE*     3.0    30.5    +      -       +      +
    234E  LEU*     3.6    39.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 218 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  VAL*     5.3     0.3    -      -       -      +
     48E  LEU*     2.8    35.9    +      -       -      +
     67E  ILE*     3.8    17.0    -      -       +      +
    216E  GLU      4.2     0.4    +      -       -      -
    217E  LEU*     1.4    74.7    -      -       -      +
    219E  THR*     1.3    61.7    +      -       -      +
    226E  PHE*     2.7    42.2    -      -       +      -
    227E  HIS      3.4     9.0    -      -       -      +
    228E  MET*     4.0     5.8    -      -       +      -
    229E  PHE      4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 219 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  VAL      3.4     9.9    -      -       -      -
     47E  CYS*     4.1     8.5    -      -       -      -
    191E  LEU*     5.7     4.0    -      -       -      +
    195E  ILE*     4.0    22.3    -      -       +      +
    217E  LEU*     3.7    28.3    -      -       +      -
    218E  ALA*     1.3    80.2    -      -       -      +
    220E  VAL*     1.4    62.3    +      -       -      +
    227E  HIS*     1.6    89.3    +      -       -      +
    229E  PHE*     3.7     3.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 220 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45E  GLY*     3.2     3.4    -      -       -      -
     46E  VAL*     3.0    47.3    +      -       +      -
     72E  ALA      5.1     1.1    -      -       -      +
     73E  HIS*     4.9    11.0    -      -       -      +
     75E  GLY*     5.2     1.1    -      -       -      +
    144E  GLY      5.0     7.9    -      -       -      +
    146E  VAL*     3.7    21.9    -      -       +      +
    191E  LEU*     4.6     1.3    -      -       -      -
    219E  THR*     1.4    69.3    -      -       -      +
    221E  GLN*     1.3    66.5    +      -       -      +
    224E  GLN*     3.3    27.6    -      -       +      +
    225E  ASN*     4.5     0.4    -      -       -      -
    226E  PHE*     3.3    47.3    -      -       +      +
----------------------------------------------------------
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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