Contacts of the strand formed by residues 182 - 186 (chain B) in PDB entry 1EFA


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 182 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  VAL*     5.9     0.2    -      -       +      -
    174B  LEU*     4.2    28.9    -      -       +      -
    175B  VAL*     5.2     2.5    -      -       +      -
    179B  HIS*     4.2    23.6    -      -       +      +
    180B  GLN      3.4    10.3    +      -       -      +
    181B  GLN*     1.3    79.9    -      -       -      +
    183B  ALA*     1.3    71.9    +      -       -      +
    184B  LEU*     4.3     4.7    -      -       +      -
    205B  LEU*     3.9    26.2    -      -       +      -
    210B  ILE*     4.4    11.4    -      -       +      -
    212B  PRO*     3.1    11.7    -      -       +      +
    213B  ILE*     3.0    27.7    +      -       -      +
    241B  ALA*     3.4    11.4    -      -       +      +
    243B  LEU*     4.1    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  ILE*     1.3    74.6    -      -       -      +
    184B  LEU*     1.3    67.0    +      -       -      +
    213B  ILE*     4.7     0.2    -      -       +      -
    214B  ALA*     3.5    16.8    -      -       +      +
    232B  MET*     3.7    30.5    -      -       -      -
    239B  PRO*     3.8    17.2    -      -       +      +
    241B  ALA      3.0     6.9    +      -       -      -
    242B  MET*     3.4    13.0    -      -       +      -
    243B  LEU      3.2    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  ILE*     4.3     2.9    -      -       +      -
    183B  ALA*     1.3    85.9    -      -       -      +
    185B  LEU*     1.3    55.5    +      -       -      +
    186B  ALA*     3.9     1.3    -      -       +      +
    198B  LEU*     4.1    12.1    -      -       +      -
    201B  TRP*     4.1    25.8    -      -       +      -
    202B  HIS*     3.8    32.8    -      -       +      +
    205B  LEU*     3.9    12.6    -      -       +      -
    212B  PRO*     3.8    16.4    -      -       +      -
    214B  ALA      2.9    10.5    +      -       -      +
    215B  GLU*     3.2     8.3    +      -       +      +
    216B  ARG*     2.7    35.7    +      -       -      +
    242B  MET*     5.6     0.9    -      -       -      -
    243B  LEU*     3.6    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  ALA      4.3     0.2    -      -       -      -
    184B  LEU*     1.3    72.0    -      -       -      +
    186B  ALA*     1.3    59.4    +      -       -      +
    201B  TRP*     3.6     3.5    -      -       -      -
    216B  ARG*     3.5    17.9    -      -       +      +
    218B  GLY*     4.1    11.7    -      -       -      +
    225B  GLY*     3.8    22.0    -      -       -      +
    228B  GLN*     3.8    28.3    -      -       +      -
    229B  THR*     3.7    22.2    -      -       -      +
    242B  MET*     4.2    15.9    -      -       +      +
    243B  LEU      3.0     8.8    +      -       -      +
    244B  VAL*     3.3    28.2    -      -       +      +
    245B  ALA      2.9    25.5    +      -       -      -
    249B  MET*     4.4     6.1    -      -       +      -
    253B  ALA*     4.4     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  LEU      3.9     1.1    -      -       -      -
    185B  LEU*     1.3    74.0    -      -       -      +
    187B  GLY*     1.3    65.4    +      -       -      +
    189B  LEU*     4.9     3.6    -      -       +      -
    194B  ALA      5.0     3.6    -      -       -      +
    198B  LEU*     3.8    34.8    -      -       +      -
    201B  TRP*     4.1     8.1    -      -       +      -
    215B  GLU*     6.1     1.6    -      -       +      -
    216B  ARG      2.8    14.5    +      -       -      +
    217B  GLU*     3.5     1.9    -      -       -      -
    218B  GLY*     2.7    33.6    +      -       -      -
    245B  ALA*     3.9     4.5    -      -       -      -
    249B  MET*     3.7     5.6    -      -       -      +
----------------------------------------------------------
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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