Contacts of the strand formed by residues 222 - 227 (chain A) in PDB entry 3ELP


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 MET 222 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     3.8    18.4    -      -       +      -
     86A  ALA*     4.1     5.4    -      -       -      -
     87A  PHE      3.6     5.8    -      -       -      +
     88A  ALA      3.9     0.9    -      -       -      -
     89A  SER      3.9     4.7    -      -       -      -
     90A  GLY      3.6     6.8    +      -       -      -
    208A  TYR      4.0     0.2    -      -       -      +
    209A  SER*     3.6     0.5    -      -       -      -
    210A  ALA*     3.0    40.4    +      -       +      +
    220A  VAL*     4.3     2.9    -      -       +      -
    221A  VAL*     1.3    85.2    -      -       -      +
    223A  GLY*     1.3    60.4    +      -       -      +
    224A  LEU*     3.7    23.1    -      -       +      -
    247A  PRO*     3.6    26.9    -      -       +      -
    251A  ASP*     3.6    25.1    -      -       +      +
    252A  CYS*     3.8     2.2    -      -       -      +
    255A  CYS*     3.4    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LEU      3.4     2.3    -      -       -      +
     86A  ALA*     3.3     4.0    -      -       -      -
     87A  PHE*     2.6    43.3    +      -       -      -
     89A  SER      3.4    22.6    -      -       -      -
     90A  GLY*     3.7     7.2    -      -       -      -
     93A  ALA*     4.0     8.5    -      -       -      -
    208A  TYR      3.9     1.6    -      -       -      -
    222A  MET*     1.3    72.7    -      -       -      +
    224A  LEU*     1.3    61.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     4.4     6.5    -      -       +      -
     72A  GLU*     5.5     1.1    -      -       +      -
     75A  VAL*     3.8    44.0    -      -       +      -
     79A  ASP*     5.5     0.8    -      -       -      +
     84A  CYS*     4.1     9.6    -      -       -      -
     85A  LEU      3.6     0.4    -      -       -      -
     86A  ALA*     4.0    26.0    -      -       +      -
     93A  ALA*     4.8     0.6    -      -       -      +
    206A  SER      3.7     1.4    -      -       -      +
    207A  MET*     3.2     5.8    -      -       -      +
    208A  TYR*     2.7    72.2    +      -       +      +
    210A  ALA*     6.0     1.8    -      -       +      -
    222A  MET*     3.7    22.0    -      -       +      -
    223A  GLY*     1.3    70.1    -      -       -      -
    225A  VAL*     1.3    61.4    +      -       -      +
    226A  SER*     4.1     0.7    -      -       -      -
    255A  CYS*     4.5    11.4    -      -       -      -
    259A  LEU*     5.6     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  CYS*     3.3     1.9    -      -       -      -
     85A  LEU*     2.7    46.2    +      -       +      +
     87A  PHE*     3.7    24.7    -      -       +      -
     93A  ALA*     3.8    20.9    -      -       +      -
     97A  ILE*     3.6    31.9    -      -       +      -
    205A  ILE*     3.8    14.1    -      -       +      -
    206A  SER      3.9     2.5    -      -       -      -
    207A  MET*     4.1     6.1    -      -       +      +
    224A  LEU*     1.3    77.2    -      -       -      +
    226A  SER*     1.3    65.1    +      -       -      +
    227A  VAL*     5.6     0.2    -      -       +      -
    236A  LEU*     3.9    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ALA*     4.2     1.9    -      -       -      -
     79A  ASP*     2.6    33.4    +      -       -      +
     81A  ALA*     3.5    13.8    -      -       -      +
     83A  TYR      3.3     8.6    +      -       -      -
     84A  CYS*     3.2    22.5    -      -       -      +
    199A  LEU*     4.2     4.5    -      -       -      -
    205A  ILE*     3.4     7.1    -      -       -      +
    206A  SER      3.1    32.1    +      -       -      -
    225A  VAL*     1.3    74.6    -      -       -      +
    227A  VAL*     1.3    68.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  ALA*     3.7     2.5    -      -       -      +
     82A  LYS      3.4     2.1    +      -       -      -
     83A  TYR*     2.9    35.5    +      -       +      +
     85A  LEU*     5.3     3.8    -      -       +      -
    199A  LEU*     3.9     9.2    -      -       -      -
    204A  ASP      2.9    21.8    -      -       -      +
    205A  ILE*     4.4     4.3    -      -       +      -
    225A  VAL      5.4     0.2    -      -       -      +
    226A  SER*     1.3    79.5    -      -       -      +
    228A  ASN*     1.3    71.9    +      -       -      +
    229A  CYS*     3.5    11.9    -      -       +      +
    232A  LEU*     3.5    24.9    -      -       +      -
    233A  HIS*     4.1    33.9    -      -       +      +
    236A  LEU*     4.8     8.5    -      -       +      -
----------------------------------------------------------
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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