Contacts of the strand formed by residues 178 - 186 (chain A) in PDB entry 2ANL


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 TYR 178 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  ILE*     3.4    23.6    -      -       +      +
    174A  GLU      3.7     7.9    -      -       -      -
    175A  GLU*     3.1    40.5    +      -       +      +
    177A  PHE*     1.3    80.2    -      -       -      +
    179A  GLU*     1.3    67.1    +      -       -      +
    180A  GLY      3.6    15.7    -      -       -      -
    182A  LEU*     3.2    31.6    -      -       +      +
    310A  PHE*     3.7    30.1    -      +       +      -
    323A  ALA*     4.1    10.8    -      -       +      -
    324A  VAL      3.1    14.4    -      -       -      +
    326A  LYS*     3.8     5.9    -      -       -      +
    203B  LYS*     2.8    53.6    +      -       +      -
    204B  THR*     3.8     4.3    -      -       -      -
    205B  SER      4.2     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  TYR*     1.3    81.1    -      -       -      +
    180A  GLY*     1.3    64.7    +      -       -      +
    181A  GLU      5.1     0.3    -      -       -      +
    323A  ALA*     4.7     1.0    -      -       -      +
    324A  VAL*     2.6    45.9    +      -       +      +
    325A  ALA      4.4     8.3    -      -       -      +
    326A  LYS*     3.2    45.4    +      -       +      +
    327A  ASN*     4.5     6.2    +      -       -      +
    203B  LYS*     4.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  TYR*     3.6    12.3    -      -       -      -
    179A  GLU*     1.3    76.4    -      -       -      +
    181A  GLU*     1.3    65.5    +      -       -      -
    202B  GLY      4.6     0.4    -      -       -      -
    203B  LYS*     3.6    26.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  GLU      5.1     0.3    -      -       -      +
    180A  GLY*     1.3    76.7    -      -       -      -
    182A  LEU*     1.3    64.1    +      -       -      +
    183A  THR*     3.9     6.3    +      -       -      +
    322A  PHE      4.3     0.2    -      -       -      +
    323A  ALA*     4.1     9.1    -      -       -      +
    200B  ASN*     2.6    36.6    +      -       -      +
    202B  GLY*     2.3    42.0    -      -       -      +
    203B  LYS      4.7     0.9    -      -       -      -
    256B  THR*     4.1    11.3    +      -       -      +
    258B  GLU*     2.4    44.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  ILE*     4.4    17.5    -      -       +      -
    178A  TYR*     3.2    36.8    -      -       +      +
    181A  GLU*     1.3    76.1    -      -       -      +
    183A  THR*     1.3    65.0    +      -       -      +
    184A  TYR*     3.9    33.4    -      -       +      +
    310A  PHE*     5.0     2.5    -      -       +      -
    312A  VAL*     3.8    28.5    -      -       +      -
    321A  GLY*     5.2     1.3    -      -       -      -
    322A  PHE      3.1     9.9    -      -       -      +
    323A  ALA*     3.8    14.4    -      -       +      -
    200B  ASN*     3.6    21.0    +      -       -      +
    203B  LYS      3.9     6.3    -      -       -      +
    205B  SER*     4.1    13.7    -      -       -      +
    260B  LYS*     6.2     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLU      4.7     4.9    +      -       -      +
    182A  LEU*     1.3    77.8    -      -       -      +
    184A  TYR*     1.3    63.0    +      -       -      +
    264A  ASN*     3.2    28.9    -      -       +      +
    266A  TYR*     2.9    33.7    +      -       -      -
    321A  GLY*     3.3     2.9    -      -       -      -
    322A  PHE*     2.6    36.0    +      -       -      +
    323A  ALA*     5.4     0.3    -      -       -      -
    200B  ASN*     5.9     0.7    -      -       -      +
    260B  LYS*     4.7    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  ILE*     5.3     5.3    -      -       +      +
    182A  LEU*     3.9    42.0    -      -       +      +
    183A  THR*     1.3    81.4    -      -       -      +
    185A  GLU*     1.3    77.7    -      -       -      +
    264A  ASN*     3.5     7.4    +      -       -      +
    312A  VAL*     5.3     7.6    -      -       +      -
    314A  ASP*     5.6     4.0    -      -       +      -
    317A  LYS*     4.6    11.3    +      -       +      -
    319A  SER*     3.7     8.3    -      -       -      +
    320A  ILE      3.2     4.9    -      -       -      -
    321A  GLY*     3.7    17.5    -      -       -      -
    322A  PHE*     4.4     0.4    -      -       -      -
    198B  ASP*     4.7    11.7    -      -       +      +
    200B  ASN*     5.3     1.3    -      -       -      -
    205B  SER*     4.4    14.7    +      -       -      -
    206B  MET*     4.4     4.1    -      -       -      -
    207B  GLU*     2.5    70.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  TYR*     1.3    79.5    -      -       -      +
    186A  LYS*     1.3    62.3    +      -       -      +
    195A  VAL*     3.9    22.4    -      -       +      -
    196A  ASP      4.5     3.6    -      -       -      +
    197A  LEU*     4.1    16.2    -      -       +      +
    261A  SER*     2.9    38.2    +      -       -      -
    264A  ASN*     2.9    15.2    +      -       -      -
    266A  TYR*     3.3    16.6    +      -       +      +
    319A  SER*     3.0     4.0    +      -       -      -
    320A  ILE*     2.8    33.0    +      -       -      +
    322A  PHE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  GLU*     1.3    74.4    +      -       -      +
    187A  LEU*     1.3    71.7    +      -       -      +
    188A  ASN*     3.2     3.3    +      -       -      +
    195A  VAL*     3.9    10.9    -      -       -      +
    196A  ASP*     4.7     2.6    +      -       -      +
    317A  LYS      4.7     7.4    -      -       -      -
    318A  GLU*     4.0     7.4    -      -       +      +
    319A  SER*     3.7    17.3    -      -       -      -
    198B  ASP*     5.3     5.9    +      -       -      -
    207B  GLU*     5.2     8.4    +      -       -      +
    208B  LYS*     4.2    34.1    -      -       -      +
----------------------------------------------------------
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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