Contacts of the strand formed by residues 16 - 21 (chain M) in PDB entry 3HOU


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 GLU 16 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14M  VAL*     3.4     7.2    -      -       -      +
     15M  LYS*     1.3    84.0    -      -       -      +
     17M  VAL*     1.3    65.0    -      -       -      +
     18M  GLN      4.1     0.7    -      -       -      -
   1418M  LEU*     3.8    20.0    -      -       +      +
   1419M  ASP      3.1    12.1    -      -       -      +
   1420M  ASP*     5.4     1.9    -      -       -      +
   1421M  CYS*     4.0     0.4    -      -       -      -
   1215N  ARG      4.0     0.2    -      -       -      +
   1217N  TYR*     3.1    30.1    +      -       +      +
   1219N  ASP      3.3     3.8    -      -       -      +
   1220N  ARG*     3.4    29.8    +      -       +      +
   1221N  SER*     2.8    27.0    +      -       -      -
   1222N  ARG*     3.3    16.1    +      -       -      +
     13P  ARG*     2.6    33.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 17 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14M  VAL*     3.9    10.3    -      -       +      -
     16M  GLU*     1.3    79.3    -      -       -      +
     18M  GLN*     1.3    59.0    +      -       -      +
     19M  PHE*     3.6    33.3    +      -       +      -
   1397M  LEU*     3.9    18.6    -      -       +      -
   1417M  GLU      3.8     0.3    -      -       -      +
   1418M  LEU*     3.5     6.9    -      -       -      -
   1419M  ASP*     2.9    36.6    +      -       +      +
   1421M  CYS*     3.5    21.8    -      -       -      -
   1430M  LEU*     4.6     2.9    -      -       +      -
   1204N  PHE*     5.3     2.0    -      -       +      -
   1214N  PRO*     4.4     7.0    -      -       +      -
   1215N  ARG      3.2    13.0    -      -       -      +
   1216N  LEU*     4.2    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 18 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16M  GLU      4.1     1.4    -      -       -      -
     17M  VAL*     1.3    69.6    -      -       -      +
     19M  PHE*     1.3    84.2    +      -       -      +
    228M  PHE*     3.3    39.7    -      -       +      -
   1416M  ALA      4.1     7.2    +      -       -      +
   1417M  GLU      3.9     3.6    +      -       -      +
   1418M  LEU*     3.8    34.3    -      -       +      +
   1213N  THR      3.2     3.5    -      -       -      +
   1214N  PRO      4.8     0.2    -      -       -      -
   1215N  ARG*     2.9    52.1    +      -       +      +
   1217N  TYR*     3.9    18.8    -      -       +      -
     12P  ARG*     4.9     4.4    -      -       -      +
     13P  ARG*     4.3     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 19 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17M  VAL*     3.6    28.0    +      -       +      -
     18M  GLN*     1.3    84.7    -      -       -      +
     20M  GLY*     1.3    58.9    +      -       -      +
    228M  PHE*     4.1     1.5    -      -       -      +
   1396M  ALA*     3.8    22.7    -      -       +      -
   1397M  LEU*     3.9    24.9    -      -       +      -
   1409M  LEU*     5.1     7.9    -      -       +      -
   1412M  ALA*     3.3    36.6    -      -       +      +
   1413M  GLY*     4.0     0.2    -      -       -      -
   1416M  ALA*     3.1    22.0    -      -       -      +
   1417M  GLU*     2.9    22.0    +      -       +      +
   1418M  LEU      5.2     0.2    -      -       -      -
   1419M  ASP*     4.6     6.5    -      -       +      -
   1204N  PHE*     5.8     1.1    -      +       -      -
   1207N  LEU*     4.5    12.6    -      -       +      -
   1212N  ILE*     4.6    10.1    -      -       +      -
   1213N  THR*     3.3     2.2    -      -       -      -
   1214N  PRO*     3.7    33.0    -      -       +      -
   1215N  ARG*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 20 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19M  PHE*     1.3    77.4    -      -       -      +
     21M  LEU*     1.3    65.0    +      -       -      +
    228M  PHE*     3.3    15.3    -      -       -      -
    229M  SER*     4.3     0.7    -      -       -      -
   1413M  GLY*     3.1    24.1    -      -       -      -
   1212N  ILE*     3.6     2.1    -      -       -      -
   1213N  THR*     3.0    35.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 21 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20M  GLY*     1.3    78.1    -      -       -      +
     22M  PHE*     1.3    62.5    +      -       -      +
     23M  SER      3.7     0.9    +      -       -      -
     26M  GLU*     5.4     0.2    -      -       -      +
     95M  PHE*     3.6    23.1    -      -       +      -
    224M  PHE*     5.1     1.3    -      -       +      -
    228M  PHE      2.8    14.4    +      -       -      +
    229M  SER*     3.4    24.5    -      -       -      -
    230M  ARG      4.8     1.3    -      -       -      +
    233M  TRP*     3.6    32.3    -      -       +      +
    234M  MET*     4.1    25.6    -      -       +      +
   1413M  GLY*     3.1    31.0    -      -       -      +
   1414M  ALA*     3.6    13.5    -      -       -      +
   1211N  ASN*     3.7     5.8    -      -       -      +
   1212N  ILE*     4.3     7.9    -      -       +      -
   1213N  THR*     4.0     9.1    +      -       -      +
   1215N  ARG*     4.6     5.4    +      -       -      -
----------------------------------------------------------
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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