Contacts of the strand formed by residues 11 - 18 (chain A) in PDB entry 5M64


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 11 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLU*     1.3    72.7    -      -       -      +
     12A  THR*     1.3    61.0    +      -       -      +
     13A  SER      4.5     5.8    -      -       -      +
   1634A  LEU*     3.6    28.5    -      -       +      +
   1643A  VAL*     4.3    24.2    -      -       +      +
   1644A  GLY      5.0     7.7    +      -       -      +
   1645A  LYS*     4.9    14.1    -      -       -      +
   1103B  VAL*     5.3     4.5    -      -       +      -
   1176B  VAL*     3.7    25.4    -      -       +      -
   1177B  ALA      5.1     4.5    -      -       -      +
   1178B  ILE*     5.6     4.0    -      -       +      -
   1198B  TYR*     4.4    28.0    -      -       +      -
   1199B  ASN      3.8     7.0    -      -       -      +
   1200B  VAL*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLU*     3.9     5.7    +      -       -      -
     11A  ILE*     1.3    73.1    -      -       -      +
     13A  SER*     1.3    69.8    +      -       -      +
   1633A  GLN*     2.9    28.3    +      -       -      +
   1634A  LEU*     3.3    12.3    -      -       -      +
   1640A  ARG*     5.9     0.5    +      -       -      -
   1199B  ASN*     4.4     1.6    +      -       -      +
   1201B  GLU*     3.3    36.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     4.5     3.3    -      -       -      +
     12A  THR*     1.3    86.3    -      -       -      +
     14A  VAL*     1.3    61.8    +      -       -      +
   1631A  ARG*     4.8     5.1    -      -       -      -
   1632A  GLU      3.4    12.1    -      -       -      -
   1633A  GLN*     3.9    21.1    -      -       -      -
   1634A  LEU*     3.5     7.3    -      -       -      +
   1198B  TYR*     4.1     1.2    -      -       -      -
   1199B  ASN*     2.5    62.8    +      -       -      +
   1201B  GLU*     4.6     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  SER*     1.3    73.4    -      -       -      +
     15A  ASP*     1.3    63.1    +      -       -      +
     16A  PHE*     4.0    11.0    -      -       +      -
   1610A  PHE*     3.6    22.2    -      -       +      -
   1631A  ARG*     4.0     4.5    -      -       -      -
   1632A  GLU*     2.8    61.9    +      -       +      +
   1634A  LEU*     4.1    13.5    -      -       +      -
   1643A  VAL*     6.3     0.2    -      -       +      -
   1196B  LEU*     3.6    20.2    -      -       +      -
   1197B  ARG      4.0     4.3    -      -       -      +
   1198B  TYR*     3.5    34.3    -      -       +      -
   1199B  ASN*     5.0     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     1.3    72.9    -      -       -      +
     16A  PHE*     1.3    82.6    +      -       -      +
   1629A  ASN*     3.4    14.0    +      -       -      +
   1630A  GLU      2.9    24.4    -      -       -      +
   1631A  ARG*     3.3    39.6    +      -       -      +
   1632A  GLU*     4.0     2.2    -      -       -      -
   1196B  LEU*     4.2     0.3    -      -       -      +
   1197B  ARG*     2.8    49.8    +      -       +      +
   1199B  ASN*     5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     4.0    11.2    -      -       +      -
     15A  ASP*     1.3    97.9    +      -       -      +
     17A  GLY*     1.3    60.4    +      -       -      +
   1609A  SER*     4.6     9.4    -      -       -      -
   1610A  PHE*     4.4    20.6    -      +       -      -
   1613A  MET*     4.9     6.1    -      -       +      -
   1622A  LEU*     5.6     6.7    -      -       +      -
   1625A  ALA*     4.3    19.1    -      -       +      -
   1626A  VAL*     4.0    33.9    -      -       +      -
   1629A  ASN*     3.1    16.0    +      -       -      +
   1630A  GLU*     4.4     3.3    +      -       -      +
   1632A  GLU*     3.6    31.0    +      -       -      -
   1189B  LEU*     6.1     2.9    -      -       +      -
   1194B  ILE*     5.3     4.0    -      -       +      -
   1195B  ARG*     3.5    12.0    +      -       -      +
   1196B  LEU*     3.6    27.4    -      -       +      -
   1197B  ARG*     5.1     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     1.3    79.7    -      -       -      +
     18A  ILE*     1.3    60.8    +      -       -      -
   1626A  VAL*     3.5    20.5    -      -       -      +
   1629A  ASN*     4.0    11.6    +      -       -      -
   1194B  ILE*     3.9     0.9    -      -       -      -
   1195B  ARG*     2.9    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLY*     1.3    76.7    -      -       -      +
     19A  LEU*     1.3    68.3    +      -       +      +
     20A  THR*     4.0     5.1    +      -       -      +
     23A  GLU*     3.4     8.7    -      -       -      +
     90A  PHE*     4.2    24.7    -      -       +      -
    350A  VAL*     6.0     5.4    -      -       +      -
    354A  SER*     3.2    52.7    -      -       -      +
    355A  PHE*     6.2     0.4    -      -       +      -
    357A  MET*     4.8     6.1    -      -       +      -
   1626A  VAL*     5.1     2.2    -      -       +      -
   1193B  GLY      3.2    23.1    -      -       -      +
   1194B  ILE*     4.7     1.6    -      -       +      -
   1195B  ARG*     3.8    12.7    -      -       -      +
----------------------------------------------------------
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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