Contacts of the strand formed by residues 659 - 664 (chain A) in PDB entry 1MUK


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 PHE 659 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  THR*     4.9     9.2    -      -       -      +
    531A  LEU*     5.0     2.2    -      -       +      -
    599A  LEU*     5.5     2.2    -      -       +      -
    654A  LEU*     3.5    38.4    -      -       +      -
    655A  TYR*     3.7    31.9    -      +       -      -
    657A  ARG*     4.6     1.3    -      -       -      +
    658A  GLY*     1.3    76.4    -      -       -      -
    660A  SER*     1.3    60.4    +      -       -      +
    661A  TYR*     3.8    26.2    -      +       +      -
    675A  HIS      3.5     1.0    -      -       -      +
    676A  MET*     2.9    19.8    -      -       -      +
    677A  THR*     2.9    31.2    +      -       -      +
    678A  THR*     4.4     7.2    -      -       -      -
    679A  THR      3.3    20.2    -      -       -      -
    680A  PHE*     4.1     7.6    -      +       -      -
    681A  PRO*     3.2    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 660 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  ALA      5.7     0.2    +      -       -      -
    512A  ASP*     2.9    28.8    +      -       -      +
    513A  THR*     2.7    34.4    +      -       -      +
    657A  ARG*     3.8    10.3    +      -       -      +
    658A  GLY      4.3     0.2    +      -       -      -
    659A  PHE*     1.3    70.8    -      -       -      +
    661A  TYR*     1.3    60.2    -      -       -      +
    674A  THR*     3.9    13.4    -      -       -      +
    675A  HIS      3.3     4.0    -      -       -      -
    676A  MET*     3.0    33.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 661 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  VAL*     5.5     2.0    -      -       +      -
    389A  TYR*     3.4    27.4    -      +       -      -
    513A  THR*     3.2    17.7    -      -       +      +
    515A  MET*     4.9     3.1    -      -       +      -
    529A  MET*     3.1    47.3    -      -       +      +
    659A  PHE*     3.8    19.9    -      +       +      +
    660A  SER*     1.3    71.8    -      -       -      +
    662A  ARG*     1.3    62.9    +      -       -      +
    663A  VAL*     3.4     9.0    +      -       +      +
    673A  PHE      3.6     0.3    -      -       -      +
    674A  THR*     3.3     2.2    -      -       -      -
    675A  HIS*     2.7    49.8    +      -       +      +
    677A  THR*     3.3    34.5    -      -       +      -
    679A  THR      3.1    17.3    +      -       -      -
    680A  PHE      3.7     1.4    +      -       -      -
    681A  PRO*     3.5    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 662 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464A  ALA*     4.6     4.4    -      -       -      +
    465A  ALA*     3.9    23.4    +      -       -      +
    468A  GLU*     2.5    47.8    +      -       -      +
    512A  ASP*     2.6    45.8    +      -       +      +
    513A  THR      2.9    12.6    +      -       -      +
    514A  SER*     3.9    15.4    -      -       -      +
    515A  MET*     3.3    22.2    +      -       -      +
    661A  TYR*     1.3    69.8    -      -       -      +
    663A  VAL*     1.3    63.0    +      -       -      +
    664A  ASN*     3.8    13.7    +      -       -      +
    673A  PHE      3.8     4.5    -      -       -      -
    674A  THR*     3.9    10.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 663 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  PRO*     4.6     5.8    -      -       +      -
    382A  THR      4.6     9.6    -      -       -      +
    385A  VAL*     3.6    36.3    -      -       +      -
    515A  MET*     4.7     9.4    -      -       +      -
    661A  TYR*     3.8    12.6    -      -       +      +
    662A  ARG*     1.3    74.4    -      -       -      +
    664A  ASN*     1.3    64.2    +      -       -      +
    665A  ASP*     4.2     9.6    -      -       +      +
    672A  ASP*     3.4     5.9    -      -       -      -
    673A  PHE*     2.8    75.0    +      -       +      +
    675A  HIS*     4.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 664 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  PRO*     5.3     3.1    -      -       -      +
    514A  SER*     5.8     2.0    +      -       -      -
    515A  MET      5.8     1.8    +      -       -      -
    662A  ARG*     3.8    15.6    +      -       -      +
    663A  VAL*     1.3    75.1    -      -       -      +
    665A  ASP*     1.3    58.9    +      -       -      +
    666A  SER*     2.9    13.2    +      -       -      -
    672A  ASP*     2.6    28.9    -      -       -      +
----------------------------------------------------------
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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