Contacts of the strand formed by residues 668 - 675 (chain P) in PDB entry 1MVW


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 HIS 668 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121P  LEU*     6.2     0.2    -      -       -      +
    165P  PHE*     4.5    22.7    -      +       -      -
    169P  ASP*     4.7     5.1    +      -       -      -
    171P  GLU*     4.2    17.4    +      -       -      +
    172P  ASN      2.7    15.0    +      -       -      +
    173P  GLN*     2.6    28.4    +      -       -      +
    174P  SER      3.2    16.1    +      -       -      -
    494P  HIS*     3.6    21.2    +      +       -      -
    498P  LEU*     5.3     4.0    -      -       -      +
    667P  THR*     1.3    70.2    -      -       -      +
    669P  PRO*     1.3    86.6    +      -       +      +
    670P  HIS*     3.3    25.6    +      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 669 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121P  LEU*     5.5     2.4    -      -       -      +
    174P  SER*     3.1    11.0    -      -       -      +
    176P  LEU*     4.5     1.6    -      -       +      -
    490P  PHE*     3.5    37.7    -      -       +      -
    494P  HIS*     3.6    37.4    +      -       +      +
    667P  THR      3.1    13.2    -      -       -      +
    668P  HIS*     1.3   106.8    +      -       +      +
    670P  HIS*     1.3    63.6    +      -       -      +
    671P  PHE*     3.7    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 670 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121P  LEU*     6.2     2.6    -      -       -      +
    158P  ILE*     4.5    18.2    +      -       +      +
    161P  ASN*     5.2     3.1    -      -       +      +
    162P  ALA*     4.1    13.6    -      -       +      -
    165P  PHE*     3.9    23.3    -      +       -      -
    173P  GLN*     3.2    34.0    +      -       +      +
    174P  SER*     2.7    17.7    +      -       -      +
    175P  ILE*     2.9    18.3    -      -       +      -
    176P  LEU*     2.7    33.1    +      -       -      +
    668P  HIS*     3.3    41.8    +      +       -      -
    669P  PRO*     1.3    72.0    +      -       -      +
    671P  PHE*     1.3    55.5    +      -       -      +
    672P  VAL*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 671 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121P  LEU*     3.7    19.8    +      -       +      +
    122P  PHE*     3.7    21.5    -      +       +      -
    123P  CYS*     3.5    18.2    +      -       -      +
    158P  ILE*     4.4     4.6    -      -       -      +
    176P  LEU*     3.9    24.7    -      -       +      -
    487P  LEU*     4.8     3.4    -      -       +      -
    490P  PHE*     4.1     8.5    -      +       -      -
    491P  PHE*     3.2    57.4    -      +       +      -
    494P  HIS*     4.2    15.3    -      +       -      -
    669P  PRO*     3.7    31.4    -      -       +      -
    670P  HIS*     1.3    71.8    -      -       -      +
    672P  VAL*     1.3    68.0    +      -       -      +
    673P  ARG*     3.9    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 672 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123P  CYS*     3.8    16.6    -      -       +      +
    125P  THR*     4.9     2.2    -      -       -      +
    155P  ILE*     4.5    24.2    -      -       +      -
    158P  ILE*     4.2    20.2    -      -       +      -
    175P  ILE*     3.8    23.6    -      -       +      -
    176P  LEU      2.8    21.5    +      -       -      +
    177P  ILE*     3.4    21.5    -      -       +      -
    178P  THR      3.3    12.3    +      -       -      -
    192P  VAL*     6.4     1.1    -      -       +      -
    671P  PHE*     1.3    78.7    -      -       -      +
    673P  ARG*     1.3    69.7    +      -       -      +
    674P  CYS*     4.5    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 673 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122P  PHE*     3.9    29.4    -      -       +      -
    123P  CYS      3.3    11.3    +      -       -      +
    124P  VAL*     3.4     5.6    -      -       -      -
    125P  THR      3.0    23.7    +      -       -      -
    176P  LEU*     3.0    36.2    +      -       -      +
    178P  THR*     3.6    31.0    +      -       -      +
    484P  ASN*     5.4     2.8    +      -       -      -
    487P  LEU*     5.2    15.8    -      -       -      +
    488P  GLN*     4.6     8.5    +      -       -      +
    491P  PHE*     5.9     1.6    -      -       -      +
    671P  PHE*     3.9    21.7    -      -       -      -
    672P  VAL*     1.3    76.5    +      -       -      +
    674P  CYS*     1.3    62.2    +      -       -      +
    675P  ILE*     3.9     5.5    -      -       +      +
    698P  ASN*     3.2    50.0    +      -       +      +
    700P  VAL*     4.7     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 674 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125P  THR*     3.6     8.1    -      -       +      +
    177P  ILE*     3.5    28.0    -      -       -      -
    178P  THR      2.9    13.3    +      -       -      +
    179P  GLY*     3.7    10.6    -      -       -      -
    183P  ALA*     3.4    31.9    -      -       +      +
    185P  LYS*     4.2     7.4    -      -       +      -
    188P  ASN*     2.9    32.5    -      -       -      +
    672P  VAL*     4.5     7.2    -      -       -      -
    673P  ARG*     1.3    74.7    -      -       -      +
    675P  ILE*     1.3    63.7    +      -       -      +
    694P  GLN*     4.6     2.6    -      -       -      +
    698P  ASN*     4.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 675 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106P  LEU*     5.4     2.2    -      -       +      -
    124P  VAL*     3.0    34.3    -      -       +      -
    125P  THR      2.5    18.8    +      -       -      +
    126P  VAL*     3.6    22.9    -      -       +      -
    127P  ASN*     3.1    28.8    +      -       -      +
    183P  ALA*     3.9     7.6    +      -       -      +
    673P  ARG*     3.9     9.4    -      -       +      +
    674P  CYS*     1.3    75.9    -      -       -      +
    676P  ILE*     1.3    71.4    +      -       -      +
    677P  PRO*     3.5     0.8    -      -       +      +
    691P  VAL*     4.3    18.2    -      -       +      -
    694P  GLN*     4.1    17.0    -      -       +      +
    695P  LEU*     4.7    11.9    -      -       +      -
    698P  ASN*     3.7    23.6    -      -       -      +
    700P  VAL*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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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