Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 1MVM


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 VAL 150 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ILE*     4.6     8.5    -      -       +      -
    148A  PHE      4.3     5.4    -      -       -      +
    149A  ASN*     1.3    75.1    -      -       -      +
    151A  VAL*     1.3    65.6    +      -       -      +
    152A  LEU*     4.2    16.2    -      -       +      -
    176A  MET*     4.0    27.6    -      -       +      -
    259A  LEU*     4.7    10.3    -      -       +      +
    260A  ARG      2.9    28.0    -      -       -      +
    261A  THR*     3.4    34.2    +      -       -      +
    263A  ASP      4.0    16.4    -      -       -      +
    524A  THR      3.4     5.6    -      -       -      +
    525A  PHE*     4.1    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ASN*     4.2     7.9    -      -       +      +
    150A  VAL*     1.3    78.3    -      -       -      +
    152A  LEU*     1.3    69.6    +      -       -      +
    153A  LYS*     3.9    34.3    -      -       +      +
    170A  ASN*     4.7     1.6    -      -       -      +
    176A  MET*     6.0     0.2    -      -       -      +
    261A  THR*     5.2     1.3    -      -       +      -
    522A  TYR*     6.2     0.7    -      -       +      -
    523A  GLY*     3.1     5.0    -      -       -      -
    524A  THR*     2.5    63.3    +      -       +      +
    526A  PHE*     6.3     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  VAL*     4.2    11.8    +      -       +      -
    151A  VAL*     1.3    84.1    -      -       -      +
    153A  LYS*     1.3    65.2    +      -       -      +
    170A  ASN*     3.6     6.6    -      -       -      +
    171A  ASP*     3.3    25.0    +      -       +      +
    172A  LEU*     5.6     0.7    -      -       -      +
    174A  ALA*     3.3    51.1    -      -       +      +
    175A  CYS*     3.7    13.7    -      -       -      +
    176A  MET*     4.8     5.4    -      -       +      -
    260A  ARG      4.4    13.2    -      -       -      +
    261A  THR*     5.0     7.7    +      -       -      +
    501A  LEU*     3.7    29.4    -      -       +      -
    521A  THR*     5.2     4.3    -      -       +      -
    522A  TYR      3.8     4.0    -      -       -      +
    523A  GLY*     4.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  VAL*     3.9    22.8    -      -       +      +
    152A  LEU*     1.3    75.0    -      -       -      +
    154A  THR*     1.3    67.0    +      -       -      +
    168A  TYR*     5.2     8.7    -      -       +      +
    169A  ASN      3.3    14.4    -      -       -      +
    170A  ASN*     2.8    33.8    -      -       -      +
    521A  THR*     3.8     5.6    -      -       -      +
    522A  TYR*     3.0    64.0    +      -       +      +
    523A  GLY*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LYS*     1.3    75.4    +      -       -      +
    155A  VAL*     1.3    69.8    +      -       -      +
    156A  THR*     5.5     4.9    -      -       +      -
    168A  TYR*     3.6     3.5    -      -       -      +
    169A  ASN*     2.7    47.2    +      -       -      +
    170A  ASN      4.7     1.0    +      -       -      -
    171A  ASP*     3.7    22.7    +      -       -      +
    504A  ASN*     4.5     6.5    +      -       -      +
    519A  ILE*     3.1    35.7    -      -       +      -
    520A  VAL      3.3    12.8    -      -       -      +
    521A  THR*     4.3     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  THR*     1.3    86.0    -      -       -      +
    156A  THR*     1.3    63.7    +      -       -      +
    157A  GLU*     3.9    16.5    +      -       -      +
    166A  LYS*     4.9    13.9    -      -       +      +
    167A  ILE      3.3     8.7    -      -       -      +
    168A  TYR*     3.5    20.2    -      -       +      -
    519A  ILE*     5.3     1.4    -      -       -      +
    520A  VAL*     3.5    39.0    +      -       +      +
    522A  TYR*     3.4    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  THR*     4.3     6.0    -      -       +      -
    155A  VAL*     1.3    77.2    -      -       -      +
    157A  GLU*     1.3    53.4    +      -       -      +
    158A  GLN*     2.7    31.2    +      -       -      +
    166A  LYS*     4.6     0.4    -      -       -      -
    167A  ILE*     3.0    36.8    +      -       -      +
    169A  ASN*     4.8    13.4    +      -       -      +
    519A  ILE*     6.3     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  VAL*     3.9    12.5    +      -       +      +
    156A  THR*     1.3    67.8    -      -       -      +
    158A  GLN*     1.3    59.6    +      -       -      +
    165A  ILE      4.2     3.8    -      -       -      -
    166A  LYS*     3.5    41.4    +      -       +      +
    520A  VAL*     4.9     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  THR*     2.7    18.1    +      -       -      +
    157A  GLU*     1.3    75.6    -      -       -      +
    159A  ASP*     1.3    72.0    +      -       -      +
    160A  SER*     5.6     0.4    -      -       -      -
    164A  ALA*     4.1     0.9    -      -       -      -
    165A  ILE*     2.0    34.3    +      -       -      +
    167A  ILE*     3.6    25.8    -      -       +      +
----------------------------------------------------------
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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