Contacts of the strand formed by residues 297 - 300 (chain 2) 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 ASN 297 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1512  ILE*     3.4    20.5    +      -       -      +
    1532  LEU*     4.5    14.5    -      -       -      +
    2782  THR*     3.2    33.6    +      -       -      +
    2822  ILE*     4.6     1.9    -      -       -      +
    2932  LEU      3.7     3.3    +      -       -      +
    2942  TYR*     5.0     2.3    -      -       -      +
    2962  ASN*     1.3    70.1    -      -       -      +
    2982  VAL*     1.3    62.3    +      -       -      +
    2992  MET*     4.8     2.4    -      -       -      -
    3132  MET*     4.4    12.9    -      -       -      +
    3172  ILE*     3.9    10.2    -      -       -      +
    3282  LYS      2.9    16.2    +      -       -      +
    3292  ILE*     3.5    26.6    -      -       +      +
    3302  ILE      2.7    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1412  SER*     4.5     9.2    -      -       -      +
    1422  LEU*     3.7    33.9    -      -       +      -
    1452  SER*     3.5    27.6    -      -       -      +
    1472  ARG*     4.3     9.2    -      -       -      -
    1512  ILE      2.9     6.6    +      -       -      +
    1522  VAL*     3.1    20.9    -      -       +      +
    1532  LEU*     2.9    26.0    +      -       -      +
    2962  ASN      3.4     2.7    +      -       -      +
    2972  ASN*     1.3    76.2    -      -       -      +
    2992  MET*     1.3    72.1    +      -       -      +
    3002  SER*     5.3     0.2    -      -       -      -
    3302  ILE*     3.3    18.2    -      -       +      +
    3322  PRO*     5.3     4.0    -      -       +      -
    3382  SER*     5.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 299 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1532  LEU*     3.6    37.0    -      -       +      -
    2972  ASN*     4.8     5.6    -      -       -      -
    2982  VAL*     1.3    77.9    -      -       -      +
    3002  SER*     1.3    64.1    +      -       -      +
    3042  THR*     3.8    17.9    -      -       -      +
    3092  ILE*     4.3    13.2    -      -       +      -
    3102  ALA*     4.0    15.3    -      -       -      +
    3132  MET*     4.8    10.8    -      -       -      -
    3292  ILE*     3.6    31.0    -      -       +      -
    3302  ILE      2.8    11.5    +      -       -      +
    3312  ALA*     3.4    30.1    -      -       +      -
    3322  PRO*     3.9    10.9    -      -       -      +
    3352  ARG*     3.8    12.8    -      -       -      +
    3382  SER*     4.4     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 300 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1412  SER*     3.0    34.3    +      -       -      -
    1522  VAL*     3.6     5.1    -      -       -      +
    1532  LEU      3.1     9.3    +      -       -      +
    1542  ASP*     3.0    23.8    +      -       -      +
    1552  SER      3.1    21.1    +      -       -      -
    2982  VAL      4.2     0.2    +      -       -      -
    2992  MET*     1.3    77.8    -      -       -      +
    3012  GLY*     1.3    60.0    +      -       -      +
    3042  THR*     3.3    10.3    -      -       -      +
    3352  ARG*     4.0     5.2    -      -       -      -
    3382  SER*     3.7    15.0    -      -       -      -
    3392  VAL*     4.5     2.2    -      -       -      +
----------------------------------------------------------
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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