Contacts of the strand formed by residues 160 - 166 (chain 7) 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 THR 160 (chain 7).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1537  LEU*     4.4     6.3    -      -       +      -
    1547  ASP      3.2     9.4    -      -       -      +
    1557  SER*     2.6    25.1    +      -       -      +
    1597  VAL*     1.4    72.2    -      -       -      +
    1617  HIS*     1.3    74.6    +      -       -      +
    1627  ASN*     5.0     2.9    -      -       -      +
    1777  ARG*     3.3     5.9    -      -       -      +
    1787  LEU*     2.9    46.3    +      -       +      -
    1807  LEU      3.1    16.7    +      -       -      -
    1817  ALA*     4.3     0.2    -      -       -      +
    2617  LEU*     5.1     0.3    -      -       -      +
    2747  ILE*     3.6    32.0    -      -       +      +
    2777  THR*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     737  HIS      5.2     0.7    -      -       -      -
    1087  ALA*     4.9     7.0    -      -       +      -
    1097  PRO*     3.6    41.2    -      -       +      +
    1107  LEU*     5.2     3.8    +      -       -      +
    1527  VAL      4.1     0.2    -      -       -      -
    1537  LEU*     3.4     4.7    -      -       -      +
    1547  ASP*     2.7    41.7    +      -       +      +
    1597  VAL*     4.0    31.6    -      -       +      +
    1607  THR*     1.3    80.4    +      -       -      +
    1627  ASN*     1.3    66.4    +      -       -      +
    1637  VAL*     4.2    11.2    -      -       +      -
    1757  ILE*     4.0     8.7    -      -       +      +
    1767  MET      3.0    17.3    -      -       -      -
    1777  ARG*     3.7    28.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 162 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1517  ILE*     4.5     6.0    -      -       +      +
    1527  VAL      3.2     6.9    +      -       -      +
    1537  LEU*     3.6    21.3    -      -       -      +
    1607  THR*     5.0     2.3    -      -       -      +
    1617  HIS*     1.3    75.1    +      -       -      +
    1637  VAL*     1.3    63.6    +      -       -      +
    1647  PRO*     3.5     1.6    -      -       -      +
    1757  ILE*     3.2    25.1    -      -       -      +
    1767  MET*     2.9    14.5    +      -       +      +
    1787  LEU*     5.8     0.5    +      -       -      +
    2777  THR*     2.9    30.9    -      -       -      +
    2787  THR*     3.4    34.6    +      -       -      +
    2817  SER*     3.6    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1097  PRO*     3.5    33.4    -      -       +      -
    1367  ILE*     5.1     2.5    -      -       +      -
    1387  ALA*     3.4    21.8    -      -       +      -
    1397  VAL*     5.0     0.9    -      -       +      -
    1517  ILE*     4.2     0.6    -      -       -      +
    1527  VAL*     2.9    28.7    +      -       -      +
    1547  ASP*     5.8     0.7    -      -       +      -
    1617  HIS*     4.2     9.2    -      -       +      -
    1627  ASN*     1.3    78.1    -      -       -      +
    1647  PRO*     1.3    62.6    -      -       -      +
    1657  ILE*     3.5    17.0    +      -       +      +
    1707  ALA*     3.6    30.5    -      -       +      -
    1757  ILE*     3.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1507  GLY      3.7     6.7    -      -       -      +
    1517  ILE*     3.9    16.2    -      -       +      -
    1627  ASN      3.5     7.0    -      -       -      +
    1637  VAL*     1.3    84.0    -      -       -      +
    1657  ILE*     1.3    59.8    +      -       -      +
    1707  ALA*     3.6     0.3    -      -       -      -
    1717  LEU*     2.8    36.3    +      -       +      +
    1747  ALA*     3.7    15.9    -      -       +      -
    1757  ILE*     4.0    18.4    -      -       +      +
    2817  SER*     3.4    20.9    -      -       -      +
    2857  CYS*     3.8    20.6    -      -       -      -
    2937  LEU*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1387  ALA*     3.7     9.6    -      -       +      +
    1397  VAL*     3.5    40.6    -      -       +      +
    1427  LEU*     3.9    18.2    -      -       +      -
    1487  THR      3.4    16.6    -      -       -      +
    1497  THR*     3.1    23.9    -      -       -      +
    1507  GLY      2.9    13.1    +      -       -      +
    1527  VAL*     4.5     2.9    -      -       +      -
    1637  VAL*     3.5    21.1    +      -       +      +
    1647  PRO*     1.3    73.6    -      -       -      +
    1667  TYR*     1.3    61.6    +      -       -      +
    1687  GLY*     3.6    25.8    -      -       -      +
    1697  TYR      3.7     3.1    -      -       -      +
    1707  ALA*     3.6    16.2    -      -       +      -
    1717  LEU*     4.7     1.3    -      -       -      -
    2937  LEU*     4.3     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain 7). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1497  THR*     3.6    18.6    -      -       +      -
    1647  PRO      4.4     0.2    -      -       -      -
    1657  ILE*     1.3    72.1    -      -       -      +
    1677  GLU*     1.3    90.5    +      -       +      +
    1687  GLY      2.9     4.8    +      -       -      -
    1697  TYR*     3.1    26.5    +      -       +      +
    1717  LEU*     4.3    21.3    -      -       +      +
    2897  ILE*     3.7    36.6    -      -       +      -
    2927  ASP*     4.0    17.0    +      -       -      -
     449  MET*     5.9     1.3    -      -       +      -
     609  SER      4.8     9.2    +      -       -      -
     619  LYS*     6.1     2.1    -      -       +      +
----------------------------------------------------------
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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