Contacts of the strand formed by residues 160 - 166 (chain 3) 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 3).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1533  LEU*     4.4     6.3    -      -       +      -
    1543  ASP      3.2     9.2    -      -       -      +
    1553  SER*     2.6    24.8    +      -       -      +
    1593  VAL*     1.4    71.8    -      -       -      +
    1613  HIS*     1.3    75.8    +      -       -      +
    1623  ASN*     5.0     3.1    -      -       -      +
    1773  ARG*     3.3     6.1    -      -       -      +
    1783  LEU*     2.9    45.6    +      -       +      -
    1803  LEU      3.1    16.9    +      -       -      -
    1813  ALA*     4.3     0.2    -      -       -      +
    2613  LEU*     5.1     0.3    -      -       -      +
    2743  ILE*     3.6    31.4    -      -       +      +
    2773  THR*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     733  HIS      5.2     1.1    -      -       -      -
    1083  ALA*     4.9     7.6    -      -       +      -
    1093  PRO*     3.6    40.9    -      -       +      +
    1103  LEU*     5.2     3.8    +      -       -      +
    1523  VAL      4.1     0.2    -      -       -      -
    1533  LEU*     3.4     4.7    -      -       -      -
    1543  ASP*     2.7    40.7    +      -       +      +
    1593  VAL*     4.0    32.1    -      -       +      +
    1603  THR*     1.3    80.8    +      -       -      +
    1623  ASN*     1.3    67.9    +      -       -      +
    1633  VAL*     4.2    11.9    -      -       +      -
    1753  ILE*     4.0     8.0    -      -       +      +
    1763  MET      3.0    17.3    -      -       -      -
    1773  ARG*     3.7    28.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 162 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1513  ILE*     4.5     6.0    -      -       +      +
    1523  VAL      3.2     6.7    +      -       -      +
    1533  LEU*     3.6    21.0    -      -       -      +
    1603  THR*     5.0     2.1    -      -       -      +
    1613  HIS*     1.3    75.1    +      -       -      +
    1633  VAL*     1.3    61.8    +      -       -      +
    1643  PRO*     3.5     2.7    -      -       -      +
    1753  ILE*     3.2    25.1    -      -       -      +
    1763  MET*     2.9    15.2    +      -       +      +
    1783  LEU*     5.8     0.3    +      -       -      +
    2773  THR*     2.9    30.7    -      -       -      +
    2783  THR*     3.4    34.8    +      -       -      +
    2813  SER*     3.6    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1093  PRO*     3.5    33.7    -      -       +      -
    1363  ILE*     5.1     2.5    -      -       +      -
    1383  ALA*     3.4    22.4    -      -       +      -
    1393  VAL*     5.0     0.9    -      -       +      -
    1513  ILE*     4.2     0.6    -      -       -      +
    1523  VAL      2.9    28.2    +      -       -      +
    1613  HIS*     4.2    10.3    -      -       +      -
    1623  ASN*     1.3    79.3    -      -       -      +
    1643  PRO*     1.3    62.6    -      -       -      +
    1653  ILE*     3.5    17.0    +      -       +      +
    1703  ALA*     3.6    31.2    -      -       +      -
    1753  ILE*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1503  GLY      3.7     7.0    -      -       -      +
    1513  ILE*     3.9    15.5    -      -       +      -
    1623  ASN      3.5     7.0    -      -       -      +
    1633  VAL*     1.3    82.9    -      -       -      +
    1653  ILE*     1.3    59.4    +      -       -      +
    1703  ALA*     3.6     0.3    -      -       -      -
    1713  LEU*     2.8    35.4    +      -       +      +
    1743  ALA*     3.7    15.9    -      -       +      -
    1753  ILE*     4.0    18.2    -      -       +      +
    2813  SER*     3.4    20.4    -      -       -      +
    2853  CYS*     3.8    21.5    -      -       -      -
    2933  LEU*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1383  ALA*     3.7     9.4    -      -       +      +
    1393  VAL*     3.5    40.8    -      -       +      +
    1423  LEU*     3.9    18.4    -      -       +      -
    1483  THR      3.4    16.6    -      -       -      +
    1493  THR*     3.1    24.1    -      -       -      +
    1503  GLY      2.9    13.3    +      -       -      +
    1523  VAL*     4.5     2.9    -      -       +      -
    1633  VAL*     3.6    20.9    -      -       +      +
    1643  PRO*     1.3    73.8    -      -       -      +
    1663  TYR*     1.3    61.8    +      -       -      +
    1683  GLY*     3.6    25.8    -      -       -      +
    1693  TYR      3.7     2.9    -      -       -      -
    1703  ALA*     3.6    16.2    -      -       +      -
    1713  LEU*     4.7     1.3    -      -       -      -
    2933  LEU*     4.3     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1493  THR*     3.6    17.9    -      -       +      -
    1653  ILE*     1.3    72.8    -      -       -      +
    1673  GLU*     1.3    89.9    +      -       +      +
    1683  GLY      2.9     4.8    +      -       -      -
    1693  TYR*     3.1    26.5    +      -       +      +
    1713  LEU*     4.3    21.0    -      -       +      +
    2893  ILE*     3.7    35.7    -      -       +      -
    2923  ASP*     4.0    17.5    +      -       -      -
     445  MET*     5.2     7.1    -      -       -      +
     605  SER      4.9     9.2    +      -       -      -
     615  LYS*     5.2     8.6    -      -       +      +
     645  ILE*     5.4    22.0    -      -       +      -
----------------------------------------------------------
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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