Contacts of the strand formed by residues 150 - 155 (chain 9) 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 GLY 150 (chain 9).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1429  LEU*     3.8    13.6    -      -       -      +
    1499  THR*     1.3    77.8    -      -       -      +
    1519  ILE*     1.3    62.7    +      -       -      +
    1639  VAL      4.8     0.2    -      -       -      -
    1649  PRO*     3.7     0.9    -      -       -      +
    1659  ILE*     2.9    28.2    +      -       -      +
    2939  LEU*     3.8    12.7    -      -       -      +
    2969  ASN*     3.2    21.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain 9). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1429  LEU*     4.9     0.2    -      -       -      -
    1509  GLY*     1.3    75.7    -      -       -      +
    1529  VAL*     1.3    65.3    +      -       -      +
    1539  LEU      4.0     0.9    +      -       -      -
    1629  ASN*     4.5     6.1    -      -       +      +
    1639  VAL      3.7     8.7    -      -       -      +
    1649  PRO*     3.9    21.5    -      -       +      -
    2789  THR*     3.6    29.8    -      -       +      +
    2819  SER*     3.6    21.8    -      -       -      +
    2829  ILE*     3.7    12.3    -      -       +      -
    2939  LEU*     3.4    33.2    -      -       +      +
    2969  ASN      2.8     8.2    +      -       -      +
    2979  ASN*     3.4    20.9    -      -       -      +
    2989  VAL*     2.9    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain 9). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1389  ALA*     3.3    41.5    -      -       +      +
    1419  SER*     4.3     2.9    -      -       -      -
    1429  LEU*     3.8    30.7    -      -       +      +
    1519  ILE*     1.3    74.4    -      -       -      +
    1539  LEU*     1.3    67.3    +      -       -      +
    1549  ASP*     3.6     9.8    +      -       +      -
    1619  HIS      4.1     0.2    -      -       -      -
    1629  ASN*     3.2     6.8    -      -       -      +
    1639  VAL*     2.9    32.6    +      -       -      +
    1659  ILE*     4.5     1.6    -      -       +      -
    2989  VAL*     3.1    14.8    -      -       +      +
    3009  SER*     3.6    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 153 (chain 9). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1519  ILE      4.0     1.0    +      -       -      -
    1529  VAL*     1.3    71.7    -      -       -      +
    1549  ASP*     1.3    60.0    +      -       -      +
    1559  SER*     5.1     2.0    -      -       -      -
    1609  THR*     4.4     8.1    -      -       +      -
    1619  HIS      3.4     8.3    -      -       -      +
    1629  ASN*     3.6    24.2    -      -       -      +
    2749  ILE*     3.6    41.3    -      -       +      +
    2789  THR*     3.9     9.9    -      -       -      +
    2979  ASN*     4.5    12.9    -      -       -      +
    2989  VAL      2.9     8.2    +      -       -      +
    2999  MET*     3.6    33.0    -      -       +      -
    3009  SER      3.1    25.1    +      -       -      +
    3049  THR*     4.0    13.7    -      -       +      -
    3099  ILE*     5.7     4.9    -      -       +      -
    3139  MET*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 154 (chain 9). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1099  PRO*     5.9     2.7    -      -       +      +
    1379  GLN*     4.0    26.2    -      -       -      +
    1389  ALA*     4.1    11.1    +      -       +      -
    1529  VAL*     3.6    12.9    +      -       +      +
    1539  LEU*     1.3    73.8    -      -       -      +
    1559  SER*     1.4    65.6    +      -       -      +
    1599  VAL      4.0     0.9    -      -       -      +
    1609  THR*     3.2     3.0    -      -       -      +
    1619  HIS*     2.7    50.4    +      -       +      +
    3009  SER*     3.0    29.3    +      -       -      +
    3019  GLY*     4.0     4.3    +      -       -      -
    3399  VAL*     4.2     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 155 (chain 9). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1539  LEU*     5.1     3.1    -      -       -      -
    1549  ASP*     1.4    76.1    +      -       -      +
    1569  GLY*     1.3    60.7    +      -       -      +
    1599  VAL      3.6     3.6    -      -       -      -
    1609  THR*     2.6    27.8    +      -       -      +
    1809  LEU      4.6     0.5    +      -       -      -
    1819  ALA*     4.5     1.9    -      -       -      +
    2619  LEU*     4.8     5.1    -      -       -      +
    2749  ILE*     5.5     1.1    -      -       -      +
    3009  SER      3.1     8.7    +      -       -      -
    3019  GLY*     3.2    13.8    -      -       -      -
    3039  THR*     3.1    38.1    +      -       -      +
    3049  THR*     3.6    19.1    -      -       -      -
----------------------------------------------------------
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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