Contacts of the strand formed by residues 150 - 155 (chain 6) 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 6).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1426  LEU*     3.8    13.9    -      -       -      +
    1496  THR*     1.3    77.6    -      -       -      +
    1516  ILE*     1.3    61.0    +      -       -      +
    1646  PRO*     3.7     0.3    -      -       -      +
    1656  ILE*     2.9    28.2    +      -       -      +
    2926  ASP      4.8     0.2    -      -       -      -
    2936  LEU*     3.8    13.0    -      -       -      +
    2966  ASN*     3.2    21.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 151 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1426  LEU*     4.4     0.6    -      -       -      +
    1506  GLY*     1.3    75.5    -      -       -      +
    1526  VAL*     1.3    64.9    +      -       -      +
    1536  LEU      4.0     0.3    +      -       -      -
    1626  ASN*     4.5     6.5    -      -       +      +
    1636  VAL      3.7     8.3    -      -       -      +
    1646  PRO*     3.9    22.0    -      -       +      -
    2786  THR*     3.6    29.6    -      -       +      +
    2816  SER*     3.6    21.3    -      -       -      +
    2826  ILE*     3.7    13.2    -      -       +      -
    2936  LEU*     3.4    33.2    -      -       +      +
    2966  ASN      2.8     8.7    +      -       -      +
    2976  ASN*     3.4    20.4    -      -       -      +
    2986  VAL      2.9    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1386  ALA*     3.3    41.1    -      -       +      +
    1416  SER*     4.3     2.7    -      -       -      -
    1426  LEU*     3.8    30.1    -      -       +      +
    1516  ILE*     1.3    75.1    -      -       -      +
    1536  LEU*     1.3    67.7    +      -       -      +
    1546  ASP*     3.6    10.2    +      -       +      -
    1616  HIS      4.1     0.2    -      -       -      -
    1626  ASN*     3.2     6.7    -      -       -      +
    1636  VAL*     2.9    32.6    +      -       -      +
    1656  ILE*     4.5     1.3    -      -       +      -
    2986  VAL*     3.1    14.8    -      -       +      +
    3006  SER*     3.6    24.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 153 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1516  ILE      4.0     1.2    +      -       -      -
    1526  VAL*     1.3    71.9    -      -       -      +
    1546  ASP*     1.3    58.4    +      -       -      +
    1556  SER*     5.1     2.5    -      -       -      -
    1606  THR*     4.4     9.0    -      -       +      -
    1616  HIS      3.4     7.9    -      -       -      +
    1626  ASN*     3.6    25.1    -      -       -      +
    2746  ILE*     3.6    40.8    -      -       +      +
    2786  THR*     3.9    10.3    -      -       -      +
    2976  ASN*     4.5    14.2    -      -       -      +
    2986  VAL      2.9     7.4    +      -       -      +
    2996  MET*     3.6    34.5    -      -       +      -
    3006  SER      3.1    24.6    +      -       -      +
    3046  THR*     4.0    13.5    -      -       +      -
    3096  ILE*     5.7     4.9    -      -       +      -
    3136  MET*     4.5     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 154 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1096  PRO*     5.9     2.6    -      -       +      +
    1376  GLN*     4.0    26.0    -      -       -      +
    1386  ALA*     4.1    10.4    +      -       +      +
    1526  VAL*     3.6    12.7    +      -       +      +
    1536  LEU*     1.3    73.8    -      -       -      +
    1556  SER*     1.4    64.5    +      -       -      +
    1596  VAL      4.0     1.1    -      -       -      +
    1606  THR*     3.2     3.3    -      -       -      +
    1616  HIS*     2.7    50.5    +      -       +      +
    3006  SER*     3.0    30.7    +      -       -      +
    3016  GLY*     4.0     5.0    +      -       -      -
    3396  VAL*     4.2     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 155 (chain 6). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1536  LEU*     5.1     3.6    -      -       -      -
    1546  ASP*     1.4    75.2    +      -       -      +
    1566  GLY*     1.3    60.4    +      -       -      +
    1596  VAL      3.6     3.8    -      -       -      -
    1606  THR*     2.6    27.9    +      -       -      +
    1806  LEU      4.6     0.7    +      -       -      -
    1816  ALA*     4.5     2.6    -      -       -      +
    2616  LEU*     4.8     4.6    -      -       -      +
    2746  ILE*     5.5     0.8    -      -       -      +
    3006  SER      3.1     8.7    +      -       -      -
    3016  GLY*     3.2    13.4    -      -       -      -
    3036  THR*     3.1    39.1    +      -       -      +
    3046  THR*     3.6    19.5    -      -       -      -
----------------------------------------------------------
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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