Contacts of the strand formed by residues 181 - 190 (chain H) in PDB entry 1MHP


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 TYR 181 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41H  PRO*     5.6     7.1    -      -       -      +
    115H  THR*     5.6     8.0    -      -       +      +
    149H  ASP      3.3     3.6    +      -       -      -
    150H  TYR*     2.8    54.2    +      -       +      +
    151H  PHE*     4.1    21.8    -      +       -      -
    152H  PRO*     4.2     3.1    -      -       +      -
    153H  GLU*     3.2    51.5    -      -       +      +
    173H  ALA*     4.0     4.9    -      -       +      -
    174H  VAL*     3.5    15.0    -      -       -      -
    175H  LEU*     3.6    42.3    -      -       +      +
    180H  LEU*     1.3    73.2    -      -       -      +
    182H  SER*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 182 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146H  LEU*     3.8    11.1    -      -       -      +
    147H  VAL      3.3    13.5    +      -       -      -
    148H  LYS*     3.7    14.3    +      -       -      +
    150H  TYR*     3.9     2.0    -      -       -      -
    172H  PRO      4.6     0.2    -      -       -      +
    173H  ALA*     3.4     2.0    -      -       -      -
    174H  VAL*     3.1    32.4    +      -       -      +
    176H  GLN*     3.5    27.4    -      -       -      -
    181H  TYR*     1.3    78.1    -      -       -      +
    183H  LEU*     1.3    66.1    +      -       -      +
    177L  THR*     6.1     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 183 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146H  LEU*     3.6     4.1    -      -       -      +
    147H  VAL*     2.8    57.0    +      -       +      +
    150H  TYR*     3.4    23.8    -      -       -      +
    153H  GLU*     5.3     1.6    -      -       -      +
    155H  VAL*     3.6    19.3    -      -       +      +
    157H  VAL*     4.5     3.4    -      -       +      -
    170H  THR*     4.0    15.3    -      -       -      +
    171H  PHE*     3.5    22.7    -      -       -      +
    172H  PRO*     4.2     3.4    -      -       +      +
    173H  ALA*     3.9    14.1    -      -       +      +
    182H  SER*     1.3    78.1    +      -       -      +
    184H  SER*     1.3    73.9    +      -       -      +
    185H  SER      4.3     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  LEU*     3.9    14.1    -      -       -      +
    145H  CYS      3.1    12.4    +      -       -      -
    146H  LEU*     3.3    25.1    -      -       -      +
    171H  PHE*     2.8    46.8    +      -       -      +
    183H  LEU*     1.3    77.9    -      -       -      +
    185H  SER*     1.3    59.8    +      -       -      +
    186H  VAL*     4.5     4.5    -      -       -      -
    132L  VAL*     4.3    14.9    -      -       -      +
    175L  SER*     5.5     3.4    -      -       -      -
    177L  THR*     5.0     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 185 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144H  GLY*     3.2     2.6    -      -       -      -
    145H  CYS*     2.7    35.5    +      -       -      +
    147H  VAL*     5.6     0.8    -      -       -      +
    157H  VAL*     3.4    26.9    -      -       -      +
    159H  TRP*     3.0    23.7    +      -       -      -
    168H  VAL*     4.0     1.4    -      -       -      +
    170H  THR*     2.8    35.6    +      -       -      +
    183H  LEU*     4.3     1.2    -      -       -      +
    184H  SER*     1.3    74.8    -      -       -      +
    186H  VAL*     1.3    57.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  LEU*     4.3    18.6    -      -       +      -
    142H  ALA*     4.9     0.4    -      -       +      -
    143H  LEU      3.5    14.8    -      -       -      +
    144H  GLY*     4.0     0.4    -      -       -      -
    159H  TRP*     4.9     0.7    -      -       -      -
    167H  GLY      3.7     0.4    -      -       -      +
    168H  VAL*     3.4     4.6    -      -       -      +
    169H  HIS*     2.5    49.4    +      -       +      +
    171H  PHE*     3.7    21.1    -      -       +      -
    184H  SER*     4.5     3.8    -      -       -      -
    185H  SER*     1.3    81.0    +      -       -      +
    187H  VAL*     1.3    69.8    +      -       -      +
    188H  THR*     5.2     1.8    -      -       +      -
    117L  PHE*     4.9     7.0    -      -       +      -
    132L  VAL*     5.9     2.7    -      -       +      -
    134L  LEU*     3.3    34.5    -      -       +      -
    136L  ASN*     5.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 187 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141H  ALA      4.1     0.2    -      -       -      +
    142H  ALA*     3.4     2.8    -      -       -      -
    143H  LEU*     2.9    66.4    +      -       +      +
    159H  TRP*     4.4    10.5    -      -       +      -
    164H  LEU*     4.1    18.8    -      -       +      -
    166H  SER      3.9     5.2    -      -       -      +
    167H  GLY      3.1    19.5    -      -       -      +
    168H  VAL*     3.8    17.7    -      -       +      -
    186H  VAL*     1.3    78.1    -      -       -      +
    188H  THR*     1.3    83.8    +      -       -      +
    189H  VAL*     4.0    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 188 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140H  THR*     4.8    10.5    -      -       -      +
    141H  ALA      3.2    10.3    -      -       -      +
    142H  ALA*     4.3    12.3    -      -       +      -
    166H  SER      4.2     7.3    -      -       -      +
    167H  GLY*     3.2    17.8    +      -       -      +
    169H  HIS*     6.0     0.4    -      -       +      -
    186H  VAL*     5.2     3.6    -      -       +      -
    187H  VAL*     1.3    84.5    -      -       -      +
    189H  VAL*     1.3    66.6    +      -       -      +
    115L  PHE*     4.6     8.7    -      -       +      -
    136L  ASN*     3.7    29.1    +      -       -      +
    137L  ASN*     5.3     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 189 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140H  THR*     3.4     7.4    -      -       -      -
    141H  ALA*     2.8    34.6    +      -       +      +
    143H  LEU*     4.0    13.0    -      -       +      -
    164H  LEU*     4.5     7.2    -      -       +      -
    166H  SER      5.8     0.2    -      -       -      +
    187H  VAL*     4.0    18.4    -      -       +      -
    188H  THR*     1.3    79.9    -      -       -      +
    190H  PRO*     1.3    73.2    -      -       +      +
    193H  SER*     3.7     4.9    -      -       -      +
    194H  LEU*     4.3     8.3    -      -       +      -
    199H  TYR*     3.2    53.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 190 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139H  GLY      3.7     8.3    -      -       -      +
    140H  THR*     4.6     1.6    -      -       +      -
    189H  VAL*     1.3    92.2    -      -       +      +
    191H  SER*     1.3    67.0    +      -       -      +
    192H  SER*     3.9    15.3    -      -       -      +
    193H  SER*     2.6    36.7    +      -       -      +
    194H  LEU*     4.4     0.2    -      -       -      +
    199H  TYR*     4.5     0.9    -      -       -      +
----------------------------------------------------------
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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