Contacts of the strand formed by residues 184 - 190 (chain B) 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 GLN 184 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  LEU      3.0     6.9    +      -       -      +
    148B  ASP*     3.5    11.2    -      -       -      +
    149B  ILE*     2.9    26.3    +      -       -      +
    178B  ILE*     4.8     2.7    -      -       +      -
    179B  GLY      3.8    12.8    -      -       -      +
    180B  PRO*     4.1    17.2    -      -       -      +
    183B  THR*     1.3    73.1    -      -       -      +
    185B  VAL*     1.3    68.5    +      -       -      +
    200B  LEU*     3.3    26.8    +      -       +      +
    201B  ASN*     3.5    19.0    -      -       -      +
    203B  TYR      5.2     4.9    +      -       -      +
    243B  GLY      2.7    25.5    -      -       -      +
    245B  ARG*     3.4    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  ILE*     3.1    16.4    -      -       +      +
    151B  ILE*     4.2    11.9    -      -       +      -
    173B  LEU*     3.8    33.0    -      -       +      -
    176B  MET*     4.4     5.4    -      -       +      -
    178B  ILE*     4.2    19.3    -      -       +      +
    183B  THR*     4.3    10.1    +      -       +      -
    184B  GLN*     1.3    82.4    -      -       -      +
    186B  GLY*     1.3    68.6    +      -       -      +
    187B  ILE*     4.3     2.9    -      -       +      -
    198B  PHE*     3.0    27.1    -      -       +      -
    199B  ASN      3.4    10.9    -      -       -      +
    200B  LEU*     3.7     9.1    +      -       -      +
    203B  TYR*     5.6     0.9    +      -       -      -
    209B  VAL*     4.5    12.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  ILE      2.9     7.9    +      -       -      +
    150B  VAL*     3.2     9.7    -      -       -      -
    151B  ILE      2.7    25.5    +      -       -      -
    185B  VAL*     1.3    75.8    -      -       -      +
    187B  ILE*     1.3    65.5    +      -       -      +
    188B  VAL*     5.6     0.2    -      -       -      -
    198B  PHE*     3.2    15.5    -      -       -      -
    199B  ASN*     4.7     0.2    -      -       -      -
    200B  LEU*     3.6    15.3    -      -       -      +
    237B  ALA*     6.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  ILE*     3.4    30.5    -      -       +      +
    153B  LEU*     3.8    18.4    -      -       +      -
    169B  LEU*     3.6    27.4    -      -       +      -
    173B  LEU*     4.8     2.7    -      -       +      -
    185B  VAL*     4.3     2.7    -      -       +      -
    186B  GLY*     1.3    78.8    -      -       -      +
    188B  VAL*     1.3    68.4    +      -       -      +
    196B  HIS*     3.8     1.4    -      -       -      -
    197B  GLU*     2.9    38.5    +      -       +      +
    198B  PHE*     3.1    38.8    +      -       +      +
    213B  ALA*     4.5     6.1    -      -       +      -
    216B  ILE*     3.8    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  VAL*     4.2    16.2    -      -       +      -
    151B  ILE      2.7    12.3    +      -       -      +
    152B  VAL*     3.3    10.6    -      -       +      +
    153B  LEU*     2.7    34.7    +      -       -      +
    187B  ILE*     1.3    80.0    -      -       -      +
    189B  GLN*     1.3    58.4    -      -       -      +
    194B  VAL*     3.4    28.9    -      -       +      -
    195B  THR      3.6     5.8    -      -       -      +
    196B  HIS*     4.0    24.2    -      -       +      +
    229B  GLY*     4.2    15.3    -      -       -      +
    232B  THR*     4.9     1.6    -      -       +      -
    233B  ALA*     4.4     9.0    -      -       +      -
    237B  ALA*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  LEU*     3.2    16.4    -      -       +      +
    155B  GLY*     3.6    16.4    -      -       -      +
    162B  TRP*     3.9    12.0    -      -       +      -
    187B  ILE*     4.3     0.6    +      -       +      -
    188B  VAL*     1.3    76.3    -      -       -      +
    190B  TYR*     1.3    69.5    +      -       -      +
    194B  VAL*     3.4     3.8    -      -       -      +
    195B  THR*     2.9    36.8    +      -       -      +
    197B  GLU*     3.1    26.6    +      -       +      +
    216B  ILE*     3.7    10.9    -      -       +      +
    217B  VAL      3.1    21.8    +      -       -      -
    218B  GLN*     3.6     2.1    -      -       -      -
    219B  ARG*     2.8    39.7    +      -       +      +
    220B  GLY      5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  VAL*     3.7    30.1    -      -       +      -
    153B  LEU      2.9    31.6    +      -       -      -
    154B  ASP*     3.6    17.0    -      -       +      -
    155B  GLY*     2.9    27.7    +      -       -      -
    156B  SER      3.6     1.0    +      -       -      -
    188B  VAL*     5.3     0.2    -      -       +      -
    189B  GLN*     1.3    76.6    -      -       -      +
    191B  GLY*     1.3    60.8    +      -       -      +
    193B  ASN      3.3    10.5    -      -       -      +
    194B  VAL*     4.1     6.1    -      -       +      -
    220B  GLY      4.9     1.3    -      -       -      -
    224B  THR*     3.7    13.7    -      -       +      -
    225B  MET*     3.5    21.8    -      -       +      +
    226B  THR*     2.9    44.9    +      -       +      +
    229B  GLY*     4.0    17.7    -      -       -      +
    254B  ILE*     4.6     2.3    -      -       +      +
    256B  THR*     3.2    26.3    +      -       -      +
----------------------------------------------------------
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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