Contacts of the strand formed by residues 84 - 89 (chain L) 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 THR 84 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35L  TYR      4.0     0.5    -      -       -      +
     37L  GLN*     3.0    51.5    +      -       +      +
     39L  PRO*     5.5     3.4    -      -       +      -
     83L  ALA*     1.3    78.7    -      -       -      +
     85L  TYR*     1.3    62.4    +      -       -      +
     86L  TYR*     4.0    23.1    +      -       +      +
    100L  GLY      4.4     1.4    -      -       -      -
    101L  THR      3.3    19.7    +      -       -      -
    102L  LYS*     3.9    29.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     2.8    28.2    +      -       -      -
     21L  ILE*     3.9    17.7    -      -       +      -
     34L  TRP*     4.6     3.1    -      -       +      -
     35L  TYR      3.3     7.0    -      -       -      +
     36L  GLN*     3.5    34.7    +      -       +      -
     46L  TRP*     3.9     8.3    -      +       -      -
     61L  PHE*     3.3    35.7    -      +       -      -
     72L  LEU*     3.4    26.7    -      -       +      -
     74L  ILE*     4.5     4.3    -      -       +      -
     81L  ASP*     2.6    29.6    +      -       -      +
     83L  ALA      3.6    22.0    -      -       -      -
     84L  THR*     1.3    73.3    -      -       -      +
     86L  TYR*     1.3    57.2    +      -       -      +
    101L  THR      2.8    22.8    +      -       -      -
    103L  VAL*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 86 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.2    22.1    +      -       -      -
     43H  LYS      4.1     5.5    +      -       -      -
     44H  GLY*     4.1    14.1    -      -       -      -
     45H  LEU*     3.5    31.0    -      -       +      -
      6L  GLN*     3.2     4.9    -      -       -      +
     34L  TRP*     3.1     8.1    -      -       -      -
     35L  TYR*     2.8    46.2    +      -       +      +
     37L  GLN*     3.4    29.6    +      -       +      -
     84L  THR*     4.0    24.4    +      -       +      +
     85L  TYR*     1.3    74.6    -      -       -      +
     87L  CYS*     1.3    64.7    +      -       -      +
     97L  PHE*     4.5     6.7    -      -       +      -
     98L  GLY      3.6    11.7    -      -       -      -
     99L  GLN      3.6    10.3    -      -       -      -
    100L  GLY*     3.3    26.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 87 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  LEU*     4.3     1.6    -      -       -      -
      6L  GLN*     2.8    30.5    +      -       -      -
     23L  CYS*     2.0    49.6    -      -       +      -
     32L  MET*     4.0     2.9    -      -       +      -
     33L  PHE      3.0     9.0    -      -       -      +
     34L  TRP*     3.5    23.3    -      -       +      -
     86L  TYR*     1.3    75.4    -      -       -      +
     88L  GLN*     1.3    61.3    +      -       -      +
     97L  PHE*     3.3     5.4    -      -       -      +
     98L  GLY*     2.9    30.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 88 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  GLY      3.0    24.4    +      -       -      +
    105H  PHE*     3.8     6.6    -      -       -      -
      4L  LEU*     3.7     1.6    -      -       -      -
     32L  MET*     3.1     8.7    -      -       -      +
     33L  PHE*     2.7    43.4    +      -       -      +
     35L  TYR*     2.7    43.9    +      -       +      -
     87L  CYS*     1.3    77.7    -      -       -      +
     89L  GLN*     1.3    86.0    +      -       -      +
     90L  TRP*     3.8     4.0    -      -       -      +
     95L  TRP*     4.3     8.5    -      -       +      +
     96L  THR      3.1    19.5    -      -       -      +
     97L  PHE*     3.9    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 89 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2L  ILE*     3.6    21.2    -      -       +      +
      4L  LEU*     3.4    30.7    -      -       +      +
     29L  VAL*     4.4     9.4    -      -       +      -
     31L  HIS      4.9     3.8    -      -       -      +
     32L  MET*     4.1    11.7    -      -       +      -
     33L  PHE*     4.9     1.8    -      -       -      -
     88L  GLN*     1.3    92.1    +      -       -      +
     90L  TRP*     1.3    56.3    +      -       -      +
     91L  SER*     3.3     4.2    +      -       -      -
     92L  GLY      2.9    43.4    +      -       -      -
     94L  PRO      3.4     3.8    +      -       -      -
     95L  TRP*     3.8     1.9    -      -       -      -
     96L  THR*     3.0    47.2    +      -       -      +
----------------------------------------------------------
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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