Contacts of the strand formed by residues 91 - 99 (chain X) 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 ALA 91 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38X  ARG*     4.7     9.4    -      -       +      -
     39X  GLN      2.9    37.7    -      -       -      +
     40X  ALA*     3.3     6.1    -      -       +      +
     41X  PRO*     3.8     9.9    -      -       -      -
     88X  GLU      5.2     0.4    -      -       -      +
     89X  ASP      3.3     7.2    +      -       -      +
     90X  THR*     1.3    77.4    -      -       -      +
     92X  VAL*     1.3    60.1    +      -       -      +
     93X  TYR*     3.3    11.2    -      -       -      -
    113X  LEU*     3.8    10.6    -      -       -      +
    114X  VAL      2.9    23.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 92 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38X  ARG*     3.5     2.4    -      -       -      -
     39X  GLN*     3.0    42.1    +      -       +      +
     41X  PRO*     5.9     2.5    -      -       +      -
     91X  ALA*     1.3    74.1    -      -       -      +
     93X  TYR*     1.3    62.2    +      -       -      +
     94X  TYR*     3.6    33.6    -      -       +      +
    110X  GLN      5.2     0.2    -      -       -      +
    111X  GLY*     3.7     5.6    -      -       -      -
    112X  THR      3.4    26.9    -      -       -      +
    113X  LEU*     4.1    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 93 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6X  GLU*     2.9    15.7    -      -       -      +
     20X  LEU*     3.3    30.3    -      -       +      -
     36X  TRP*     4.4     6.1    -      +       +      -
     37X  VAL      3.7     3.4    -      -       -      -
     38X  ARG*     2.9    49.3    +      -       +      -
     48X  VAL*     4.0    12.8    -      -       +      -
     67X  PHE*     4.1     1.3    -      +       -      -
     80X  LEU*     4.0    21.5    -      -       +      -
     82X  MET*     3.9    11.7    -      -       -      -
     89X  ASP*     2.7    33.9    +      -       -      +
     91X  ALA      3.3    17.3    -      -       -      -
     92X  VAL*     1.3    73.4    -      -       -      +
     94X  TYR*     1.3    62.8    +      -       -      +
    111X  GLY*     3.1    13.7    -      -       -      -
    112X  THR*     2.9    14.6    +      -       +      +
    114X  VAL*     3.7    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 94 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6X  GLU*     3.3     4.7    -      -       -      +
     36X  TRP*     3.2     9.1    -      -       -      -
     37X  VAL*     2.8    57.4    +      -       +      +
     39X  GLN*     3.6    19.6    +      -       +      -
     45X  LEU*     4.3     5.2    -      -       +      -
     92X  VAL*     3.6    28.0    -      -       +      +
     93X  TYR*     1.3    73.6    -      -       -      +
     95X  CYS*     1.3    66.0    +      -       -      +
     96X  THR*     4.2     0.4    -      -       +      +
    108X  TRP*     4.0    29.2    -      +       +      -
    109X  GLY      4.7     4.0    -      -       -      +
    110X  GLN      3.7     2.0    -      -       -      -
    111X  GLY*     3.5    29.6    -      -       -      -
     37Y  GLN*     3.4    19.4    +      -       -      -
     41Y  LYS      4.3     1.6    +      -       -      -
     42Y  ALA*     3.5    29.6    -      -       +      -
     43Y  PRO*     3.8    12.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 95 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4X  LEU*     3.7    16.6    -      -       +      +
      6X  GLU*     3.5    20.2    +      -       -      -
     22X  CYS*     2.0    53.6    -      -       +      -
     34X  MET*     6.2     0.4    -      -       +      -
     35X  SER      3.4     4.7    -      -       -      -
     36X  TRP*     3.7    16.2    -      -       +      -
     78X  LEU*     4.0     8.5    -      -       +      -
     94X  TYR*     1.3    73.2    -      -       -      +
     96X  THR*     1.3    68.3    +      -       -      +
    108X  TRP*     3.7     0.3    -      -       -      -
    109X  GLY*     3.2    21.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 96 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4X  LEU*     4.1     2.0    -      -       -      -
     34X  MET*     3.3    14.4    -      -       -      +
     35X  SER*     2.7    57.7    +      -       -      -
     36X  TRP      4.1     0.2    +      -       -      -
     37X  VAL*     4.1    17.8    -      -       +      +
     78X  LEU*     4.9     0.2    -      -       -      +
     94X  TYR      4.2     4.5    -      -       -      +
     95X  CYS*     1.3    84.3    -      -       -      +
     97X  ARG*     1.3    60.4    +      -       -      +
     98X  GLY      3.8     0.2    +      -       -      -
    105X  PHE*     3.5    22.1    -      -       +      -
    107X  VAL      3.5    12.3    -      -       -      +
    108X  TRP*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 97 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292B  GLY*     5.7     7.5    -      -       -      -
      2X  VAL*     4.1     9.3    -      -       -      +
      4X  LEU*     4.0     2.3    -      -       +      +
     27X  PHE*     3.1    64.3    -      -       +      +
     32X  TYR*     3.4    32.4    +      -       +      -
     34X  MET*     3.8    20.0    -      -       +      -
     96X  THR*     1.3    72.4    -      -       -      +
     98X  GLY*     1.3    54.7    +      -       -      +
    105X  PHE*     3.2     2.4    -      -       -      -
    106X  ASP*     2.5    71.1    +      -       -      +
    107X  VAL*     3.2    28.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32X  TYR*     4.0    19.8    -      -       -      +
     33X  THR      3.4    14.4    +      -       -      +
     35X  SER*     5.5     1.4    +      -       -      +
     96X  THR      3.8     1.6    +      -       -      -
     97X  ARG*     1.3    76.9    -      -       -      +
     99X  PHE*     1.3    62.2    +      -       -      -
    100X  GLY      4.3     0.2    +      -       -      -
    102X  GLY*     3.5    25.1    -      -       -      -
    104X  TYR      3.0    10.8    -      -       -      -
    105X  PHE*     4.1     2.8    -      -       -      -
    106X  ASP*     3.6     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 99 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  GLU*     6.1     0.2    -      -       -      -
    288B  HIS*     4.4    27.8    -      +       +      -
    289B  TYR*     3.9    34.5    -      +       -      -
    292B  GLY*     5.7     5.2    -      -       -      -
    294B  LEU*     3.9    25.4    -      -       +      -
     32X  TYR*     5.7     1.6    -      +       -      -
     98X  GLY*     1.3    74.2    -      -       -      -
    100X  GLY*     1.3    74.7    +      -       -      +
    101X  ASP      3.0     1.0    +      -       -      -
    102X  GLY*     3.0    17.0    +      -       -      -
    104X  TYR*     2.6    35.4    +      +       +      -
    106X  ASP*     3.6    17.7    -      -       -      +
     49Y  LEU*     4.6     9.4    -      -       +      -
     90Y  TRP*     3.8    35.7    -      +       -      -
----------------------------------------------------------
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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