Contacts of the strand formed by residues 136 - 146 (chain H) in PDB entry 1ZMD


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 136 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  THR*     3.6    25.7    -      -       +      +
    129H  ALA      3.4     4.5    -      -       -      -
    130H  THR*     3.9    11.4    +      -       -      +
    131H  LYS*     3.5    12.8    +      -       -      +
    134H  GLY      3.6     7.1    +      -       -      -
    135H  GLY*     1.3    77.5    +      -       -      -
    137H  GLN*     1.3    71.1    +      -       -      +
    138H  VAL*     4.1     9.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  PRO*     3.2    26.1    -      -       -      +
      5H  ILE*     4.2    23.2    -      -       +      +
    115H  VAL*     4.3    20.2    -      -       +      -
    129H  ALA      2.8    36.0    +      -       -      +
    131H  LYS*     4.5    10.5    -      -       +      +
    136H  THR*     1.3    80.1    -      -       -      +
    138H  VAL*     1.3    89.3    +      -       -      +
    139H  ILE*     3.4    17.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 138 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  PRO*     4.4    16.4    -      -       +      +
      5H  ILE      3.3    13.7    +      -       -      +
    126H  GLN*     4.7    18.6    -      -       +      +
    127H  VAL      3.4     3.8    -      -       -      +
    128H  THR*     3.4    28.0    -      -       +      +
    136H  THR*     4.1     9.4    -      -       +      -
    137H  GLN*     1.3    92.2    +      -       -      +
    139H  ILE*     1.3    62.0    +      -       -      +
    140H  ASP*     4.9    10.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 139 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5H  ILE*     3.1    35.7    -      -       +      +
      7H  ALA*     4.2     4.5    -      -       +      -
     10H  THR*     3.5    27.8    -      -       +      +
     33H  VAL*     4.2    18.4    -      -       +      -
     35H  ILE*     4.2    19.5    -      -       +      -
    115H  VAL*     4.7     3.8    -      -       +      -
    126H  GLN*     3.3     5.8    -      -       -      +
    127H  VAL*     2.7    45.2    +      -       +      +
    129H  ALA*     4.7     3.4    -      -       +      +
    137H  GLN*     3.4    21.1    -      -       +      +
    138H  VAL*     1.3    79.1    -      -       -      +
    140H  ASP*     1.3    71.7    +      -       -      +
    141H  THR*     3.8     1.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  PRO*     5.5     4.5    -      -       -      +
      5H  ILE      2.9    12.0    +      -       -      +
      6H  ASP*     2.9    17.2    -      -       +      +
      7H  ALA      2.8    23.9    +      -       -      +
    125H  ASN*     3.3     6.7    -      -       +      +
    126H  GLN*     3.7    27.4    +      -       -      +
    138H  VAL*     4.9     9.9    -      -       -      +
    139H  ILE*     1.3    73.1    -      -       -      +
    141H  THR*     1.3    59.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  ALA      3.0    12.9    +      -       -      -
      8H  ASP      3.5     3.5    +      -       -      -
      9H  VAL      3.7     0.2    +      -       -      -
     10H  THR*     3.0    36.5    +      -       +      +
    125H  ASN*     2.8    41.5    +      -       -      +
    127H  VAL*     4.4     4.5    -      -       +      -
    139H  ILE*     4.2     8.1    -      -       -      +
    140H  ASP*     1.3    75.5    -      -       -      +
    142H  LYS*     1.3    64.7    +      -       -      +
    143H  ASN      2.8    25.8    +      -       -      +
    144H  ILE*     3.9    16.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  ALA      3.1     8.2    +      -       -      +
      8H  ASP*     3.1    36.8    -      -       +      +
     30H  PHE*     6.4     0.7    -      -       +      -
    125H  ASN*     3.3     8.3    -      -       -      +
    141H  THR*     1.3    74.3    +      -       -      +
    143H  ASN*     1.3    71.5    +      -       -      +
    314H  ASN*     2.9    30.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8H  ASP*     2.9    18.1    +      -       -      +
      9H  VAL*     3.5     9.8    -      -       +      +
     10H  THR      2.9    15.9    +      -       -      -
     30H  PHE*     5.2     6.1    -      -       -      -
    141H  THR*     2.8    18.1    +      -       -      +
    142H  LYS*     1.3    90.6    -      -       -      +
    144H  ILE*     1.3    63.3    +      -       -      +
    314H  ASN*     3.3    15.0    -      -       -      +
    316H  TYR*     3.7    19.3    +      -       +      -
    342H  MET*     4.0    30.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  THR      3.5     6.1    -      -       -      +
     12H  ILE*     3.8    19.1    -      -       +      -
    121H  ILE*     3.6    47.8    -      -       +      -
    123H  GLY      4.0     3.1    -      -       -      +
    124H  LYS      3.6    23.8    -      -       -      +
    125H  ASN*     5.1     0.4    -      -       -      -
    126H  GLN      4.2     2.9    -      -       -      +
    127H  VAL*     3.8    13.7    -      -       +      -
    141H  THR*     3.9    16.2    -      -       +      -
    143H  ASN*     1.3    77.4    -      -       -      +
    145H  LEU*     1.3    59.9    +      -       -      +
    146H  ILE*     4.5     0.7    -      -       +      -
    314H  ASN*     2.9     7.7    +      -       -      +
    315H  ILE*     3.3    17.8    -      -       +      -
    316H  TYR*     2.7    36.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9H  VAL*     4.8     2.5    -      -       +      -
     10H  THR      2.8    14.4    +      -       -      +
     11H  VAL*     3.5    19.4    -      -       +      +
     12H  ILE*     2.9    28.4    +      -       -      +
     21H  ALA*     3.5    32.5    -      -       +      -
    143H  ASN      4.2     0.2    -      -       -      -
    144H  ILE*     1.3    74.8    -      -       -      +
    146H  ILE*     1.3    66.2    +      -       -      +
    147H  ALA      3.5     0.3    +      -       -      -
    316H  TYR*     3.5    24.2    -      -       +      -
    317H  ALA      3.9     1.1    -      -       -      +
    318H  ILE*     3.9    33.4    -      -       +      -
    338H  CYS*     4.0     7.2    -      -       +      -
    339H  VAL*     4.1    17.0    -      -       +      -
    342H  MET*     4.3     8.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  ILE*     4.3     6.5    -      -       +      -
    121H  ILE*     3.8    30.7    -      -       +      -
    144H  ILE*     4.5     2.5    -      -       +      -
    145H  LEU*     1.3    73.8    -      -       -      +
    147H  ALA*     1.3    60.1    +      -       -      +
    148H  THR*     3.5    25.1    -      -       +      +
    287H  LEU*     3.6    15.3    -      -       +      -
    289H  LEU*     3.9    21.1    -      -       +      -
    294H  ILE*     5.1     0.2    -      -       +      -
    302H  ILE*     3.8    21.1    -      -       +      -
    310H  THR*     4.7     4.9    -      -       +      -
    315H  ILE*     3.8    15.7    -      -       +      -
    316H  TYR      2.5    17.7    +      -       -      +
    317H  ALA*     3.0    24.4    -      -       +      +
    318H  ILE      3.0    10.0    +      -       -      +
    321H  VAL*     3.8     2.6    -      -       +      +
----------------------------------------------------------
 Back to top of page


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