Contacts of the helix formed by residues 103 - 123 (chain H) in PDB entry 3AZL


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 PRO 103 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  GLU*     3.6    40.8    -      -       +      +
     95G  LYS*     4.0    27.1    -      -       +      -
     96G  LEU*     4.2    18.4    -      -       +      +
    101H  LEU      3.9     5.6    -      -       -      +
    102H  LEU*     1.3    87.8    -      -       +      +
    104H  GLY*     1.3    67.7    +      -       -      +
    105H  GLU      3.7     1.1    -      -       -      -
    106H  LEU*     3.0    13.5    +      -       +      +
    107H  ALA      2.8    17.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 104 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  GLU*     3.7     4.1    +      -       -      -
    102H  LEU      3.9     0.8    +      -       -      -
    103H  PRO*     1.3    71.7    -      -       -      +
    105H  GLU*     1.3    63.5    +      -       -      -
    107H  ALA*     3.1    12.6    +      -       -      +
    108H  LYS*     3.2    24.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 105 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  GLU*     2.7    29.6    +      -       -      +
    104H  GLY*     1.3    68.9    -      -       -      -
    106H  LEU*     1.3    63.0    +      -       +      -
    108H  LYS*     3.2    13.2    +      -       -      +
    109H  HIS*     3.0    53.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 106 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57G  TYR*     3.9    27.3    -      -       +      +
     58G  LEU*     3.9    20.2    -      -       +      -
     61G  GLU*     4.4    16.8    -      -       +      -
     90G  ASP*     5.7     1.3    -      -       -      +
     92G  GLU*     3.1    50.4    +      -       +      +
     93G  LEU*     4.0    16.6    -      -       +      +
     96G  LEU*     4.9     4.5    -      -       +      -
    102H  LEU*     3.8    12.7    -      -       +      +
    103H  PRO*     3.0    16.3    +      -       +      +
    105H  GLU*     1.3    76.3    -      -       +      +
    107H  ALA*     1.3    57.7    +      -       -      +
    110H  ALA*     2.9    33.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 107 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98H  VAL*     4.4     9.9    -      -       -      +
     99H  ARG*     4.5    19.7    -      -       +      +
    102H  LEU*     3.7    22.9    -      -       +      +
    103H  PRO      2.8    12.7    +      -       -      +
    104H  GLY*     3.3    10.3    -      -       -      +
    106H  LEU*     1.3    74.5    -      -       -      +
    108H  LYS*     1.3    57.8    +      -       +      +
    110H  ALA*     3.4     3.1    +      -       -      +
    111H  VAL*     2.7    41.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 108 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  ARG*     3.8    25.5    -      -       -      +
    104H  GLY*     3.2    20.4    +      -       -      +
    105H  GLU*     3.2    18.8    +      -       -      +
    107H  ALA*     1.3    77.7    -      -       -      +
    109H  HIS*     1.3    71.4    +      -       +      +
    111H  VAL*     3.1     8.7    +      -       -      +
    112H  SER*     2.9    23.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 109 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57G  TYR*     3.0    40.6    -      +       +      +
     61G  GLU*     5.6     0.4    -      -       -      -
    105H  GLU*     3.0    35.9    +      -       +      +
    108H  LYS*     1.3    81.0    -      -       +      +
    110H  ALA*     1.3    62.2    +      -       -      +
    112H  SER*     2.8    24.4    +      -       -      -
    113H  GLU*     3.0    13.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 110 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54G  VAL*     4.0    20.9    -      -       +      +
     57G  TYR*     3.8    18.5    -      -       +      -
     98H  VAL*     3.8     9.2    -      -       +      -
    102H  LEU*     3.6    22.2    -      -       +      -
    106H  LEU      2.9    20.3    +      -       -      +
    107H  ALA      3.7     2.5    -      -       -      +
    109H  HIS*     1.3    76.6    -      -       -      +
    111H  VAL*     1.3    63.8    +      -       -      +
    113H  GLU*     3.4     3.8    +      -       -      +
    114H  GLY*     2.9    21.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 111 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  TYR*     3.3    13.1    +      -       -      +
     95H  GLN*     3.3    29.6    -      -       +      +
     98H  VAL*     4.2    10.5    -      -       +      -
     99H  ARG*     3.6    43.3    -      -       +      +
    107H  ALA      2.7    28.8    +      -       -      +
    108H  LYS*     3.4     5.4    -      -       -      +
    110H  ALA*     1.3    73.6    -      -       -      +
    112H  SER*     1.3    64.9    +      -       -      +
    114H  GLY      3.3     0.9    +      -       -      -
    115H  THR*     3.0    31.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 112 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108H  LYS      2.9    12.2    +      -       -      -
    109H  HIS*     2.8    17.0    +      -       -      -
    111H  VAL*     1.3    78.8    -      -       -      +
    113H  GLU*     1.3    80.4    +      -       -      +
    114H  GLY      3.0     0.3    +      -       -      -
    115H  THR*     3.1     8.2    +      -       -      -
    116H  LYS*     2.7    35.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 113 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23G  LEU*     5.9     2.9    -      -       -      +
     53G  ALA*     3.6    11.6    -      -       +      +
     57G  TYR*     3.9    38.4    -      -       +      +
    109H  HIS      3.0    16.0    +      -       -      +
    110H  ALA      3.7     4.5    -      -       -      +
    112H  SER*     1.3    85.5    +      -       -      +
    114H  GLY*     1.3    61.7    +      -       -      +
    116H  LYS*     3.4    29.8    +      -       -      +
    117H  ALA*     2.9    25.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 114 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  TYR*     3.7    25.2    -      -       -      -
     53G  ALA*     3.8    13.7    -      -       -      +
     54G  VAL*     4.7     0.9    -      -       -      +
    110H  ALA      2.9    15.6    +      -       -      -
    111H  VAL      3.7     2.7    -      -       -      -
    113H  GLU*     1.3    77.5    -      -       -      +
    115H  THR*     1.3    62.4    +      -       -      +
    117H  ALA*     3.2     4.3    +      -       -      +
    118H  VAL*     3.0    26.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 115 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  TYR*     3.6     8.0    -      -       +      +
     95H  GLN*     3.4    26.2    -      -       -      +
    111H  VAL*     3.0    20.7    +      -       +      +
    112H  SER*     3.6     7.0    +      -       -      -
    114H  GLY*     1.3    75.7    -      -       -      +
    116H  LYS*     1.3    60.3    +      -       -      +
    118H  VAL*     4.0     5.5    -      -       -      +
    119H  THR*     2.9    33.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 116 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  SER*     2.7    31.8    +      -       -      +
    113H  GLU*     3.5    32.9    +      -       -      +
    115H  THR*     1.3    74.8    +      -       -      +
    117H  ALA*     1.3    58.0    +      -       -      +
    119H  THR*     3.5     8.6    -      -       +      +
    120H  LYS*     3.0    47.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 117 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21G  ALA*     3.8    16.8    -      -       -      +
     23G  LEU*     3.9    15.7    -      -       +      -
     49G  VAL*     3.3    15.2    -      -       +      +
     53G  ALA*     3.7    21.1    -      -       +      -
    113H  GLU      2.9    17.6    +      -       -      +
    114H  GLY      3.2     2.0    +      -       -      +
    116H  LYS*     1.3    78.2    -      -       -      +
    118H  VAL*     1.3    59.4    +      -       -      +
    120H  LYS*     4.7     0.2    -      -       -      -
    121H  TYR*     3.0    29.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46G  GLY*     3.6    35.0    -      -       -      +
     49G  VAL*     3.7     8.1    -      -       +      -
     50G  TYR*     3.7    25.6    -      -       +      +
     91H  SER*     4.7     8.3    -      -       -      +
    114H  GLY      3.0    18.9    +      -       -      +
    115H  THR*     4.0     6.3    -      -       -      +
    116H  LYS      3.3     0.2    -      -       -      -
    117H  ALA*     1.3    72.8    -      -       -      +
    119H  THR*     1.3    67.6    +      -       -      +
    121H  TYR*     3.2     4.1    +      -       +      +
    122H  THR*     2.9    37.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 119 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115H  THR*     2.9    19.5    +      -       -      -
    116H  LYS*     3.5     8.7    -      -       +      +
    118H  VAL*     1.3    76.1    -      -       -      +
    120H  LYS*     1.3    70.9    +      -       +      +
    122H  THR*     2.9    18.2    +      -       -      -
    123H  SER*     3.2    17.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19G  SER      5.3     0.7    -      -       -      +
     20G  ARG*     3.5    16.0    -      -       -      +
     21G  ALA      3.8    18.0    +      -       -      +
     22G  GLY*     4.1    14.6    +      -       -      -
    116H  LYS*     3.0    29.9    +      -       -      +
    117H  ALA*     4.0     3.8    -      -       -      +
    119H  THR*     1.3    84.0    -      -       +      +
    121H  TYR*     1.3    62.0    +      -       -      +
    123H  SER*     3.2    21.4    +      -       -      +
    124H  ALA*     4.4     2.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 121 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17G  ARG*     3.0    66.6    +      -       +      +
     20G  ARG*     3.7    44.3    +      -       +      +
     21G  ALA*     3.8     7.4    -      -       +      -
     45G  ALA*     4.4    22.2    -      -       +      +
     46G  GLY*     5.5     2.7    -      -       -      -
     49G  VAL*     3.8    25.6    -      -       +      -
    117H  ALA      3.0    19.7    +      -       -      +
    118H  VAL*     3.6     4.5    -      -       +      +
    119H  THR      3.2     0.2    -      -       -      -
    120H  LYS*     1.3    76.9    -      -       -      +
    122H  THR*     1.3    71.4    +      -       -      +
    123H  SER      3.5     5.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 122 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118H  VAL*     2.9    23.2    +      -       -      +
    119H  THR*     2.9     8.3    +      -       -      -
    121H  TYR*     1.3    82.4    -      -       -      +
    123H  SER*     1.3    66.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 123 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  THR*     3.2    12.7    +      -       -      +
    120H  LYS*     3.2    16.0    +      -       -      -
    121H  TYR      4.0     2.3    -      -       -      +
    122H  THR*     1.3    83.7    -      -       -      +
    124H  ALA*     1.3    72.1    +      -       -      +
----------------------------------------------------------
 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