Contacts of the helix formed by residues 18 - 33 (chain B) in PDB entry 5I1U


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 HIS 18 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ASN*     2.8    20.5    +      -       -      +
     17B  PRO*     1.3    94.4    +      -       +      +
     19B  GLN*     1.3    64.8    +      -       -      +
     20B  THR      3.3     3.2    +      -       -      -
     21B  GLU*     3.3    13.3    +      -       +      +
     22B  ALA*     2.9    21.3    +      -       -      +
     61B  SER      3.5    16.6    -      -       -      -
     62B  SER*     3.9     3.8    -      -       -      -
     63B  ALA*     3.6    38.4    +      -       +      +
     66B  LEU*     3.7     5.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ARG*     3.0    29.2    +      -       -      -
     16B  ASN      3.3    10.5    +      -       -      +
     17B  PRO      3.3     2.4    +      -       -      -
     18B  HIS*     1.3    76.3    -      -       -      +
     20B  THR*     1.3    59.3    +      -       -      +
     22B  ALA*     3.4     1.7    +      -       -      +
     23B  ALA*     2.9    30.1    +      -       +      +
     49B  ASP*     4.5     3.4    +      -       -      -
     51B  THR*     4.6     8.8    +      -       -      +
     52B  GLU*     3.0    37.1    +      -       -      +
     55B  SER*     3.3    31.0    -      -       -      +
     66B  LEU*     3.7     5.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PRO      5.1     1.0    +      -       -      -
     18B  HIS      3.4     1.0    -      -       -      -
     19B  GLN*     1.3    78.8    -      -       -      +
     21B  GLU*     1.3    65.5    +      -       -      +
     23B  ALA*     3.2     8.1    +      -       -      +
     24B  ASP*     3.0    32.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  HIS*     3.3    15.4    +      -       -      +
     20B  THR*     1.3    79.8    -      -       -      +
     22B  ALA*     1.3    63.3    +      -       -      +
     24B  ASP*     3.2     9.3    +      -       -      +
     25B  ARG*     3.1    56.7    +      -       +      +
     63B  ALA*     3.4    23.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  HIS      2.9    17.6    +      -       -      +
     19B  GLN      3.8     2.2    -      -       -      +
     21B  GLU*     1.3    76.6    -      -       -      +
     23B  ALA*     1.3    57.7    +      -       -      +
     25B  ARG*     3.2     4.3    +      -       -      +
     26B  HIS*     2.8    30.3    +      -       -      +
     51B  THR*     4.7     3.1    -      -       +      -
     63B  ALA      4.0     6.2    +      -       -      +
     66B  LEU*     3.6    33.2    -      -       +      +
     67B  ALA*     3.8    24.7    -      -       -      +
     70B  ALA*     5.5     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLN*     2.9    19.7    +      -       +      +
     20B  THR*     3.2     8.0    +      -       -      +
     22B  ALA*     1.3    77.0    -      -       -      +
     24B  ASP*     1.3    59.9    +      -       -      +
     26B  HIS*     3.2     3.1    +      -       -      +
     27B  LEU*     3.0    35.5    +      -       +      +
     51B  THR*     3.6    31.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  THR*     3.0    24.4    +      -       -      +
     21B  GLU*     3.2    10.4    +      -       +      +
     23B  ALA*     1.3    80.2    -      -       -      +
     25B  ARG*     1.3    63.0    +      -       +      +
     27B  LEU*     3.3    17.8    +      -       -      +
     28B  GLU*     3.2    31.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLU*     3.1    50.2    +      -       +      +
     22B  ALA*     3.6     5.6    -      -       -      +
     24B  ASP*     1.3    76.8    -      -       +      +
     26B  HIS*     1.3    61.7    +      -       -      +
     28B  GLU*     3.2    18.0    +      -       -      +
     29B  TRP*     3.1    20.3    +      -       -      +
     32B  ARG*     5.3     0.3    +      -       -      -
     63B  ALA*     4.3     7.2    +      -       -      +
     64B  GLU*     3.9    36.6    -      -       -      +
     67B  ALA*     3.7    24.7    -      -       +      +
     71B  ASP*     4.4     2.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ALA      2.8    17.2    +      -       -      +
     23B  ALA      3.5     5.4    -      -       -      +
     24B  ASP      3.2     0.2    -      -       -      -
     25B  ARG*     1.3    76.0    -      -       -      +
     27B  LEU*     1.3    62.1    +      -       +      +
     29B  TRP*     3.2     9.3    +      +       -      +
     30B  LEU*     3.0    43.6    +      -       +      +
     45B  TYR*     2.5    33.9    +      +       -      -
     50B  ILE*     4.0     5.2    -      -       +      +
     51B  THR*     3.8    23.6    -      -       +      -
     67B  ALA*     4.9     1.3    -      -       -      +
     70B  ALA*     3.3    28.3    -      -       +      -
     71B  ASP*     2.7    37.2    +      -       -      +
     74B  GLY*     4.3     2.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  ALA*     3.0    20.3    +      -       +      +
     24B  ASP*     3.3    22.0    +      -       -      +
     26B  HIS*     1.3    77.9    -      -       +      +
     28B  GLU*     1.3    58.5    +      -       +      +
     30B  LEU*     3.2    22.2    +      -       +      +
     31B  GLN*     3.0    43.7    +      -       -      +
     46B  THR*     6.4     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ASP*     3.2    18.9    +      -       -      +
     25B  ARG*     3.4    17.4    -      -       -      +
     26B  HIS      3.2     0.2    -      -       -      -
     27B  LEU*     1.3    77.1    -      -       +      +
     29B  TRP*     1.3    62.1    +      -       -      +
     31B  GLN*     3.2    19.6    +      -       -      +
     32B  ARG*     3.0    39.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  ARG      3.1     9.8    +      -       -      +
     26B  HIS*     3.2     9.4    +      +       -      +
     28B  GLU*     1.3    76.8    -      -       -      +
     30B  LEU*     1.3    86.2    +      -       +      +
     32B  ARG*     3.1    22.4    +      -       -      +
     33B  HIS*     3.0    50.6    +      +       +      -
     36B  LEU*     4.4     5.6    -      -       +      -
     71B  ASP*     3.2    51.4    -      -       +      +
     75B  PHE*     4.2    15.9    -      -       +      -
     78B  LEU*     4.6     5.4    -      -       +      -
    119B  ALA*     3.9    29.2    -      -       +      -
    122B  ASP*     2.9    22.6    +      -       -      -
    123B  LEU*     4.1    17.4    -      -       +      +
    126B  ARG*     3.4    22.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  HIS*     3.0    40.0    +      -       +      +
     27B  LEU*     3.2    24.6    +      -       +      +
     29B  TRP*     1.3    90.3    -      -       +      +
     31B  GLN*     1.3    62.8    +      -       +      +
     33B  HIS      3.2     4.9    -      -       -      +
     34B  ARG*     3.1    22.7    +      -       -      -
     37B  ALA*     3.8    27.1    -      -       +      +
     45B  TYR*     3.6    36.8    -      -       +      +
     78B  LEU*     4.0    13.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LEU*     3.0    32.2    +      -       -      +
     28B  GLU*     3.4    19.3    -      -       -      +
     30B  LEU*     1.3    78.4    -      -       +      +
     32B  ARG*     1.3    59.8    +      -       -      +
     33B  HIS      3.4     0.7    +      -       -      -
     34B  ARG*     3.5    18.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  ARG      5.3     0.4    +      -       -      -
     28B  GLU*     3.0    37.6    +      -       -      +
     29B  TRP*     3.1    32.7    +      -       -      +
     31B  GLN*     1.3    75.8    -      -       -      +
     33B  HIS*     1.3    71.0    +      -       +      +
     34B  ARG*     3.4     2.5    +      -       -      +
    118B  ARG*     4.0    30.0    +      -       -      +
    122B  ASP*     5.0     6.2    +      -       -      -
    126B  ARG*     5.6     0.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  TRP*     3.0    67.9    +      +       +      +
     30B  LEU*     3.2     5.2    -      -       +      -
     32B  ARG*     1.3    89.8    +      -       +      +
     34B  ARG*     1.3    64.8    +      -       -      +
     35B  GLU      3.3     2.5    -      -       -      -
     36B  LEU*     3.3    14.9    +      -       +      -
     37B  ALA*     3.0    21.0    +      -       -      +
     78B  LEU*     5.9     0.2    -      -       -      +
    115B  PRO      4.9     1.2    +      -       -      +
    118B  ARG*     3.7    44.0    +      -       +      +
    119B  ALA*     3.7    25.9    +      -       +      +
    122B  ASP*     4.3    11.6    -      -       +      +
----------------------------------------------------------
 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