Contacts of the helix formed by residues 25 - 36 (chain F) in PDB entry 1HCQ
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.
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 GLU 25 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F SER* 2.8 31.8 + - - +
18F HIS* 3.6 11.1 + - - -
24F CYS* 1.3 74.6 - - - +
26F GLY* 1.3 52.0 - - - +
28F LYS* 3.0 23.5 + - - +
29F ALA* 2.6 35.9 + - - +
13G G 4.4 2.9 - - - -
14G A 3.7 40.8 + - + +
15G C 2.9 33.8 + - + -
16G C 5.7 1.3 - - - -
22H G 4.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F CYS* 3.2 8.2 - - - +
25F GLU* 1.3 74.5 - - - +
27F CYS* 1.3 63.9 + - - +
28F LYS 2.8 4.2 + - - -
29F ALA* 2.9 12.6 + - - +
30F PHE* 2.9 13.3 + - - +
63F ARG* 3.6 8.7 - - - -
13G G 3.9 35.4 + - - +
14G A 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F CYS* 4.3 2.2 - - - -
9F VAL* 3.5 35.4 - - + -
10F CYS* 3.9 5.2 - - - -
23F SER* 4.9 0.7 - - - -
24F CYS* 3.0 8.9 - - - +
26F GLY* 1.3 72.2 - - - -
28F LYS* 1.3 64.1 + - - +
30F PHE* 3.6 4.4 - - - +
31F PHE* 3.0 24.8 + - - +
63F ARG* 3.7 19.3 - - - +
67F CYS* 4.5 2.9 - - - -
72F MET* 4.1 13.7 - - + +
598F ZN 2.1 38.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F HIS* 3.6 39.8 + - + +
19F TYR* 3.9 23.5 - - + -
23F SER* 4.0 10.5 + - - +
24F CYS 2.9 18.4 + - - +
25F GLU* 3.1 31.9 - - - +
26F GLY 2.8 2.4 + - - -
27F CYS* 1.3 82.0 - - - +
29F ALA* 1.3 61.6 + - - +
31F PHE* 3.9 0.3 - - - -
32F LYS* 3.1 24.9 + - - +
72F MET* 5.5 1.3 - - - -
15G C 4.6 1.6 - - - +
21H A 4.1 11.4 + - - -
22H G 3.0 44.1 + - - -
23H G 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLU 2.6 16.4 + - - +
26F GLY 3.5 3.4 - - - +
28F LYS* 1.3 74.1 - - - +
30F PHE* 1.3 63.3 + - - +
32F LYS* 3.1 20.6 + - - +
33F ARG* 3.1 38.2 + - - +
13G G 3.4 37.7 - - + +
14G A 4.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F GLY 2.9 15.7 + - - +
27F CYS* 3.6 4.9 - - - +
29F ALA* 1.3 79.0 - - - +
31F PHE* 1.3 57.8 + - - +
33F ARG* 3.3 11.9 + - - +
34F SER* 2.5 37.3 + - - -
41F TYR* 4.0 21.1 - + - -
60F GLN* 3.4 27.4 - - + -
63F ARG* 3.0 51.6 - - + +
64F LEU* 3.5 28.0 - - + -
67F CYS* 4.2 10.5 - - - -
12G T 3.5 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 3.7 26.5 - + + -
27F CYS 3.0 14.4 + - - +
28F LYS 4.0 2.2 - - - +
30F PHE* 1.3 79.8 - - - +
32F LYS* 1.3 68.1 + - - +
33F ARG 3.1 0.2 + - - -
34F SER* 3.2 4.7 + - - -
35F ILE* 2.8 62.5 + - + +
64F LEU* 4.3 5.8 - - + -
67F CYS* 3.5 24.5 - - + -
68F TYR* 3.8 35.2 - + - -
72F MET* 3.7 39.0 - - + -
73F MET* 4.0 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 3.8 24.7 - - + +
28F LYS* 3.1 14.1 + - - +
29F ALA* 3.2 25.1 - - - +
31F PHE* 1.3 79.2 - - - +
33F ARG* 1.3 71.7 + - + +
35F ILE* 3.3 10.3 - - + +
36F GLN* 3.1 18.2 + - - -
13G G 5.3 0.2 + - - -
14G A 4.6 1.4 - - - +
22H G 3.7 36.4 + - + +
23H G 3.1 34.1 + - + +
24H T 3.5 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F ALA* 3.1 23.5 + - - +
30F PHE* 3.4 21.4 - - + +
32F LYS* 1.3 90.7 - - + +
34F SER* 1.3 55.1 + - - +
36F GLN* 2.7 24.6 + - - +
37F GLY 2.9 14.7 + - - +
41F TYR* 5.4 5.3 + - - +
11G G 4.3 3.6 - - - +
12G T 3.1 81.4 + - - +
13G G 3.2 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F PHE* 2.5 26.7 + - - -
31F PHE 3.2 6.5 + - - -
33F ARG* 1.3 76.3 - - - +
35F ILE* 1.3 60.6 + - - +
37F GLY* 2.9 23.1 + - - +
41F TYR* 4.7 10.3 + - - -
64F LEU* 3.3 41.0 - - - +
68F TYR* 5.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 3.9 32.3 - - + +
31F PHE* 2.8 52.4 + - + +
32F LYS* 3.3 11.9 - - + +
34F SER* 1.3 77.6 - - - +
36F GLN* 1.3 62.2 + - - +
37F GLY* 3.2 1.9 + - - -
68F TYR* 4.3 10.5 - - - +
73F MET 5.3 3.8 - - - +
74F LYS* 5.5 3.4 - - - +
22H G 4.3 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LYS 3.1 11.8 + - - -
33F ARG* 2.7 12.6 + - - +
35F ILE* 1.3 80.1 - - - +
37F GLY* 1.4 52.8 + - - -
----------------------------------------------------------
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