Contacts of the helix formed by residues 6 - 18 (chain A) in PDB entry 2H1R
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 ASN 6 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.9 6.0 - - + +
5A LYS* 1.3 78.9 - - - +
7A PRO* 1.4 72.5 - - - +
8A GLY* 3.2 14.0 + - - -
9A ILE* 3.0 37.8 + - + +
10A LEU* 3.2 17.8 + - - +
34A ASN* 5.8 0.8 - - - +
159A SER* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.9 25.1 - - + +
6A ASN* 1.4 87.7 - - - +
8A GLY* 1.3 61.4 - - - +
10A LEU* 3.3 15.3 + - + +
11A ASP* 3.1 28.2 + - - +
38A LYS* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 3.2 8.5 + - - -
7A PRO* 1.3 78.5 - - - +
9A ILE* 1.3 63.2 + - - +
11A ASP* 3.5 12.2 + - - +
12A LYS* 3.3 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.9 23.1 - - + -
6A ASN* 3.0 39.4 + - + +
8A GLY* 1.3 75.7 - - - +
10A LEU* 1.3 67.8 + - - +
12A LYS* 3.0 12.2 + - + +
13A ILE* 3.0 21.3 + - + +
153A CYS* 4.6 8.5 - - + -
154A ASN 4.2 17.5 - - - +
155A VAL* 4.0 10.5 - - + -
159A SER* 4.4 5.2 - - - +
170A ILE* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 30.3 - - + +
6A ASN 3.2 13.6 + - - +
7A PRO* 3.6 13.2 - - + +
9A ILE* 1.3 76.7 - - - +
11A ASP* 1.3 62.5 + - - +
13A ILE* 3.2 14.1 + - + +
14A ILE* 3.1 26.7 + - - +
34A ASN* 3.7 46.0 - - + +
35A LEU* 3.9 19.4 - - + +
38A LYS* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.1 15.9 + - - +
8A GLY* 3.5 14.6 - - - +
9A ILE 3.2 0.2 - - - -
10A LEU* 1.3 76.0 - - - +
12A LYS* 1.3 57.2 + - + +
14A ILE* 3.4 4.8 + - - +
15A TYR* 3.0 28.6 + - - +
38A LYS* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 3.3 15.5 - - - +
9A ILE* 3.0 16.6 + - + +
11A ASP* 1.3 75.5 - - + +
13A ILE* 1.3 65.9 + - + +
15A TYR* 3.5 6.4 + - - +
16A ALA* 3.0 25.1 + - - +
152A VAL* 3.8 24.0 + - + +
153A CYS* 3.5 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.3 10.1 - - + -
9A ILE 3.0 16.4 + - - +
10A LEU* 3.2 26.2 + - + +
12A LYS* 1.3 77.6 - - - +
14A ILE* 1.3 59.4 + - + +
16A ALA* 3.3 4.7 + - - +
17A ALA* 3.0 30.6 + - + +
35A LEU* 4.0 22.7 - - + -
39A LEU* 5.8 0.9 - - + -
90A THR* 3.7 24.2 - - + +
116A VAL* 4.2 21.6 - - + +
118A MET* 5.8 3.6 - - + -
152A VAL* 5.2 1.1 - - + -
170A ILE* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.1 17.3 + - - +
11A ASP* 3.7 6.5 - - - +
13A ILE* 1.3 75.8 - - + +
15A TYR* 1.3 64.8 + - - +
17A ALA* 3.3 13.3 + - + +
18A LYS* 3.4 10.0 + - - -
19A ILE* 4.6 3.9 + - + +
35A LEU* 3.8 13.0 - - + -
38A LYS* 3.9 28.3 - - + +
39A LEU* 3.6 30.7 - - + -
42A LEU* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 3.0 17.6 + - - +
12A LYS* 3.8 7.9 - - - +
14A ILE* 1.3 80.3 - - - +
16A ALA* 1.3 66.5 + - + +
18A LYS* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS 3.0 18.4 + - - +
13A ILE 3.6 4.3 - - - +
15A TYR* 1.3 83.7 - - - +
17A ALA* 1.3 60.7 + - - +
18A LYS* 3.5 8.0 + - - +
114A CYS* 4.4 2.3 - - - -
116A VAL* 4.1 11.2 - - + -
152A VAL* 3.9 29.8 - - + -
172A LYS* 3.5 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.0 19.0 + - + +
14A ILE* 3.3 6.0 + - - +
16A ALA* 1.3 76.7 - - - +
18A LYS* 1.3 68.5 + - - +
19A ILE* 3.3 28.3 + - + +
39A LEU* 5.7 0.9 - - + -
88A VAL* 4.1 15.9 - - + +
90A THR* 6.1 2.7 - - - -
114A CYS* 3.7 15.6 - - - -
116A VAL* 3.7 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE 3.4 8.1 + - - -
15A TYR 3.6 16.6 - - - +
16A ALA 3.3 7.8 - - - +
17A ALA* 1.3 79.8 - - - +
19A ILE* 1.3 64.3 + - - +
20A LYS* 3.5 9.5 + - - +
23A ASP* 4.1 3.6 - - - +
88A VAL* 5.5 0.3 - - - +
172A LYS* 6.2 1.1 - - - +
----------------------------------------------------------
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