Contacts of the helix formed by residues 3 - 27 (chain A) in PDB entry 2HR3
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 THR 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 1.3 76.1 - - - +
4A ASN* 1.3 77.6 + - + +
5A GLN* 3.1 17.3 - - + +
6A ASP* 2.5 32.9 + - - +
7A LEU* 3.1 19.8 + - - +
116B VAL* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO 4.9 2.5 - - - +
3A THR* 1.3 80.0 - - + +
5A GLN* 1.3 52.2 + - - +
7A LEU* 3.0 16.9 + - + +
8A GLN* 2.8 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.1 14.8 - - + +
4A ASN* 1.3 77.1 - - - +
6A ASP* 1.3 62.4 + - - +
8A GLN* 3.9 8.7 + - - +
9A LEU* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.5 0.9 - - + +
3A THR* 2.5 45.8 + - - +
5A GLN* 1.3 78.0 - - - +
7A LEU* 1.3 60.8 + - - +
9A LEU* 3.3 11.3 + - + +
10A ALA* 3.0 29.1 + - - +
116B VAL* 3.7 15.7 - - + +
119B MSE 5.4 1.4 - - - +
120B HIS* 3.4 38.9 + - + +
128B ARG* 5.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 5.0 5.6 - - + +
3A THR 3.1 17.9 + - - +
4A ASN* 3.0 21.7 + - + +
6A ASP* 1.3 75.6 - - - +
8A GLN* 1.3 55.3 + - + +
10A ALA* 3.4 4.2 + - - +
11A ALA* 3.0 27.9 + - - +
112B GLU* 4.6 5.4 - - + +
113B GLU* 6.4 2.0 - - + -
116B VAL* 4.0 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 2.8 21.9 + - + +
5A GLN* 4.3 6.7 - - - +
7A LEU* 1.3 70.4 - - + +
9A LEU* 1.3 62.2 + - - +
11A ALA* 3.7 7.9 - - + +
12A HIS* 2.9 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN 3.2 19.5 + - - +
6A ASP* 3.3 13.4 + - + +
8A GLN* 1.3 75.5 - - - +
10A ALA* 1.3 58.3 + - - +
12A HIS* 3.5 8.9 - - + +
13A LEU* 2.9 32.4 + - + +
119B MSE 3.2 35.7 - - + -
120B HIS* 6.0 0.4 - - - +
128B ARG* 4.0 25.8 - - + +
131B LEU* 4.6 1.8 - - + -
132B ALA* 3.7 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP 3.0 12.9 + - - +
7A LEU 3.5 8.7 - - - +
9A LEU* 1.3 76.8 - - - +
11A ALA* 1.3 54.7 + - - +
14A ARG* 2.9 29.2 + - - +
112B GLU* 3.7 17.5 - - - +
115B LEU* 3.2 25.4 - - + +
116B VAL* 3.6 23.1 - - + +
119B MSE 4.5 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 3.0 15.0 + - - +
8A GLN* 3.7 11.0 - - + +
10A ALA* 1.3 73.7 - - - +
12A HIS* 1.3 62.9 + - + +
14A ARG* 3.5 7.9 + - - +
15A SER* 3.0 28.9 + - - -
112B GLU* 3.6 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 2.9 33.3 + - + +
9A LEU* 3.5 10.3 - - + +
11A ALA* 1.3 78.5 - - + +
13A LEU* 1.3 66.8 + - - +
15A SER* 3.1 8.4 + - - -
16A GLN* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 2.9 24.8 + - + +
10A ALA* 3.9 2.7 - - - +
12A HIS* 1.3 73.2 - - - +
14A ARG* 1.3 64.1 + - - +
16A GLN* 3.3 13.7 + - - +
17A VAL* 3.1 42.8 + - + +
138A LEU* 4.0 13.7 - - + -
141A LEU* 4.1 15.7 - - + -
20B LEU* 4.8 3.8 - - + -
115B LEU* 4.0 12.6 - - + -
119B MSE 3.8 29.4 - - + -
131B LEU* 4.0 23.8 - - + +
135B GLY* 5.5 1.1 - - - -
138B LEU* 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 2.9 19.1 + - - +
11A ALA* 3.5 13.0 + - - +
13A LEU* 1.3 75.3 - - - +
15A SER* 1.3 78.7 + - - +
18A THR* 3.0 39.9 + - + +
24B LEU* 4.0 25.1 - - + -
108B ARG* 4.2 30.5 + - - +
111B ARG* 4.2 31.9 - - - +
112B GLU* 2.6 39.8 + - + +
115B LEU* 3.7 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.0 15.4 + - - -
12A HIS* 3.1 14.4 + - - -
14A ARG* 1.3 90.2 - - - +
16A GLN* 1.3 61.8 + - - +
18A THR* 3.5 5.3 + - - -
19A THR* 2.7 43.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A HIS* 2.9 38.0 + - - +
13A LEU* 3.3 18.1 + - - +
15A SER* 1.3 82.2 + - - +
17A VAL* 1.3 58.7 + - - +
19A THR* 4.1 3.4 - - - -
20A LEU* 3.1 27.3 + - - +
131B LEU 4.9 0.7 - - - +
135B GLY* 3.2 30.3 - - - +
136B PRO* 3.7 23.6 - - - +
138B LEU* 3.8 15.8 - - + +
139B THR* 3.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.1 35.3 + - + +
14A ARG* 4.3 1.6 - - - +
16A GLN* 1.3 78.1 - - - +
18A THR* 1.3 59.2 + - - +
20A LEU* 3.7 3.0 + - - +
21A THR* 2.8 31.4 + - - -
138A LEU* 4.2 14.8 - - + -
17B VAL* 3.4 18.6 - - + +
20B LEU* 4.2 16.2 - - + -
21B THR* 2.9 27.1 - - - +
24B LEU* 4.6 5.6 - - + -
138B LEU* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 35.9 + - + +
15A SER* 3.5 5.9 + - - -
17A VAL* 1.3 75.4 - - - +
19A THR* 1.3 67.3 + - - +
21A THR* 3.2 2.6 + - - -
22A ARG* 3.0 46.4 + - - +
21B THR* 3.8 23.1 - - + +
24B LEU* 3.8 24.2 - - + -
25B ARG* 6.0 0.7 - - - -
111B ARG* 4.4 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.7 29.9 + - - -
16A GLN* 4.1 4.5 - - - -
18A THR* 1.3 80.1 + - - +
20A LEU* 1.3 60.6 + - - +
22A ARG* 3.5 19.2 + - - +
23A ARG* 3.3 21.3 + - - +
139B THR* 5.6 7.0 - - + +
142B ALA* 3.7 18.6 - - + +
143B GLN* 6.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN 3.1 20.7 + - - +
17A VAL* 4.2 4.0 - - - +
18A THR 3.4 0.2 - - - -
19A THR* 1.3 75.7 - - - +
21A THR* 1.3 62.1 + - - +
23A ARG* 3.4 3.1 + - + +
24A LEU* 3.1 27.9 + - + +
114A TRP* 4.6 15.0 - - + -
115A LEU* 5.1 5.4 - - + -
13B LEU* 4.9 6.1 - - + -
17B VAL* 4.0 21.1 - - + -
138B LEU* 3.6 38.6 - - + +
141B LEU* 4.0 20.4 - - + +
142B ALA* 3.7 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL 2.8 22.4 + - - -
18A THR 3.2 5.6 + - - -
20A LEU* 1.3 76.6 - - - +
22A ARG* 1.3 57.5 + - - +
24A LEU* 3.6 13.3 + - - +
25A ARG* 3.1 31.9 + - + +
17B VAL* 3.4 13.7 + - - +
18B THR* 3.6 22.7 - - + +
21B THR* 2.9 30.8 + - + -
25B ARG* 4.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.0 38.2 + - - +
19A THR* 3.8 22.5 + - - +
20A LEU 3.3 0.2 - - - -
21A THR* 1.3 74.2 - - - +
23A ARG* 1.3 65.3 + - - +
25A ARG* 3.2 13.0 - - + +
26A ARG* 3.2 20.1 + - - +
25B ARG* 5.9 4.6 - - - +
46B ARG* 3.6 52.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR 3.3 12.6 + - - +
20A LEU* 3.5 9.9 - - + +
22A ARG* 1.3 72.5 - - - +
24A LEU* 1.3 66.6 + - - +
26A ARG* 3.1 14.7 + - - +
27A GLU* 3.0 49.6 + - - +
114A TRP* 3.4 30.6 - - + +
142B ALA* 2.7 45.6 + - - +
143B GLN 3.7 1.8 - - - -
144B PHE* 2.9 41.8 + - - +
145B GLU* 3.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.1 23.6 + - + +
21A THR* 3.7 7.6 - - - +
23A ARG* 1.3 78.4 - - - +
25A ARG* 1.3 62.9 + - - +
27A GLU* 3.3 12.4 + - - -
28A ALA 3.5 0.2 + - - -
111A ARG* 3.1 58.8 - - + +
114A TRP* 4.3 16.4 - - + -
115A LEU* 4.4 10.5 - - + -
14B ARG* 4.0 25.8 - - + -
17B VAL* 3.8 29.4 - - + -
18B THR* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.1 23.0 + - + +
22A ARG* 3.2 17.0 - - + +
23A ARG 3.1 1.0 - - - -
24A LEU* 1.3 75.2 - - - +
26A ARG* 1.3 61.5 + - - +
28A ALA* 3.1 23.2 + - - +
29A GLN 4.6 0.2 + - - -
35A PHE* 3.8 35.4 - - + -
111A ARG* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG 3.2 7.8 + - - +
23A ARG* 3.1 19.7 + - - +
25A ARG* 1.3 76.9 - - - +
27A GLU* 1.3 64.7 + - + +
28A ALA 3.2 1.4 + - - -
29A GLN* 3.4 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.0 45.7 + - - +
24A LEU* 3.6 11.2 - - - +
25A ARG 3.2 0.8 - - - -
26A ARG* 1.3 77.4 - - - +
28A ALA* 1.3 64.8 + - - +
29A GLN* 3.1 7.2 + - - +
110A LYS* 4.6 11.8 - - - +
111A ARG* 4.0 17.0 - - + +
114A TRP* 3.3 49.3 + - + +
----------------------------------------------------------
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