Contacts of the helix formed by residues 15 - 30 (chain A) in PDB entry 1QMU
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 HIS 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A HIS* 4.0 9.9 + - + +
14A HIS* 1.3 75.4 - - - +
16A PHE* 1.3 68.4 + - - +
17A SER* 3.3 4.7 - - - +
18A ASP* 3.0 17.5 + - - +
19A MET* 2.9 17.5 + - - +
81A ARG* 3.5 0.4 - - - -
121A TYR* 3.4 25.0 + + - -
122A GLU* 2.8 33.1 + - - +
124A SER 5.7 3.6 - - - -
278A TYR* 4.1 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 1.3 70.6 - - - +
17A SER* 1.3 67.9 + - - +
19A MET* 2.9 13.5 + - - +
20A GLU* 2.7 47.6 + - + +
46A ARG* 3.9 32.5 - - + +
47A GLU* 3.4 40.6 - - + -
49A TYR* 3.8 19.1 - + - -
81A ARG* 3.3 11.2 - - - +
115A SER* 6.1 0.2 - - - -
118A PRO* 3.7 27.6 - - + -
122A GLU* 2.9 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 3.3 3.7 - - - +
16A PHE* 1.3 80.6 - - - +
18A ASP* 1.3 65.0 + - - +
20A GLU* 3.3 7.5 + - - +
21A ILE* 3.0 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 4.2 31.2 + - - +
14A HIS* 4.3 10.1 - - + -
15A HIS* 3.0 22.4 + - - +
17A SER* 1.3 78.0 + - - +
19A MET* 1.3 56.3 + - - +
20A GLU 3.2 1.3 - - - -
21A ILE* 3.5 19.2 - - + +
22A PHE* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 4.1 10.5 - - + +
15A HIS 2.9 12.6 + - - +
16A PHE* 3.5 20.4 - - - +
18A ASP* 1.3 73.8 - - - +
20A GLU* 1.3 62.4 + - - +
22A PHE* 3.6 5.5 - - - +
23A LEU* 2.8 49.2 + - + +
49A TYR* 5.8 2.7 - - - -
81A ARG* 2.9 63.0 - - + +
85A LEU* 3.9 20.2 - - + -
114A PRO* 4.0 20.4 - - + -
115A SER* 4.0 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 2.7 28.7 + - + +
17A SER* 3.4 11.4 - - - +
19A MET* 1.3 78.4 - - - +
21A ILE* 1.3 65.5 + - + +
23A LEU* 3.5 5.1 - - - +
24A ARG* 2.8 70.0 + - + +
47A GLU* 5.0 1.6 - - - +
49A TYR* 3.1 39.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.0 24.5 + - - +
18A ASP* 3.5 23.3 - - - +
20A GLU* 1.3 77.8 - - + +
22A PHE* 1.3 55.7 + - - +
24A ARG* 3.1 8.7 + - - +
25A ARG* 2.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 3.2 30.3 - - + -
14A HIS* 4.1 13.2 - + + -
18A ASP 2.7 21.7 + - - +
19A MET* 3.6 6.7 - - - +
21A ILE* 1.3 74.0 - - - +
23A LEU* 1.3 68.7 + - + +
25A ARG* 3.2 17.0 + - - +
26A TYR* 3.2 53.0 + + - -
85A LEU* 3.5 57.0 - - + -
86A ASN* 4.8 1.1 - - - -
88A ILE* 4.3 9.6 - - + -
89A GLU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 2.8 46.8 + - + +
20A GLU* 3.5 3.4 - - - +
22A PHE* 1.3 76.8 - - + +
24A ARG* 1.3 58.3 + - - +
26A TYR* 3.2 7.0 + - - +
27A ALA* 2.9 26.5 + - - +
36A LEU* 3.9 14.2 - - + +
49A TYR* 3.8 38.4 - - + -
51A MET* 3.6 30.8 - - + +
85A LEU* 4.3 15.7 - - + -
88A ILE* 4.6 9.4 - - + -
114A PRO* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 2.8 63.6 + - + +
21A ILE* 3.7 7.4 - - - +
23A LEU* 1.3 71.0 - - - +
25A ARG* 1.3 66.7 + - - +
27A ALA* 3.1 3.0 + - - +
28A ASN* 2.9 38.3 + - - +
36A LEU* 4.0 19.7 - - + +
49A TYR* 3.6 14.0 + - + +
----------------------------------------------------------
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 ILE* 2.8 18.6 + - + +
22A PHE* 3.2 13.7 + - - +
24A ARG* 1.3 76.8 - - - +
26A TYR* 1.3 80.6 + - + +
28A ASN* 3.4 5.0 + - - +
29A GLU* 2.8 68.7 + - + +
93A LYS* 5.1 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.2 57.3 + + - -
23A LEU 3.2 7.2 + - - +
25A ARG* 1.3 95.8 + - + +
27A ALA* 1.3 67.5 + - - +
29A GLU* 5.3 2.7 - - + -
30A TYR* 3.2 52.3 + + - +
34A THR* 3.6 8.8 + - - +
51A MET* 5.0 2.0 - - - -
88A ILE* 4.2 17.3 - - + -
89A GLU* 3.0 43.4 + - + +
92A CYS* 3.9 14.8 - - + -
93A LYS* 3.2 21.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.9 14.0 + - - +
24A ARG* 3.1 8.5 + - - +
26A TYR* 1.3 77.6 - - - +
28A ASN* 1.3 66.2 + - - +
31A PRO* 3.5 16.5 - - - +
34A THR* 3.3 23.5 + - - +
35A ARG* 5.8 0.2 - - - -
36A LEU* 3.8 33.4 - - + +
51A MET* 4.5 2.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.9 29.3 + - - +
25A ARG* 3.8 4.8 - - - +
27A ALA* 1.3 81.3 - - - +
29A GLU* 1.3 63.8 + - + +
31A PRO* 3.3 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 2.8 59.8 + - + +
26A TYR* 5.3 1.4 - - - -
28A ASN* 1.3 73.9 - - - +
30A TYR* 1.3 95.6 + - + +
31A PRO* 3.4 5.7 - - - +
93A LYS* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.2 41.8 + + - +
27A ALA 3.8 0.7 - - - -
29A GLU* 1.3 107.9 + - + +
31A PRO* 1.3 55.8 - - - +
32A SER* 3.1 8.1 - - - +
33A ILE* 3.1 14.7 + - + -
34A THR* 2.8 40.9 + - + -
92A CYS* 3.3 38.1 - - + -
93A LYS* 3.6 25.1 - - - +
----------------------------------------------------------
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