Contacts of the helix formed by residues 4 - 23 (chain A) in PDB entry 4QYD
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 GLN 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 1.3 68.6 + - + +
6A THR* 3.5 10.1 + - - +
7A PRO* 3.2 28.9 - - + +
8A PHE* 3.2 22.9 + - - +
114A MET* 5.2 5.6 - - - +
115A GLY* 4.7 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 1.3 77.4 - - + +
6A THR* 1.3 58.7 + - - +
8A PHE* 3.2 13.0 + - + +
9A LEU* 2.9 52.6 + - + +
60A TYR* 3.9 24.5 - - + -
63A LEU* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.5 10.9 + - - +
5A LEU* 1.3 78.8 - - - +
7A PRO* 1.4 73.6 - - + +
9A LEU* 3.3 5.9 + - - +
10A ILE* 3.1 38.7 + - + +
13A ARG* 5.2 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
4A GLN* 3.2 36.6 - - + +
6A THR* 1.4 97.5 - - + +
8A PHE* 1.3 55.2 + - - +
10A ILE* 3.5 11.4 + - + +
11A LEU* 3.0 26.7 + - - +
114A MET* 3.6 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN 3.2 17.8 + - - +
5A LEU* 3.6 12.6 - - + +
6A THR 3.2 0.6 - - - -
7A PRO* 1.3 79.0 - - - +
9A LEU* 1.3 62.4 + - + +
11A LEU* 3.2 14.4 + - + +
12A LEU* 2.9 63.7 + - + +
62A TYR 3.6 17.3 - - - -
63A LEU 4.0 4.5 - - - -
64A ASN* 3.5 34.1 - - - -
65A PHE* 3.6 4.3 - + - -
111A ALA* 4.3 10.5 - - + -
114A MET* 3.9 13.9 - - + -
116A ILE* 3.9 27.1 - - + -
----------------------------------------------------------
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 LEU* 2.9 37.3 + - + +
6A THR* 3.9 5.6 - - - +
8A PHE* 1.3 77.8 - - + +
10A ILE* 1.3 60.4 + - - +
12A LEU* 3.2 7.3 + - + +
13A ARG* 2.9 60.8 + - - +
57A LEU* 4.1 27.0 - - + +
58A GLU* 5.9 0.2 - - - -
60A TYR* 3.4 39.0 - - + +
62A TYR 4.0 17.5 - - - +
63A LEU* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.1 31.3 + - + +
7A PRO* 3.7 11.7 - - + +
8A PHE 3.3 0.2 - - - -
9A LEU* 1.3 75.4 - - - +
11A LEU* 1.3 64.2 + - - +
13A ARG* 3.4 19.8 + - - +
14A LYS* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO 3.0 14.5 + - - +
8A PHE* 3.2 15.2 + - + +
10A ILE* 1.3 78.1 - - - +
12A LEU* 1.3 60.2 + - + +
14A LYS* 3.4 12.1 + - + +
15A THR* 2.8 45.0 + - - +
65A PHE* 5.0 3.1 - - + -
107A ALA* 3.8 10.1 - - + +
110A GLN* 3.9 20.6 - - + -
111A ALA* 3.6 41.7 - - + +
114A MET* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 2.9 54.2 + - + +
9A LEU* 3.2 14.1 + - + +
11A LEU* 1.3 80.1 - - + +
13A ARG* 1.3 52.2 + - - +
15A THR* 3.2 3.5 + - - +
16A LEU* 2.8 37.1 + - - +
57A LEU* 3.7 13.9 - - + +
62A TYR* 3.6 32.1 - - + +
65A PHE* 3.9 20.6 - - + -
68A PHE* 3.8 30.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 2.9 55.0 + - - +
10A ILE* 3.7 21.2 - - - +
12A LEU* 1.3 76.9 - - - +
14A LYS* 1.3 57.3 + - - +
16A LEU* 3.4 3.0 + - - +
17A GLU* 2.9 41.6 + - - +
54A LYS* 3.8 13.2 - - - +
57A LEU* 3.6 21.0 - - + +
58A GLU* 2.7 39.5 + - - +
60A TYR* 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.1 26.2 + - - +
11A LEU* 3.7 12.3 - - + +
13A ARG* 1.3 76.7 - - - +
15A THR* 1.3 62.9 + - - +
17A GLU* 3.3 13.0 + - + +
18A GLN* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.8 31.9 + - - +
12A LEU* 3.5 6.6 - - - -
14A LYS* 1.3 77.2 - - - +
16A LEU* 1.3 58.0 + - - +
18A GLN* 3.2 8.1 + - - +
19A LEU* 3.0 32.4 + - + +
65A PHE* 4.9 0.7 - - + -
68A PHE* 3.6 24.9 - - + -
103A VAL* 3.9 15.9 - - + -
104A LEU* 4.1 4.7 - - + -
107A ALA* 3.3 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 2.8 21.2 + - - +
13A ARG* 3.7 4.5 - - - +
15A THR* 1.3 74.2 - - - +
17A GLU* 1.3 56.8 + - + +
19A LEU* 3.3 5.4 + - + +
20A GLN* 2.9 39.5 + - - +
50A PHE* 3.6 35.2 - - + +
53A MET* 4.1 20.9 - - + -
54A LYS* 3.7 43.7 - - + +
57A LEU* 4.1 14.1 - - + -
68A PHE* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.9 31.5 + - + +
14A LYS* 3.6 9.7 + - + +
16A LEU* 1.3 76.4 - - + +
18A GLN* 1.3 57.7 + - + +
20A GLN* 3.4 8.4 + - - +
21A GLU* 2.9 41.0 + - - +
54A LYS* 6.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 3.0 32.4 + - + +
15A THR* 3.7 8.3 - - - +
17A GLU* 1.3 74.6 - - + +
19A LEU* 1.3 64.8 + - - +
21A GLU* 3.2 25.9 + - - +
22A LYS* 3.2 24.9 + - - +
103A VAL* 3.9 28.4 - - + +
106A GLN* 4.8 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.0 32.9 + - + +
16A LEU* 3.3 11.4 + - + +
18A GLN* 1.3 74.2 - - - +
20A GLN* 1.3 62.8 + - - +
22A LYS* 3.1 21.3 + - - +
23A ASP 3.5 4.2 + - - -
50A PHE* 3.8 21.0 - - + -
68A PHE* 4.1 18.4 - - + -
72A PHE* 3.8 30.1 - - + -
96A LEU* 3.9 3.5 - - + +
100A GLY* 3.6 39.0 - - - +
103A VAL* 3.8 13.0 - - + -
104A LEU* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 2.9 25.7 + - - +
17A GLU* 3.7 6.8 - - - +
19A LEU* 1.3 76.8 - - - +
21A GLU* 1.3 62.0 + - - +
23A ASP* 3.1 23.3 + - + +
26A ASN* 5.1 5.2 - - - +
29A SER* 4.0 24.0 + - - +
50A PHE* 3.4 49.6 - - + +
51A PHE* 5.0 0.8 - - - +
54A LYS* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 2.9 27.9 + - + +
18A GLN* 3.5 20.9 - - - +
19A LEU 3.2 0.4 - - - -
20A GLN* 1.3 77.0 - - - +
22A LYS* 1.3 64.8 + - + +
23A ASP 3.5 0.7 + - - -
24A THR* 3.8 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.2 20.2 - - - +
19A LEU* 3.1 12.0 + - - +
21A GLU* 1.3 78.9 - - + +
23A ASP* 1.3 57.9 + - - +
24A THR* 3.0 16.0 + - - +
96A LEU* 3.8 17.3 - - + +
99A GLN* 3.9 51.5 - - + +
100A GLY 4.8 0.9 - - - +
103A VAL* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU 3.5 1.8 + - - +
20A GLN* 3.1 18.8 + - + +
21A GLU 4.2 0.7 - - - -
22A LYS* 1.3 75.3 - - - +
24A THR* 1.3 61.4 + - - +
25A GLY 3.8 2.4 + - - -
26A ASN* 3.1 20.6 + - - +
27A ILE* 2.9 26.8 + - - +
28A PHE* 2.8 48.6 + - + +
29A SER* 3.8 4.5 + - - -
50A PHE* 3.9 17.8 - - + -
92A ALA* 5.5 1.6 - - - +
96A LEU* 4.5 5.3 - - + +
----------------------------------------------------------
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