Contacts of the helix formed by residues 2 - 19 (chain M) in PDB entry 2WQT
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 2 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0M LEU 5.0 3.1 + - - -
1M MET* 1.3 81.9 + - + +
3M LYS* 1.3 60.4 + - - +
4M HIS 3.3 2.2 - - - -
5M THR* 3.1 16.3 + - - +
6M LEU* 2.8 47.7 + - - +
29M LEU 6.1 1.1 - - - +
34M ASN* 5.6 8.4 + - - +
37M ALA* 5.7 1.4 - - - +
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Residues in contact with LYS 3 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLN* 2.9 29.7 + - - +
53C GLY* 4.9 5.2 - - - +
0M LEU* 3.9 33.6 - - + +
1M MET 3.2 2.6 - - - -
2M THR* 1.3 79.2 + - - +
4M HIS* 1.3 63.4 + - - +
6M LEU* 3.3 14.5 + - + +
7M GLU* 3.0 45.3 + - + +
44M ILE* 4.8 11.0 - - + -
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Residues in contact with HIS 4 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP* 3.7 29.3 + - - -
52C GLN* 4.4 9.2 + - - +
54C ARG* 3.6 47.0 + - + +
85C ASP* 4.0 13.9 - - - +
98C ARG* 5.3 5.6 - - - -
1263C K 4.3 11.9 - - - -
1310C NA 4.3 8.6 - - - -
0M LEU 5.3 1.2 + - - -
1M MET 4.5 2.3 + - - +
2M THR 3.3 0.4 - - - -
3M LYS* 1.3 78.0 - - - +
5M THR* 1.3 66.4 + - - +
7M GLU* 3.3 9.5 + - - +
8M GLN* 3.1 49.3 + - - +
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Residues in contact with THR 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG* 5.3 13.6 + - - -
1M MET 4.4 3.3 + - - -
2M THR* 3.1 22.6 + - + +
4M HIS* 1.3 79.9 - - - +
6M LEU* 1.3 62.2 + - + +
8M GLN* 3.2 20.5 + - - +
9M LEU* 2.9 46.2 + - + +
29M LEU* 4.9 20.2 - - + +
30M ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M THR* 2.8 38.5 + - + +
3M LYS* 3.5 14.6 - - + +
4M HIS 3.2 0.2 - - - -
5M THR* 1.3 80.1 - - - +
7M GLU* 1.3 57.5 + - - +
9M LEU* 3.3 3.4 + - - +
10M ALA* 2.9 31.9 + - - +
30M ILE* 4.1 25.8 - - + -
37M ALA* 4.1 20.0 - - + +
40M ALA* 4.1 20.6 - - + -
41M ILE* 4.0 22.0 - - + +
44M ILE* 5.1 11.9 - - + -
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Residues in contact with GLU 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 5.5 0.4 - - - -
52C GLN* 3.5 44.9 - - + +
1263C K 4.7 3.4 - - - -
3M LYS* 3.0 47.3 + - + +
4M HIS* 3.3 9.2 + - - +
6M LEU* 1.3 74.0 - - - +
8M GLN* 1.3 58.0 + - - +
10M ALA* 3.5 6.1 + - - +
11M ALA* 3.0 29.3 + - - +
14M ARG* 5.2 2.3 + - - -
44M ILE* 3.6 30.5 - - + +
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Residues in contact with GLN 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA* 3.9 17.5 + - - +
18C GLU* 3.8 45.6 - - + +
1263C K 4.5 4.3 - - - -
4M HIS* 3.1 44.3 + - + +
5M THR* 3.4 24.1 - - + +
7M GLU* 1.3 76.4 - - - +
9M LEU* 1.3 59.3 + - + +
11M ALA* 3.3 4.6 + - - +
12M ASP* 3.0 35.1 + - - +
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Residues in contact with LEU 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M THR* 2.9 28.4 + - + +
6M LEU 3.8 3.8 - - - +
8M GLN* 1.3 74.7 - - + +
10M ALA* 1.3 65.8 + - - +
12M ASP* 3.1 18.6 + - - +
13M LEU* 3.0 26.2 + - - +
26M LEU* 4.0 32.1 - - + +
29M LEU* 4.2 30.5 - - + -
30M ILE* 3.4 33.0 - - + -
41M ILE* 4.0 18.4 - - + -
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Residues in contact with ALA 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU 2.9 18.7 + - - +
7M GLU 3.6 4.5 - - - +
9M LEU* 1.3 75.9 - - - +
11M ALA* 1.3 57.4 + - - +
13M LEU 3.3 1.7 + - - -
14M ARG* 3.0 24.1 + - - +
41M ILE* 3.8 16.9 - - + +
44M ILE* 3.9 26.9 - - + -
45M ASN* 3.2 33.7 + - - +
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Residues in contact with ALA 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.7 26.5 - - - +
7M GLU 3.0 18.3 + - - +
8M GLN 3.5 5.4 - - - +
10M ALA* 1.3 73.6 - - - +
12M ASP* 1.3 65.5 + - - +
14M ARG* 3.1 28.8 + - - +
15M ARG* 2.9 29.9 + - - +
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Residues in contact with ASP 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.9 32.5 - - - +
19C GLN* 4.3 2.8 - - - +
8M GLN 3.0 18.2 + - - +
9M LEU* 3.1 25.7 + - + +
11M ALA* 1.3 75.1 - - - +
13M LEU* 1.3 58.1 + - - +
15M ARG* 2.7 36.4 + - - +
16M ALA* 2.9 28.1 + - - +
23M ILE* 3.9 26.1 - - + +
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Residues in contact with LEU 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LEU 3.0 9.9 + - - +
10M ALA 3.4 9.0 - - - +
11M ALA 3.2 0.2 - - - -
12M ASP* 1.3 76.2 - - - +
14M ARG* 1.3 63.3 + - - +
16M ALA* 3.5 4.1 + - - +
17M ALA* 3.2 21.7 + - - +
23M ILE* 3.7 23.3 - - + -
26M LEU* 3.7 28.5 - - + -
41M ILE* 3.8 16.8 - - + -
45M ASN* 3.8 8.5 - - - +
143M ARG* 3.9 23.7 - - + +
144M ILE* 4.7 5.2 - - + -
156M ALA 3.6 25.6 - - - +
157M ASP* 4.0 18.4 - - - +
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Residues in contact with ARG 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M GLU* 5.2 2.6 + - - -
10M ALA* 3.0 17.7 + - - +
11M ALA* 3.1 29.6 + - - +
13M LEU* 1.3 75.5 - - - +
15M ARG* 1.3 59.2 + - - +
17M ALA* 3.3 6.7 + - - +
18M GLU* 3.0 42.8 + - - +
44M ILE* 4.5 6.9 - - - +
45M ASN* 2.8 48.3 + - - +
48M HIS* 3.7 52.8 + - - +
49M ASP* 4.8 5.4 - - - -
1307M NA 4.4 8.5 - - - -
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Residues in contact with ARG 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 3.7 28.3 - - - +
18C GLU* 3.3 23.4 + - - +
19C GLN* 3.1 37.7 + - - +
11M ALA* 2.9 16.4 + - - +
12M ASP* 2.7 36.9 + - - +
14M ARG* 1.3 74.8 - - - +
16M ALA* 1.3 65.4 + - - +
18M GLU* 3.7 14.5 - - - +
19M GLN* 3.0 55.5 + - + +
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Residues in contact with ALA 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ASP 2.9 18.5 + - - +
13M LEU* 3.5 8.1 - - - +
15M ARG* 1.3 77.4 - - - +
17M ALA* 1.3 56.4 + - - +
19M GLN* 5.0 1.8 - - - +
20M GLY* 3.0 25.5 + - - -
21M GLU 3.2 30.6 + - - +
23M ILE* 4.1 11.0 - - + +
100M LEU* 4.2 1.6 - - - +
143M ARG* 3.8 28.3 - - + +
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Residues in contact with ALA 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LEU 3.2 10.2 + - - +
14M ARG* 3.6 9.2 - - - +
15M ARG 3.2 0.4 - - - -
16M ALA* 1.3 79.1 - - - +
18M GLU* 1.3 63.2 + - + +
19M GLN 3.2 0.9 + - - -
20M GLY* 3.4 10.0 + - - -
100M LEU* 5.3 2.7 - - - -
143M ARG* 4.1 20.2 - - + +
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Residues in contact with GLU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ARG* 3.0 32.9 + - - +
15M ARG* 3.7 15.9 - - - +
17M ALA* 1.3 76.2 - - + +
19M GLN* 1.3 62.8 + - + +
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Residues in contact with GLN 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLN* 5.5 1.4 + - - -
15M ARG* 3.0 46.7 + - + +
16M ALA* 5.1 1.0 - - - +
18M GLU* 1.3 79.7 - - + +
20M GLY* 1.3 63.1 + - - +
21M GLU* 3.3 40.0 + - + +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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