Contacts of the helix formed by residues 2 - 19 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C LEU 5.2 2.6 + - - -
1C MET* 1.3 81.8 - - + +
3C LYS* 1.3 65.1 + - - +
4C HIS 3.3 2.0 - - - -
5C THR* 3.1 16.6 + - + +
6C LEU* 2.9 41.5 + - + +
29C LEU 6.1 1.1 - - - +
34C ASN* 5.6 7.7 + - - +
37C ALA* 5.7 2.0 - - - +
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Residues in contact with LYS 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C LEU* 3.8 39.6 - - + +
1C MET 3.3 2.6 - - - -
2C THR* 1.3 78.5 + - - +
4C HIS* 1.3 62.8 + - - +
6C LEU* 3.3 15.1 + - + +
7C GLU* 3.1 47.1 + - + +
44C ILE* 4.8 9.6 - - + -
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Residues in contact with HIS 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C LEU 4.9 1.6 + - - +
1C MET 4.5 6.1 + - - +
2C THR 3.3 0.4 - - - -
3C LYS* 1.3 78.9 - - - +
5C THR* 1.3 65.5 + - - +
7C GLU* 3.3 10.4 + - + +
8C GLN* 3.1 53.8 + - + +
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Residues in contact with THR 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 4.4 2.9 + - - -
2C THR* 3.1 22.8 + - + +
4C HIS* 1.3 79.9 - - - +
6C LEU* 1.3 61.8 + - + +
8C GLN* 3.2 19.2 + - - +
9C LEU* 3.0 46.0 + - + +
29C LEU* 4.9 21.3 - - + +
30C ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 2.9 35.2 + - + +
3C LYS* 3.5 17.5 - - + +
4C HIS 3.2 0.2 - - - -
5C THR* 1.3 76.3 - - - +
7C GLU* 1.3 58.1 + - - +
9C LEU* 3.3 1.7 + - - +
10C ALA* 2.9 32.4 + - - +
30C ILE* 4.1 25.4 - - + -
37C ALA* 4.1 19.5 - - + +
40C ALA* 4.1 20.9 - - + -
41C ILE* 4.0 22.6 - - + +
44C ILE* 5.1 11.7 - - + -
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 3.1 47.2 + - + +
4C HIS* 3.5 14.4 - - + +
6C LEU* 1.3 73.9 - - - +
8C GLN* 1.3 62.0 + - + +
10C ALA* 3.5 6.0 + - - +
11C ALA* 3.0 23.9 + - - +
14C ARG* 5.2 2.6 + - - -
44C ILE* 3.6 30.5 - - + +
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 3.1 44.8 + - + +
5C THR* 3.4 23.9 - - + +
7C GLU* 1.3 76.3 - - + +
9C LEU* 1.3 59.9 + - + +
11C ALA* 3.3 7.3 + - - +
12C ASP* 3.0 36.1 + - - +
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 3.0 27.9 + - + +
6C LEU* 3.8 2.9 - - - +
8C GLN* 1.3 73.1 - - + +
10C ALA* 1.3 67.9 + - - +
12C ASP* 3.1 18.9 + - - +
13C LEU* 3.0 25.7 + - - +
23C ILE* 5.3 0.2 - - - +
26C LEU* 3.9 32.8 - - + +
29C LEU* 4.2 31.6 - - + -
30C ILE* 3.4 33.2 - - + -
41C ILE* 3.9 18.8 - - + -
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU 2.9 18.1 + - - +
7C GLU 3.6 5.4 - - - +
9C LEU* 1.3 75.3 - - - +
11C ALA* 1.3 58.4 + - - +
13C LEU* 3.2 2.5 + - - -
14C ARG* 3.0 23.9 + - - +
41C ILE* 3.8 16.5 - - + +
44C ILE* 3.9 26.9 - - + -
45C ASN* 3.3 32.5 + - - +
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU 3.0 18.7 + - - +
8C GLN* 3.6 6.7 - - - +
9C LEU 3.2 0.2 - - - -
10C ALA* 1.3 72.3 - - - +
12C ASP* 1.3 62.2 + - - +
14C ARG* 3.2 28.1 + - - +
15C ARG* 2.9 41.5 + - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.0 22.6 + - - +
9C LEU* 3.1 26.2 + - + +
11C ALA* 1.3 76.5 - - - +
13C LEU* 1.3 55.4 + - - +
15C ARG* 2.6 36.2 + - - +
16C ALA* 2.9 28.6 + - - +
23C ILE* 3.9 26.0 - - + +
26C LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 3.0 9.5 + - - +
10C ALA 3.4 8.3 - - - +
12C ASP* 1.3 73.4 - - - +
14C ARG* 1.3 64.9 + - - +
16C ALA* 3.4 4.7 + - - +
17C ALA* 3.2 22.0 + - - +
23C ILE* 3.7 23.1 - - + -
26C LEU* 3.7 28.5 - - + -
41C ILE* 3.8 17.5 - - + -
45C ASN* 3.8 9.2 - - - +
143C ARG* 3.9 22.6 - - + +
144C ILE* 4.7 4.7 - - + -
156C ALA 3.6 24.7 - - - +
157C ASP* 4.0 18.8 - - - +
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Residues in contact with ARG 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 5.2 2.6 + - - -
10C ALA* 3.0 18.3 + - - +
11C ALA* 3.2 29.4 + - - +
13C LEU* 1.3 75.1 - - - +
15C ARG* 1.3 59.2 + - - +
17C ALA* 3.2 7.9 + - - +
18C GLU* 3.0 40.9 + - - +
44C ILE* 4.5 6.9 - - - +
45C ASN* 2.8 48.8 + - - +
48C HIS* 3.7 52.8 + - - +
49C ASP* 4.8 4.3 - - - -
1263C K 4.6 8.1 - - - -
1310C NA 4.5 8.1 - - - -
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 2.9 22.3 + - - +
12C ASP* 2.6 38.6 + - - +
14C ARG* 1.3 74.9 - - - +
16C ALA* 1.3 65.1 + - - +
18C GLU* 3.2 9.2 + - - +
19C GLN* 3.0 43.9 + - - +
15M ARG* 3.7 37.0 - - - +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP 2.9 18.0 + - - +
13C LEU* 3.5 9.2 - - - +
14C ARG 3.3 0.2 - - - -
15C ARG* 1.3 76.0 - - - +
17C ALA* 1.3 57.2 + - - +
19C GLN* 5.0 2.5 - - - +
20C GLY* 3.0 24.8 + - - -
21C GLU 3.2 29.9 + - - +
23C ILE* 4.1 11.0 - - + +
100C LEU* 4.2 2.3 - - - +
143C ARG* 3.8 28.3 - - + +
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU 3.2 10.4 + - - +
14C ARG* 3.2 10.0 + - - +
16C ALA* 1.3 79.4 - - - +
18C GLU* 1.3 61.8 + - - +
19C GLN 3.3 0.7 + - - -
20C GLY* 3.4 9.8 + - - -
100C LEU* 5.4 2.4 - - - +
143C ARG* 3.8 21.2 - - + +
8M GLN* 3.9 19.6 + - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG* 3.0 30.3 + - + +
15C ARG* 3.7 8.5 - - - +
17C ALA* 1.3 75.7 - - - +
19C GLN* 1.3 59.6 + - - +
1263C K 3.5 17.8 - - - -
8M GLN* 3.8 35.0 - - + +
11M ALA* 3.7 21.4 - - - +
12M ASP* 2.9 32.9 - - - +
15M ARG* 3.3 26.3 + - - +
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Residues in contact with GLN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 3.0 34.3 + - - +
16C ALA* 5.3 0.4 - - - +
18C GLU* 1.3 77.0 - - - +
20C GLY* 1.3 63.4 + - - +
21C GLU* 3.4 42.2 + - + +
12M ASP* 4.3 2.9 - - - +
15M ARG* 3.1 40.0 + - - +
19M GLN* 5.5 1.4 + - - -
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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