Contacts of the helix formed by residues 2 - 19 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B LEU 5.0 3.6 + - - -
1B MET* 1.3 82.0 + - + +
3B LYS* 1.3 65.2 + - - +
4B HIS 3.3 2.2 - - - -
5B THR* 3.1 15.5 + - - +
6B LEU* 2.9 41.8 + - - +
29B LEU 6.1 1.1 - - - +
34B ASN* 5.6 8.3 + - - +
37B ALA* 5.7 2.2 - - - +
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Residues in contact with LYS 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B LEU* 3.7 43.7 + - + +
1B MET 3.2 2.8 - - - -
2B THR* 1.3 78.8 + - - +
4B HIS* 1.3 62.3 + - - +
6B LEU* 3.3 14.8 + - + +
7B GLU* 3.0 45.3 + - + +
44B ILE* 4.9 9.2 - - + -
52G GLN* 3.2 28.7 + - - +
53G GLY* 5.2 2.6 - - - -
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Residues in contact with HIS 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B LEU 4.7 1.6 + - - +
1B MET 4.4 2.3 + - - +
2B THR 3.3 0.6 - - - -
3B LYS* 1.3 78.0 - - - +
5B THR* 1.3 65.2 + - - +
7B GLU* 3.3 8.8 + - - +
8B GLN* 3.1 48.8 + - - +
49G ASP* 3.8 25.5 + - - -
52G GLN* 4.3 12.1 + - - +
54G ARG* 3.8 45.6 + - + +
85G ASP* 4.2 12.8 - - - +
98G ARG* 5.4 5.8 - - - -
1265G K 4.3 13.2 - - - -
1313G NA 4.4 5.2 - - - -
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Residues in contact with THR 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.4 2.9 + - - -
2B THR* 3.1 23.4 + - + +
4B HIS* 1.3 79.8 - - - +
6B LEU* 1.3 62.1 + - + +
8B GLN* 3.2 20.5 + - + +
9B LEU* 2.9 46.4 + - + +
29B LEU* 4.9 20.9 - - + +
30B ILE* 5.7 0.7 - - + -
98G ARG* 5.4 11.5 + - - -
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 2.9 37.0 + - - +
3B LYS* 3.4 13.7 - - + +
5B THR* 1.3 76.3 - - - +
7B GLU* 1.3 59.4 + - - +
9B LEU* 3.3 2.9 + - - +
10B ALA* 2.9 31.4 + - - +
30B ILE* 4.1 19.1 - - + -
37B ALA* 4.1 26.2 - - + +
40B ALA* 4.1 21.8 - - + -
41B ILE* 3.9 22.6 - - + +
44B ILE* 5.1 11.2 - - + -
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 3.0 47.1 + - + +
4B HIS* 3.5 8.7 - - + +
6B LEU* 1.3 74.7 - - - +
8B GLN* 1.3 64.0 + - + +
10B ALA* 3.4 5.3 + - - +
11B ALA* 3.0 24.8 + - - +
14B ARG* 5.3 3.1 + - - -
44B ILE* 3.6 31.5 - - + +
18G GLU* 5.5 0.7 - - - -
52G GLN* 3.6 42.3 - - + +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS* 3.1 43.1 + - + +
5B THR* 3.2 23.8 + - + +
7B GLU* 1.3 77.2 - - - +
9B LEU* 1.3 59.2 + - + +
11B ALA* 3.3 4.5 + - - +
12B ASP* 3.0 33.7 + - - +
17G ALA* 3.8 17.3 + - - +
18G GLU* 3.6 48.7 - - + +
1265G K 4.4 3.8 - - - -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR* 2.9 27.1 + - + +
6B LEU 3.9 3.6 - - - +
8B GLN* 1.3 74.0 - - + +
10B ALA* 1.3 67.1 + - - +
12B ASP* 3.1 18.5 + - - +
13B LEU* 3.0 26.7 + - - +
26B LEU* 3.9 32.2 - - + +
29B LEU* 4.2 30.3 - - + -
30B ILE* 3.4 32.8 - - + -
41B ILE* 3.9 18.6 - - + -
18G GLU 5.7 0.7 - - - +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU 2.9 17.7 + - - +
7B GLU 3.6 4.7 - - - +
9B LEU* 1.3 77.1 - - - +
11B ALA* 1.3 57.2 + - - +
13B LEU* 3.3 2.0 + - - -
14B ARG* 3.0 24.7 + - - +
41B ILE* 3.8 16.5 - - + +
44B ILE* 3.8 27.4 - - + -
45B ASN* 3.3 31.1 + - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU 3.0 13.9 + - - +
8B GLN 3.5 9.0 - - - +
10B ALA* 1.3 72.7 - - - +
12B ASP* 1.3 60.4 + - - +
14B ARG* 3.2 27.9 + - - +
15B ARG* 2.9 33.5 + - - +
18G GLU* 3.7 25.4 - - - +
1262G PO4 4.8 7.5 + - - +
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.0 19.2 + - - +
9B LEU* 3.1 25.9 + - + +
11B ALA* 1.3 75.5 - - - +
13B LEU* 1.3 56.8 + - - +
15B ARG* 2.6 35.7 + - - +
16B ALA* 2.9 28.1 + - - +
23B ILE* 3.9 25.5 - - + +
18G GLU* 3.0 28.3 - - - +
19G GLN* 4.2 3.3 - - - +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.0 9.4 + - - +
10B ALA 3.5 8.3 - - - +
12B ASP* 1.3 74.7 - - - +
14B ARG* 1.3 63.7 + - - +
16B ALA* 3.4 3.9 + - - +
17B ALA* 3.2 22.3 + - - +
23B ILE* 3.7 22.9 - - + -
26B LEU* 3.7 28.5 - - + -
41B ILE* 3.8 17.7 - - + -
45B ASN* 3.9 8.7 - - - +
143B ARG* 3.9 22.6 - - + +
144B ILE* 4.7 4.9 - - + -
156B ALA 3.6 25.6 - - - +
157B ASP* 4.0 18.6 - - - +
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 5.3 2.4 + - - -
10B ALA* 3.0 18.3 + - - +
11B ALA* 3.2 29.4 + - - +
13B LEU* 1.3 74.6 - - - +
15B ARG* 1.3 58.3 - - - +
17B ALA* 3.3 7.1 + - - +
18B GLU* 3.0 40.1 + - - +
44B ILE* 4.5 7.5 - - - +
45B ASN* 2.8 50.2 + - + +
48B HIS* 3.7 52.2 + - - +
49B ASP* 4.8 4.7 - - - +
1264B K 4.3 8.7 - - - -
1262G PO4 5.8 0.8 + - - -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA 2.9 12.7 + - - +
12B ASP* 2.6 37.7 + - - +
14B ARG* 1.3 74.0 - - - +
16B ALA* 1.3 65.2 + - - +
18B GLU* 3.2 14.7 + - - +
19B GLN* 2.9 48.7 + - + +
1262B PO4 3.8 13.7 - - - -
15G ARG* 3.7 7.7 - - - +
18G GLU* 3.4 16.6 + - - +
19G GLN* 3.1 39.8 - - - +
1262G PO4 2.6 49.5 + - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASP 2.9 17.8 + - - +
13B LEU* 3.5 9.2 - - - +
14B ARG 3.3 0.2 - - - -
15B ARG* 1.3 76.2 - - - +
17B ALA* 1.3 56.4 + - - +
19B GLN* 5.0 2.2 - - - -
20B GLY* 3.0 25.5 + - - -
21B GLU 3.2 28.0 + - - +
23B ILE* 4.1 11.6 - - + +
100B LEU* 4.2 1.6 - - - +
143B ARG* 3.8 28.3 - - + +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 3.2 9.8 + - - +
14B ARG* 3.6 8.7 - - - +
15B ARG 3.2 0.6 - - - -
16B ALA* 1.3 79.8 - - - +
18B GLU* 1.3 63.0 + - + +
19B GLN 3.3 0.7 + - - -
20B GLY* 3.4 10.0 + - - -
100B LEU* 5.3 2.5 - - - -
143B ARG* 3.8 21.0 - - + +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.0 28.7 + - - +
15B ARG* 3.2 15.2 + - - +
17B ALA* 1.3 76.6 - - - +
19B GLN* 1.3 61.3 + - + +
20B GLY 3.9 0.2 + - - -
1264B K 3.4 18.7 - - - -
1262G PO4 4.1 14.1 + - - -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 2.9 37.4 + - + +
16B ALA* 4.1 1.3 - - - +
18B GLU* 1.3 81.0 - - + +
20B GLY* 1.3 63.7 + - - +
21B GLU* 3.3 34.6 + - + +
1262B PO4 2.7 40.0 + - - -
19G GLN* 5.5 0.2 + - - -
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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
------------------------------------------------------------
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