Contacts of the helix formed by residues 2 - 19 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0T LEU 4.5 6.1 + - - -
1T MET* 1.3 81.8 - - + +
3T LYS* 1.3 59.8 + - - +
4T HIS 3.3 1.8 - - - -
5T THR* 3.1 16.6 + - + +
6T LEU* 2.9 48.3 + - + +
29T LEU 6.0 1.3 - - - +
30T ILE* 6.6 0.4 - - - -
34T ASN* 5.6 8.1 + - - +
37T ALA* 5.7 1.7 - - - +
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Residues in contact with LYS 3 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLN* 3.1 29.1 + - - +
53L GLY* 5.1 2.6 - - - -
0T LEU* 3.5 46.7 + - + +
1T MET 3.2 2.6 - - - -
2T THR* 1.3 79.4 + - - +
4T HIS* 1.3 63.1 + - - +
6T LEU* 3.2 14.2 + - + +
7T GLU* 3.0 45.7 + - + +
44T ILE* 4.8 9.4 - - + -
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Residues in contact with HIS 4 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L ASP* 3.8 16.9 + - - -
52L GLN* 4.5 9.0 + - - +
54L ARG* 3.7 55.9 + - + +
85L ASP* 4.1 13.5 - - - +
98L ARG* 5.3 7.0 - - - -
1264L K 4.3 11.4 - - - -
1314L NA 4.1 11.1 - - - -
0T LEU 4.6 1.8 + - - -
1T MET 4.4 2.8 + - - +
2T THR 3.3 0.4 - - - -
3T LYS* 1.3 78.3 - - - +
5T THR* 1.3 66.0 + - - +
7T GLU* 3.3 9.8 + - - +
8T GLN* 3.1 47.5 + - + +
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Residues in contact with THR 5 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L ARG* 5.2 13.9 + - - -
1T MET 4.4 2.9 + - - -
2T THR* 3.1 23.4 + - + +
4T HIS* 1.3 80.5 - - - +
6T LEU* 1.3 61.9 + - + +
8T GLN* 3.1 20.3 + - + +
9T LEU* 2.9 47.0 + - + +
29T LEU* 4.9 20.2 - - + +
30T ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 6 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0T LEU 6.4 0.2 - - - +
2T THR* 2.9 37.7 + - - +
3T LYS* 3.4 13.5 - - + +
5T THR* 1.3 78.9 - - - +
7T GLU* 1.3 57.4 + - - +
9T LEU* 3.3 3.3 + - - +
10T ALA* 2.9 31.3 + - - +
30T ILE* 4.1 25.8 - - + -
37T ALA* 4.1 19.1 - - + +
40T ALA* 4.1 20.9 - - + -
41T ILE* 4.0 22.4 - - + +
44T ILE* 5.1 12.1 - - + -
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Residues in contact with GLU 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 5.5 0.9 - - - -
52L GLN* 3.6 42.8 - - + +
1264L K 4.7 4.0 - - - -
3T LYS* 3.0 47.2 + - + +
4T HIS* 3.5 8.1 - - - +
6T LEU* 1.3 75.7 - - - +
8T GLN* 1.3 61.0 + - - +
10T ALA* 3.4 5.7 + - - +
11T ALA* 3.0 24.1 + - - +
14T ARG* 5.3 2.6 + - - -
44T ILE* 3.6 30.7 - - + +
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Residues in contact with GLN 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L ARG 5.1 0.2 + - - -
17L ALA* 3.7 18.2 + - - +
18L GLU* 3.6 50.1 - - + +
1264L K 4.5 3.1 - - - -
4T HIS* 3.1 44.2 + - + +
5T THR* 3.1 23.7 + - + +
7T GLU* 1.3 76.4 - - - +
9T LEU* 1.3 59.9 + - + +
11T ALA* 3.3 4.7 + - - +
12T ASP* 3.0 33.7 + - - +
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Residues in contact with LEU 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU 5.6 0.4 - - - +
5T THR* 2.9 27.6 + - + +
6T LEU* 3.8 3.6 - - - +
8T GLN* 1.3 74.9 - - + +
10T ALA* 1.3 65.5 + - - +
12T ASP* 3.1 19.3 + - - +
13T LEU* 3.0 26.2 + - - +
23T ILE* 5.3 0.2 - - - +
26T LEU* 3.9 30.8 - - + +
29T LEU* 4.2 30.1 - - + -
30T ILE* 3.4 32.5 - - + -
41T ILE* 3.9 18.4 - - + -
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Residues in contact with ALA 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T LEU 2.9 17.5 + - - +
7T GLU 3.6 5.2 - - - +
9T LEU* 1.3 75.3 - - - +
11T ALA* 1.3 58.3 + - - +
13T LEU* 3.3 1.8 + - - -
14T ARG* 3.0 24.1 + - - +
41T ILE* 3.9 17.3 - - + +
44T ILE* 3.8 27.4 - - + -
45T ASN* 3.2 33.5 + - - +
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Residues in contact with ALA 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 3.7 26.9 - - - +
7T GLU 3.0 17.2 + - - +
8T GLN 3.5 5.2 - - - +
10T ALA* 1.3 73.3 - - - +
12T ASP* 1.3 60.1 + - - +
14T ARG* 3.2 28.5 + - - +
15T ARG* 2.9 34.9 + - - +
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Residues in contact with ASP 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 2.9 28.7 - - - +
19L GLN* 4.1 3.6 - - - +
8T GLN 3.0 19.5 + - - +
9T LEU* 3.1 26.5 + - + +
11T ALA* 1.3 75.0 - - - +
13T LEU* 1.3 56.4 + - - +
15T ARG* 2.6 37.6 + - - +
16T ALA* 2.9 28.2 + - - +
23T ILE* 4.0 25.7 - - + +
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Residues in contact with LEU 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T LEU 3.0 9.9 + - - +
10T ALA 3.4 8.7 - - - +
11T ALA 3.3 0.2 - - - -
12T ASP* 1.3 75.5 - - - +
14T ARG* 1.3 63.2 + - - +
16T ALA* 3.5 4.3 + - - +
17T ALA* 3.2 21.1 + - - +
23T ILE* 3.7 23.6 - - + -
26T LEU* 3.7 28.3 - - + -
41T ILE* 3.8 17.3 - - + -
45T ASN* 3.8 8.5 - - - +
143T ARG* 3.9 23.0 - - + +
144T ILE* 4.7 4.9 - - + -
156T ALA 3.7 25.1 - - - +
157T ASP* 4.0 18.6 - - - +
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Residues in contact with ARG 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T GLU* 5.3 2.2 + - - -
10T ALA* 3.0 17.3 + - - +
11T ALA* 3.2 30.6 + - - +
13T LEU* 1.3 74.4 - - - +
15T ARG* 1.3 59.7 - - - +
17T ALA* 3.3 7.2 + - - +
18T GLU* 3.0 41.4 + - - +
44T ILE* 4.5 7.3 - - - +
45T ASN* 2.8 47.5 + - - +
48T HIS* 3.7 53.7 + - - +
49T ASP* 4.8 3.8 - - - -
1263T K 4.3 8.3 - - - -
1303T NA 4.4 9.2 - - - -
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Residues in contact with ARG 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L ARG* 3.6 21.3 - - - +
18L GLU* 3.4 23.4 + - - +
19L GLN* 3.0 32.3 - - - +
1263L PO4 3.6 20.9 - - - -
11T ALA* 2.9 15.6 + - - +
12T ASP* 2.6 37.1 + - - +
14T ARG* 1.3 75.1 - - - +
16T ALA* 1.3 65.2 + - - +
18T GLU* 3.3 15.4 + - - +
19T GLN* 3.0 44.6 + - + +
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Residues in contact with ALA 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T ASP 2.9 18.0 + - - +
13T LEU* 3.5 9.4 - - - +
15T ARG* 1.3 76.2 - - - +
17T ALA* 1.3 57.0 + - - +
19T GLN* 5.0 1.3 - - - -
20T GLY* 3.0 25.1 + - - -
21T GLU 3.2 30.2 + - - +
23T ILE* 4.1 10.7 - - + +
100T LEU* 4.2 1.6 - - - +
143T ARG* 3.8 27.8 - - + +
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Residues in contact with ALA 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T LEU 3.2 9.8 + - - +
14T ARG* 3.6 9.4 - - - +
15T ARG 3.2 0.6 - - - -
16T ALA* 1.3 77.3 - - - +
18T GLU* 1.3 64.6 + - + +
19T GLN 3.3 0.9 + - - -
20T GLY* 3.4 10.3 + - - -
100T LEU* 5.4 2.6 - - - +
143T ARG* 3.8 21.0 - - + +
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Residues in contact with GLU 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ARG* 3.0 30.9 + - - +
15T ARG* 3.3 15.8 + - - +
17T ALA* 1.3 76.8 - - + +
19T GLN* 1.3 63.3 + - + +
1263T K 3.6 16.8 - - - -
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Residues in contact with GLN 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L GLN* 5.4 0.2 + - - -
1263L PO4 2.8 38.6 + - - -
15T ARG* 3.0 37.6 + - + +
16T ALA* 5.2 0.9 - - - -
18T GLU* 1.3 80.4 - - + +
20T GLY* 1.3 62.8 + - - +
21T GLU* 3.4 35.0 + - + +
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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
------------------------------------------------------------
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