Contacts of the helix formed by residues 34 - 52 (chain N) 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 ASN 34 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N THR* 5.6 8.5 + - - +
30N ILE* 3.2 30.4 + - + +
31N GLY* 3.0 8.3 + - - +
32N ILE 3.6 0.2 - - - -
33N ASP* 1.3 73.3 - - - +
35N ALA* 1.3 64.4 + - - +
36N GLU* 3.7 9.4 + - - +
37N ALA* 3.3 30.0 + - + +
38N ALA 3.3 12.8 + - - -
152N VAL* 3.3 15.6 - - - +
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Residues in contact with ALA 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASP 3.4 7.2 + - - +
34N ASN* 1.3 72.2 + - - +
36N GLU* 1.3 66.5 - - - +
38N ALA* 3.2 3.6 + - - +
39N TYR* 3.0 35.9 + - + -
151N PHE* 4.0 24.9 - - + -
152N VAL* 4.2 7.1 - - - +
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Residues in contact with GLU 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N ASN* 3.3 8.6 + - - +
35N ALA* 1.3 78.1 - - - +
37N ALA* 1.3 57.7 + - - +
39N TYR* 3.5 6.3 + - - +
40N ALA* 3.0 27.0 + - + +
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Residues in contact with ALA 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2N THR* 5.7 2.2 - - - +
6N LEU* 4.1 24.3 - - + +
30N ILE* 4.4 10.8 - - + -
34N ASN* 3.3 32.3 + - + +
35N ALA 3.2 0.6 - - - -
36N GLU* 1.3 77.2 - - - +
38N ALA* 1.3 60.6 + - - +
40N ALA* 3.0 9.0 + - - +
41N ILE* 2.9 34.8 + - - +
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Residues in contact with ALA 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N ILE* 4.5 6.4 - - + +
34N ASN 3.3 2.2 + - - -
35N ALA* 3.2 9.5 + - - +
37N ALA* 1.3 77.5 - - - +
39N TYR* 1.3 62.2 + - - +
41N ILE* 3.3 2.9 + - - +
42N GLN* 3.1 18.2 + - - +
151N PHE* 5.7 0.2 - - + -
152N VAL* 3.4 43.1 - - + +
155N VAL* 3.8 17.5 - - + -
156N ALA* 3.4 20.1 + - - +
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Residues in contact with TYR 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ALA* 3.0 30.6 + - + +
36N GLU* 3.9 5.6 - - - +
38N ALA* 1.3 75.6 - - - +
40N ALA* 1.3 58.1 + - - +
42N GLN* 3.4 10.2 + - - +
43N HIS* 2.9 29.2 + - - +
77N PRO 4.3 4.2 + - - -
78N ASP* 3.8 10.9 + - - -
79N PHE* 3.2 71.6 + + - -
151N PHE* 4.5 15.2 - + - -
155N VAL* 3.4 26.1 - - + +
210N TRP* 4.4 4.0 - - - -
214N LYS* 4.2 18.4 + - - -
218N LEU* 6.1 2.9 - - + -
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Residues in contact with ALA 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N LEU* 4.0 20.6 - - + -
36N GLU* 3.0 16.1 + - + +
37N ALA* 3.0 9.6 + - - +
39N TYR* 1.3 74.3 - - - +
41N ILE* 1.3 58.8 + - - +
43N HIS* 3.3 7.9 + - - +
44N ILE* 2.8 38.5 + - + +
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Residues in contact with ILE 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N LEU* 3.9 24.0 - - + +
9N LEU* 3.9 31.0 - - + -
10N ALA* 3.8 23.8 - - - +
13N LEU* 3.8 21.1 - - + -
26N LEU* 5.1 1.8 - - + -
30N ILE* 4.2 17.3 - - + -
37N ALA 2.9 18.4 + - - +
38N ALA 3.3 6.3 + - - +
40N ALA* 1.3 72.7 - - - +
42N GLN* 1.3 65.7 + - - +
44N ILE* 3.3 10.2 + - - +
45N ASN* 3.2 22.6 + - - +
156N ALA* 3.9 18.2 - - + +
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Residues in contact with GLN 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ALA 3.1 8.2 + - - +
39N TYR* 3.4 12.5 + - - +
41N ILE* 1.3 74.9 - - - +
43N HIS* 1.3 58.4 + - - +
45N ASN* 3.2 7.3 + - - +
46N VAL* 2.9 30.9 + - + +
79N PHE* 3.0 40.5 + - - -
81N THR* 3.1 23.6 + - - -
155N VAL* 3.1 30.5 + - - +
156N ALA 3.8 8.0 + - - +
158N ASN* 3.2 34.7 + - + +
159N ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N TYR 2.9 18.1 + - - +
40N ALA* 3.4 9.4 - - - +
42N GLN* 1.3 75.1 - - - +
44N ILE* 1.3 70.1 + - + +
46N VAL* 3.2 9.2 + - + +
47N GLN* 2.9 57.0 + - + +
220N GLU* 4.1 27.7 + - - -
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Residues in contact with ILE 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N LYS* 4.8 10.5 - - + -
6N LEU* 4.9 11.0 - - + +
7N GLU* 3.6 42.8 - - + +
10N ALA* 3.8 20.0 - - + -
14N ARG* 4.5 8.5 - - - +
40N ALA* 2.8 37.2 + - + +
41N ILE* 3.6 10.1 - - - +
43N HIS* 1.3 77.2 - - + +
45N ASN* 1.3 59.2 + - - +
47N GLN* 3.3 5.7 + - - +
48N HIS* 2.9 28.3 + - + +
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Residues in contact with ASN 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N ALA* 3.2 27.2 + - - +
13N LEU* 3.8 19.6 - - - +
14N ARG* 2.8 45.5 + - + +
41N ILE* 3.2 11.5 + - - +
42N GLN* 3.2 8.3 + - - +
43N HIS 3.2 0.2 - - - -
44N ILE* 1.3 78.2 - - - +
46N VAL* 1.3 63.2 + - - +
48N HIS* 3.6 4.0 + - - +
49N ASP* 3.2 31.3 + - - +
156N ALA 4.8 3.4 + - - -
158N ASN* 6.6 0.2 - - + -
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N GLN* 2.9 29.6 + - + +
43N HIS* 3.7 9.2 - - - +
45N ASN* 1.3 75.0 - - + +
47N GLN* 1.3 65.5 + - - +
49N ASP* 3.2 3.3 + - - +
50N VAL* 2.9 38.9 + - + +
56N VAL* 4.4 5.2 - - + -
59N ARG* 5.3 3.4 - - - +
81N THR* 3.6 39.5 - - + +
83N PHE* 4.1 22.9 - - + -
158N ASN* 4.7 3.6 - - - +
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Residues in contact with GLN 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N HIS* 2.9 50.4 + - + +
44N ILE* 3.5 6.7 - - - +
46N VAL* 1.3 82.7 - - - +
48N HIS* 1.3 62.5 + - - +
50N VAL* 3.4 20.1 + - - +
51N ALA* 3.1 22.7 + - - +
220N GLU* 5.4 0.9 - - - +
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Residues in contact with HIS 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N ARG* 3.7 42.3 + - - +
44N ILE* 2.9 19.0 + - + +
45N ASN* 3.7 8.5 - - - +
47N GLN* 1.3 76.5 - - - +
49N ASP* 1.3 75.4 + - - +
51N ALA* 3.3 16.0 + - - +
52N GLN* 3.3 38.2 + - + +
1263N K 4.1 5.5 - - - -
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Residues in contact with ASP 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E HIS* 3.6 15.5 - - - -
14N ARG* 4.8 1.2 - - - -
45N ASN 3.2 17.1 + - - +
46N VAL 3.7 3.4 - - - +
48N HIS* 1.3 88.8 - - - +
50N VAL* 1.3 66.1 + - - +
52N GLN* 3.0 24.0 + - - +
53N GLY 3.4 0.3 + - - -
54N ARG* 3.0 58.9 + - + +
83N PHE* 4.1 9.5 - - + -
1263N K 4.2 2.8 - - - -
1315N NA 3.4 18.8 - - - -
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Residues in contact with VAL 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N VAL* 2.9 25.6 + - + +
47N GLN* 3.8 20.2 - - - +
48N HIS 3.3 0.2 - - - -
49N ASP* 1.3 76.5 - - - +
51N ALA* 1.3 57.8 + - - +
53N GLY* 2.8 21.3 + - - -
54N ARG 3.6 19.0 - - - +
56N VAL* 4.0 24.5 - - + +
83N PHE* 4.3 2.2 - - + -
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Residues in contact with ALA 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N GLN 3.1 12.8 + - - +
48N HIS* 3.4 13.0 - - - +
49N ASP 3.2 0.2 - - - -
50N VAL* 1.3 78.4 - - - +
52N GLN* 1.3 58.8 + - + +
53N GLY 3.3 1.4 + - - -
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Residues in contact with GLN 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LYS* 3.0 32.5 + - - +
4E HIS* 4.3 9.7 + - - +
7E GLU* 3.4 43.0 - - + +
48N HIS* 3.3 31.8 + - + +
49N ASP* 3.0 21.4 + - - +
51N ALA* 1.3 77.9 - - + +
53N GLY* 1.3 58.8 + - - +
54N ARG* 3.4 4.0 + - + +
1263N K 3.7 18.3 - - - -
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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