Contacts of the helix formed by residues 34 - 52 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 5.6 8.1 + - - +
30D ILE* 3.2 30.1 + - + +
31D GLY* 2.9 8.3 + - - +
32D ILE 3.6 0.4 - - - -
33D ASP* 1.3 73.7 - - - +
35D ALA* 1.3 63.8 + - - +
36D GLU* 3.7 9.5 + - - +
37D ALA* 3.3 28.8 + - + +
38D ALA 3.3 12.1 + - - -
152D VAL* 3.3 15.2 - - + +
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASP 3.4 8.0 + - - +
34D ASN* 1.3 73.8 - - - +
36D GLU* 1.3 63.1 + - - +
38D ALA* 3.2 3.6 + - - +
39D TYR* 3.0 35.9 + - + -
151D PHE* 4.0 28.5 - - + -
152D VAL* 4.2 3.3 - - - +
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ASN* 3.3 8.8 + - - +
35D ALA* 1.3 79.0 - - - +
37D ALA* 1.3 55.9 + - - +
39D TYR* 3.5 7.2 + - - +
40D ALA* 3.0 26.2 + - + +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D THR* 5.7 2.5 - - - +
6D LEU* 4.1 24.1 - - + +
30D ILE* 4.4 10.3 - - + -
34D ASN* 3.3 33.0 + - + +
35D ALA 3.2 0.8 - - - -
36D GLU* 1.3 75.8 - - - +
38D ALA* 1.3 60.9 + - - +
40D ALA* 3.1 9.1 + - - +
41D ILE* 2.9 34.7 + - - +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.5 5.9 - - + +
34D ASN 3.3 2.2 + - - -
35D ALA* 3.2 8.9 + - - +
37D ALA* 1.3 78.4 - - - +
39D TYR* 1.3 62.9 + - - +
41D ILE* 3.3 2.1 + - - +
42D GLN* 3.1 18.0 + - - +
151D PHE* 5.7 0.2 - - + -
152D VAL* 3.4 43.1 - - + +
155D VAL* 3.7 17.0 - - + -
156D ALA* 3.4 20.1 + - - +
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 3.0 31.8 + - + +
36D GLU* 3.9 6.3 - - - +
38D ALA* 1.3 73.6 - - - +
40D ALA* 1.3 59.1 + - - +
42D GLN* 3.4 10.2 + - - +
43D HIS* 2.9 29.5 + - - +
77D PRO 4.3 4.5 + - - -
78D ASP* 3.8 10.7 + - - -
79D PHE* 3.2 70.8 + + - -
151D PHE* 4.4 15.3 - + - -
155D VAL* 3.4 24.9 - - + +
210D TRP* 4.4 3.8 - - - -
214D LYS* 4.3 18.2 + - - -
218D LEU* 5.9 2.5 - - + -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.0 20.6 - - + -
36D GLU* 3.0 16.8 + - + +
37D ALA* 3.1 9.6 + - - +
39D TYR* 1.3 72.9 - - - +
41D ILE* 1.3 61.7 + - - +
43D HIS* 3.3 8.3 + - - +
44D ILE* 2.8 37.8 + - + +
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.0 24.5 - - + +
9D LEU* 3.9 30.7 - - + -
10D ALA* 3.9 16.2 - - - +
13D LEU* 3.8 27.8 - - + -
26D LEU* 5.0 2.0 - - + -
30D ILE* 4.2 17.9 - - + -
37D ALA 2.9 18.3 + - - +
38D ALA 3.6 6.5 - - - +
40D ALA* 1.3 72.4 - - - +
42D GLN* 1.3 65.9 + - - +
44D ILE* 3.2 10.1 + - - +
45D ASN* 3.2 21.9 + - - +
156D ALA* 3.8 18.4 - - + +
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA 3.1 8.4 + - - +
39D TYR* 3.6 17.5 - - - +
40D ALA 3.4 0.2 - - - -
41D ILE* 1.3 75.7 - - - +
43D HIS* 1.3 58.1 + - - +
45D ASN* 3.3 6.5 + - - +
46D VAL* 2.9 30.5 + - + +
59D ARG* 4.9 0.2 + - - -
79D PHE* 3.0 41.5 + - - -
81D THR* 3.1 23.4 + - - -
155D VAL* 3.1 27.1 + - - +
156D ALA 3.9 7.8 + - - -
158D ASN* 3.2 35.9 + - + +
159D ALA 4.0 0.6 - - - +
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Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR 2.9 18.3 + - - +
40D ALA* 3.5 10.1 - - - +
42D GLN* 1.3 74.5 - - - +
44D ILE* 1.3 71.7 + - + +
46D VAL* 3.2 8.7 + - + +
47D GLN* 2.9 58.7 + - + +
220D GLU* 4.2 27.6 + - - -
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 4.8 10.5 - - + -
6D LEU* 4.9 10.8 - - + +
7D GLU* 3.6 43.1 - - + +
10D ALA* 3.8 19.7 - - + -
14D ARG* 4.5 8.7 - - - +
40D ALA* 2.8 37.6 + - + +
41D ILE* 3.2 11.2 + - - +
43D HIS* 1.3 75.7 - - + +
45D ASN* 1.3 59.5 + - - +
47D GLN* 3.4 5.9 + - - +
48D HIS* 2.9 27.2 + - + +
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 3.2 27.8 + - - +
13D LEU* 3.8 19.6 - - - +
14D ARG* 2.8 42.3 + - + +
41D ILE* 3.2 10.7 + - - +
42D GLN* 3.7 8.3 - - - +
44D ILE* 1.3 78.6 - - - +
46D VAL* 1.3 64.0 + - + +
48D HIS* 3.5 3.9 + - - +
49D ASP* 3.1 31.6 + - - +
156D ALA 4.8 3.8 + - - -
158D ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLN* 2.9 28.8 + - + +
43D HIS* 3.8 9.2 - - + +
45D ASN* 1.3 74.6 - - - +
47D GLN* 1.3 66.4 + - - +
49D ASP* 3.2 4.2 + - - +
50D VAL* 2.9 39.1 + - + +
56D VAL* 4.4 4.9 - - + -
59D ARG* 5.3 3.1 - - - +
81D THR* 3.6 39.7 - - + +
83D PHE* 4.1 22.6 - - + -
158D ASN* 4.6 3.8 - - - +
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D HIS* 2.9 49.3 + - + +
44D ILE* 3.5 6.5 - - - +
46D VAL* 1.3 82.9 - - - +
48D HIS* 1.3 61.3 + - - +
50D VAL* 3.4 19.4 + - - +
51D ALA* 3.1 23.6 + - - +
220D GLU* 5.4 0.7 - - - +
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Residues in contact with HIS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 3.7 43.3 + - - +
44D ILE* 2.9 18.1 + - + +
45D ASN* 3.7 8.7 - - - +
47D GLN* 1.3 75.9 - - - +
49D ASP* 1.3 75.9 + - - +
51D ALA* 3.3 16.0 + - - +
52D GLN* 3.3 39.4 + - + +
1265D K 4.0 5.3 - - - -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 4.7 1.7 - - - -
45D ASN 3.1 17.6 + - - +
46D VAL 3.7 3.4 - - - +
48D HIS* 1.3 89.7 - - - +
50D VAL* 1.3 64.0 + - - +
52D GLN* 3.0 26.7 + - - +
53D GLY 3.4 0.2 + - - -
54D ARG* 3.0 62.1 + - + +
83D PHE* 4.1 9.1 - - + -
1265D K 4.1 6.1 - - - -
1304D NA 3.5 18.0 - - - -
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 2.9 25.9 + - + +
47D GLN* 3.7 20.9 - - - +
48D HIS 3.4 0.2 - - - -
49D ASP* 1.3 76.7 - - - +
51D ALA* 1.3 57.2 + - - +
53D GLY* 2.9 20.8 + - - -
54D ARG 3.6 18.8 - - - +
56D VAL* 4.0 24.7 - - + +
83D PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN 3.1 13.8 + - - +
48D HIS* 3.4 13.2 - - - +
49D ASP 3.2 0.4 - - - -
50D VAL* 1.3 75.6 - - - +
52D GLN* 1.3 60.6 + - + +
53D GLY 3.3 1.0 + - - -
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Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D HIS* 3.3 32.5 + - + +
49D ASP* 3.0 22.6 + - - +
51D ALA* 1.3 78.0 - - + +
53D GLY* 1.3 58.6 + - - +
54D ARG* 3.4 3.8 + - + +
1265D K 3.7 19.3 - - - -
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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