Contacts of the helix formed by residues 30 - 45 (chain D) in PDB entry 2QB0
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 SER 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D TYR 3.5 2.9 + - - -
29D TRP* 1.3 76.9 - - - +
31D ARG* 1.3 64.2 + - - +
32D ASP* 3.5 9.1 + - - +
33D ASP* 2.8 45.1 + - - +
34D VAL* 3.2 10.6 + - - +
58D ASN* 3.9 7.2 - - - -
153D LYS* 6.6 0.4 - - - -
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Residues in contact with ARG 31 (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 SER* 1.3 74.0 - - - +
32D ASP* 1.3 68.8 + - - +
34D VAL* 3.5 7.1 + - - +
35D ALA* 3.4 19.5 + - + +
55D PHE 4.6 1.1 - - - +
56D GLU* 3.5 36.7 + - - +
57D MET* 3.3 41.0 - - - +
58D ASN* 3.8 7.5 - - + +
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Residues in contact with ASP 32 (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 SER* 3.3 8.3 + - - +
31D ARG* 1.3 82.1 - - - +
33D ASP* 1.3 61.0 + - - +
35D ALA* 3.3 9.1 + - - +
36D GLN* 3.0 39.3 + - + +
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Residues in contact with ASP 33 (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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21D HIS* 3.2 16.9 - - - -
22D LEU* 3.5 16.6 - - + +
28D TYR 4.1 2.3 - - - +
29D TRP* 3.5 19.3 - - + -
30D SER* 2.8 37.9 + - - +
32D ASP* 1.3 74.8 - - - +
34D VAL* 1.3 60.5 + - - +
36D GLN* 3.2 9.9 + - - +
37D TRP* 2.9 27.5 + - - +
154D ASP* 3.7 1.6 - - - +
257D MN 2.7 35.4 + - - -
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Residues in contact with VAL 34 (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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29D TRP* 4.4 15.7 - - + -
30D SER 3.2 15.2 + - - +
31D ARG 3.7 4.3 - - - +
32D ASP 3.4 0.2 - - - -
33D ASP* 1.3 74.3 - - - +
35D ALA* 1.3 63.0 + - + +
37D TRP* 3.2 15.9 + - + +
38D LEU* 2.9 36.0 + - + +
55D PHE* 3.4 37.9 - - + +
57D MET 3.5 16.4 - - - +
58D ASN 3.9 15.0 - - - +
59D GLY* 4.0 4.3 - - - +
62D LEU* 4.8 9.9 - - + -
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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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31D ARG* 3.4 9.6 + - + +
32D ASP* 3.3 14.1 + - - +
33D ASP 3.2 0.2 - - - -
34D VAL* 1.3 84.6 - - + +
36D GLN* 1.3 57.2 + - + +
38D LEU* 3.5 12.8 - - - +
39D LYS* 3.2 25.1 + - - +
52D SER* 4.7 20.8 - - - +
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Residues in contact with GLN 36 (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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19D PRO* 5.9 0.2 - - - +
21D HIS* 3.4 32.8 + - - +
22D LEU* 4.3 11.3 - - + +
32D ASP* 3.0 24.9 + - + +
33D ASP* 3.2 12.2 + - - +
35D ALA* 1.3 76.7 - - + +
37D TRP* 1.3 60.1 + - - +
39D LYS* 3.4 16.0 + - - +
40D TRP* 3.0 28.9 + - - +
154D ASP* 3.6 14.5 + - - +
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Residues in contact with TRP 37 (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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18D LEU* 5.2 2.7 - - + -
22D LEU* 3.9 15.2 - - + +
29D TRP* 3.6 33.4 - + + -
33D ASP 2.9 12.9 + - - +
34D VAL* 3.2 13.9 + - + +
36D GLN* 1.3 77.1 - - - +
38D LEU* 1.3 79.5 + - + +
40D TRP* 3.3 15.9 + + - +
41D ALA* 2.8 36.7 + - + +
55D PHE* 5.3 0.9 - + - -
62D LEU* 4.2 21.1 - - + -
70D PHE* 4.2 11.4 - + - -
81D LEU* 3.5 39.5 - - + -
84D LEU* 3.5 28.0 - - + +
85D LEU* 4.2 17.9 - - + -
88D ILE* 3.6 16.9 - - + +
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Residues in contact with LEU 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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34D VAL* 2.9 16.6 + - + +
35D ALA* 3.5 16.6 - - - +
37D TRP* 1.3 109.0 - - + +
39D LYS* 1.3 57.3 + - - +
41D ALA* 3.3 4.5 + - - +
42D GLU* 3.0 30.1 + - - +
50D ILE* 3.8 33.8 - - + +
51D ASP 4.4 9.0 - - - +
52D SER* 4.8 8.1 - - - +
54D THR* 4.5 2.7 - - - -
55D PHE* 3.9 39.7 - - + +
81D LEU* 4.5 11.2 - - + +
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Residues in contact with LYS 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 3.2 14.2 + - - +
36D GLN* 3.7 15.3 + - + +
37D TRP 3.4 0.2 - - - -
38D LEU* 1.3 79.9 - - - +
40D TRP* 1.3 63.6 + - - +
42D GLU* 3.7 10.7 + - - +
43D ASN* 3.6 17.7 + - - +
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Residues in contact with TRP 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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16D ILE* 4.7 10.1 - - + -
17D ARG 3.5 26.2 + - - -
18D LEU* 3.8 17.7 - - + -
19D PRO* 3.6 35.3 - - + +
22D LEU* 5.3 0.7 - - + -
36D GLN 3.0 16.9 + - - +
37D TRP* 3.6 19.3 - + - +
39D LYS* 1.3 77.5 - - - +
41D ALA* 1.3 74.4 + - + +
43D ASN* 3.2 8.5 + - - +
44D GLU* 2.9 63.6 + - + +
45D PHE* 4.1 10.8 - + - -
84D LEU* 4.0 30.3 - - + -
88D ILE* 5.5 0.4 - - + -
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Residues in contact with ALA 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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37D TRP* 2.8 22.0 + - - +
38D LEU 3.8 4.0 - - - +
40D TRP* 1.3 81.3 - - + +
42D GLU* 1.3 63.0 + - - +
45D PHE* 3.0 36.8 + - + +
47D LEU* 3.7 2.5 - - - +
81D LEU* 3.8 21.1 - - + -
84D LEU* 3.8 26.7 - - + -
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Residues in contact with GLU 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 LEU 3.0 15.2 + - - +
39D LYS* 3.8 12.5 - - - +
40D TRP 3.3 0.2 - - - -
41D ALA* 1.3 77.7 - - - +
43D ASN* 1.3 56.2 + - - +
46D SER* 3.2 7.3 + - - -
47D LEU* 3.0 50.3 + - - +
48D ARG 4.1 6.5 - - - +
49D PRO* 3.6 16.3 - - - +
50D ILE* 2.9 40.4 + - + +
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Residues in contact with ASN 43 (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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39D LYS 3.6 8.4 + - - +
40D TRP* 3.2 10.6 + - - +
42D GLU* 1.3 79.2 - - - +
44D GLU* 1.3 69.2 + - - +
45D PHE 3.2 0.7 + - - -
46D SER* 3.6 12.1 + - - +
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Residues in contact with GLU 44 (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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58A ASN* 2.9 16.6 + - - -
60A LYS* 2.8 41.8 + - - +
15D SER 5.7 0.5 - - - +
16D ILE* 6.0 2.6 - - + -
17D ARG 5.1 5.3 + - - +
40D TRP* 2.9 54.8 + - + +
41D ALA 4.0 2.9 - - - +
43D ASN* 1.3 81.4 + - - +
45D PHE* 1.3 79.4 + - + +
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Residues in contact with PHE 45 (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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57A MET* 3.6 6.2 - - - +
58A ASN* 3.2 25.3 + - - +
60A LYS* 3.8 23.8 - - + -
61A ALA* 3.5 30.3 - - + -
64A LEU* 3.8 22.9 - - + -
16D ILE* 4.1 19.3 - - + -
40D TRP* 4.1 7.2 - + - -
41D ALA* 3.0 29.6 + - + +
44D GLU* 1.3 94.7 - - + +
46D SER* 1.3 66.9 + - - +
47D LEU* 3.2 13.6 + - + +
80D VAL* 4.7 7.0 - - + -
84D LEU* 3.6 29.8 - - + -
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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
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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