Contacts of the helix formed by residues 20 - 41 (chain B) in PDB entry 1QO0
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 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B SER* 4.8 0.3 - - - -
17B THR 5.3 0.2 + - - -
18B GLY 3.3 0.6 - - - -
19B VAL* 1.3 81.5 - - + +
21B ALA* 1.3 63.1 + - - +
22B ASP* 3.2 3.8 + - - -
23B ILE* 3.4 7.2 + - + -
24B GLU* 2.4 48.1 + - - +
58B GLY* 4.9 3.4 - - - -
63B TYR* 4.8 0.5 + - - -
83B TYR* 3.9 17.4 - - + -
84B MET* 3.9 30.5 - - + +
206B VAL* 3.6 31.0 - - + -
207B GLY* 4.4 7.2 - - - -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.9 12.1 - - - +
16B GLU 3.4 22.9 - - - +
17B THR* 3.7 13.2 + - - -
18B GLY 3.0 18.2 + - - +
19B VAL 3.4 1.0 + - - -
20B THR* 1.3 76.3 - - - +
22B ASP* 1.3 58.9 + - - +
24B GLU 3.9 0.2 - - - -
25B ARG* 2.9 42.9 + - - +
208B THR* 5.5 0.6 + - - +
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR 3.2 1.4 + - - -
21B ALA* 1.3 77.9 - - - +
23B ILE* 1.3 62.1 + - - +
25B ARG* 3.0 24.8 + - - +
26B SER* 3.1 21.4 + - - -
208B THR* 4.7 7.8 + - - -
237B ALA* 3.9 23.5 - - + +
238B GLU* 4.8 8.1 - - - +
241B LYS* 3.6 31.6 + - - +
279B ASN 4.2 5.6 - - - +
280B ALA* 5.6 2.1 - - - -
281B THR 5.6 0.9 + - - -
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Residues in contact with ILE 23 (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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20B THR* 3.4 9.7 + - + +
22B ASP* 1.3 77.6 - - - +
24B GLU* 1.3 57.8 + - - +
26B SER* 3.0 9.8 - - - -
27B GLN* 2.9 23.8 + - - +
83B TYR* 3.2 53.2 - - + +
206B VAL* 6.3 1.3 - - + -
207B GLY* 5.6 4.9 - - - +
233B THR 4.5 5.4 - - - +
235B SER* 3.3 34.3 - - - +
237B ALA* 4.4 1.6 - - + -
238B GLU* 3.5 20.8 + - - +
283B THR* 4.4 6.7 - - + +
285B TRP* 3.8 20.2 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 3.3 23.3 - - + +
15B SER* 2.9 44.5 + - - +
20B THR* 2.4 38.2 + - - +
23B ILE* 1.3 73.2 - - - +
25B ARG* 1.3 61.0 + - - +
27B GLN* 3.3 22.3 + - - +
28B ARG* 3.0 20.6 + - - +
63B TYR* 2.5 29.0 + - - -
83B TYR* 3.7 19.7 + - + +
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Residues in contact with ARG 25 (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 SER 4.0 4.0 + - - +
16B GLU* 2.8 58.4 + - - +
21B ALA* 2.9 28.3 + - - +
22B ASP* 3.0 34.1 + - - +
24B GLU* 1.3 75.5 - - - +
26B SER* 1.3 63.4 + - - +
28B ARG* 3.0 6.8 + - - -
29B TYR* 3.0 50.4 + - + -
279B ASN* 3.1 47.9 + - - +
280B ALA* 4.2 5.2 - - + -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 3.1 12.5 + - - -
23B ILE* 3.0 17.9 - - - -
25B ARG* 1.3 77.8 - - - +
27B GLN* 1.4 57.5 + - - -
29B TYR 3.6 0.2 + - - -
30B GLY 3.1 11.6 + - - -
237B ALA* 5.7 0.4 - - - -
276B PHE* 3.9 7.9 - - - -
280B ALA* 4.9 4.3 - - - +
281B THR 3.0 26.8 + - - -
283B THR* 2.9 27.3 + - - -
286B ALA* 3.1 26.7 - - - +
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Residues in contact with GLN 27 (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 PHE* 3.2 39.6 - - + -
23B ILE 2.9 16.1 + - - +
24B GLU* 3.3 17.4 + - - +
25B ARG 3.2 0.4 - - - -
26B SER* 1.4 73.0 - - - +
28B ARG* 1.3 67.9 + - - +
30B GLY 3.2 0.9 + - - -
31B ALA* 3.0 20.4 + - - +
83B TYR* 3.3 22.6 - - - +
105B PRO* 3.0 30.9 + - - +
106B THR* 3.1 15.4 + - - -
285B TRP* 3.5 32.1 - - + +
289B ALA* 3.2 10.7 - - + +
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Residues in contact with ARG 28 (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 LEU* 4.3 10.1 - - + -
14B PHE* 3.9 25.5 + - + +
15B SER 5.6 0.6 + - - -
16B GLU* 2.6 35.9 + - - +
24B GLU 3.0 13.8 + - - +
25B ARG* 3.0 10.4 + - - +
27B GLN* 1.3 77.4 - - - +
29B TYR* 1.3 93.8 + - - +
31B ALA* 3.2 5.7 + - - +
32B LEU* 2.9 44.4 + - + +
53B SER* 3.2 32.5 + - - +
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Residues in contact with TYR 29 (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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25B ARG* 3.0 39.6 + - + +
28B ARG* 1.3 108.6 + - - +
30B GLY* 1.3 60.6 + - - +
32B LEU* 3.7 15.1 - - + +
33B LEU* 2.7 30.8 + - - +
275B PHE* 3.8 24.2 - + - -
276B PHE* 3.4 30.5 - - + -
277B PRO* 3.4 41.7 - - + +
280B ALA* 4.1 2.7 - - + -
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Residues in contact with GLY 30 (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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26B SER 3.1 15.6 + - - -
27B GLN 3.2 2.8 + - - -
29B TYR* 1.3 77.5 - - - +
31B ALA* 1.3 60.7 + - - +
33B LEU* 3.4 5.4 + - - +
34B ALA 3.2 16.3 + - - -
268B PHE* 5.5 2.0 - - - -
276B PHE* 3.8 11.5 - - - -
286B ALA 3.6 19.5 - - - -
290B TYR* 3.3 20.4 - - - +
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Residues in contact with ALA 31 (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 LEU* 3.8 27.1 - - + -
14B PHE* 4.8 0.4 - - + -
27B GLN 3.0 13.2 + - - +
28B ARG* 3.5 8.3 - - - +
30B GLY* 1.3 75.0 - - - +
32B LEU* 1.3 63.5 + - - +
34B ALA* 3.3 4.9 + - - +
35B VAL* 3.1 27.2 + - - +
80B VAL* 4.5 4.3 - - + -
289B ALA* 3.9 9.3 - - + +
293B THR* 3.5 24.8 - - + +
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Residues in contact with LEU 32 (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 LEU* 3.7 15.3 - - + -
28B ARG* 2.9 51.8 + - + +
29B TYR* 3.7 19.1 - - + +
31B ALA* 1.3 72.3 - - - +
33B LEU* 1.3 67.1 - - - +
35B VAL* 3.2 5.5 + - + +
36B GLU* 3.2 24.1 + - - +
51B THR* 3.7 29.6 - - + +
53B SER* 5.5 0.7 - - - +
275B PHE* 3.8 17.9 - - + -
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Residues in contact with LEU 33 (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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29B TYR 2.7 20.5 + - - +
30B GLY* 3.5 7.2 - - - +
32B LEU* 1.3 74.5 - - - +
34B ALA* 1.3 61.0 + - - +
36B GLU* 3.3 9.0 - - + +
37B GLN* 3.1 24.5 + - + +
40B ARG* 5.7 4.3 - - - +
268B PHE* 4.1 17.5 - - + -
271B ALA* 3.8 40.6 - - + +
272B CYS* 4.2 7.0 - - - -
275B PHE* 3.8 27.3 - - + -
276B PHE* 4.8 3.6 - - + -
290B TYR* 3.8 24.2 - - + -
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Residues in contact with ALA 34 (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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30B GLY 3.2 7.2 + - - +
31B ALA 3.5 8.5 - - - +
33B LEU* 1.3 79.0 - - - +
35B VAL* 1.3 56.3 + - - +
37B GLN* 3.1 3.8 + - - +
38B LEU* 2.8 34.5 + - - +
290B TYR* 3.5 38.1 - - + +
293B THR* 3.6 16.2 - - + -
294B LEU* 3.7 13.0 - - + +
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Residues in contact with VAL 35 (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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10B ILE* 4.0 11.4 - - + -
12B LEU* 6.2 0.4 - - + -
31B ALA* 3.1 18.3 + - + +
32B LEU* 3.2 10.9 + - + +
34B ALA* 1.3 74.0 - - - +
36B GLU* 1.3 53.4 + - - +
38B LEU* 3.2 9.9 + - + +
39B ASN* 2.8 39.0 + - - +
49B ILE* 3.5 33.0 - - + +
50B GLU 5.1 0.2 - - - -
51B THR* 3.6 31.0 - - + -
293B THR* 3.9 15.7 - - + -
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Residues in contact with GLU 36 (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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32B LEU 3.2 10.2 + - - +
33B LEU* 3.3 15.7 - - + +
35B VAL* 1.3 79.3 - - - +
37B GLN* 1.3 61.7 + - - +
39B ASN* 3.3 7.4 + - - +
40B ARG* 3.1 43.9 + - + +
275B PHE* 3.3 29.8 - - + -
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Residues in contact with GLN 37 (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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33B LEU* 3.1 11.4 + - + +
34B ALA 3.1 8.8 + - - +
36B GLU* 1.3 80.8 - - - +
38B LEU* 1.3 61.1 + - - +
40B ARG* 3.1 38.6 + - - +
41B GLU* 3.1 42.7 + - + +
290B TYR* 2.6 37.4 + - - -
294B LEU* 3.9 10.0 - - + +
298B ARG* 3.4 16.0 - - - +
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Residues in contact with LEU 38 (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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10B ILE* 5.4 1.3 - - + -
34B ALA 2.8 25.0 + - - +
35B VAL* 3.5 15.3 - - + +
37B GLN* 1.3 72.4 - - - +
39B ASN* 1.3 56.2 + - - +
41B GLU* 3.0 31.9 + - - +
42B GLY 3.4 1.0 + - - -
43B GLY* 3.0 16.1 + - - -
49B ILE* 3.6 28.7 - - + -
293B THR* 3.5 26.0 - - + +
294B LEU* 3.7 26.9 - - + +
297B GLY* 3.7 26.2 - - - +
298B ARG* 4.1 3.4 - - - +
301B GLN* 3.7 6.9 + - - +
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Residues in contact with ASN 39 (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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35B VAL* 2.8 28.7 + - - +
36B GLU* 3.8 7.1 - - - +
37B GLN 3.3 0.4 - - - -
38B LEU* 1.3 71.6 - - - +
40B ARG* 1.3 59.1 + - - +
41B GLU 3.5 0.5 + - - -
42B GLY* 3.6 8.3 + - - -
43B GLY* 3.5 15.8 + - - +
48B PRO* 3.6 14.7 - - + +
49B ILE* 2.7 52.4 + - - +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.7 5.3 - - - +
36B GLU* 3.1 37.2 + - + +
37B GLN* 3.1 42.4 + - - +
39B ASN* 1.3 76.4 - - - +
41B GLU* 1.3 60.9 + - + +
42B GLY 3.4 1.2 + - - -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 3.1 34.5 + - + +
38B LEU* 3.0 21.6 + - - +
40B ARG* 1.3 80.0 - - + +
42B GLY* 1.3 55.9 + - - +
298B ARG* 2.5 49.5 + - - +
301B GLN* 4.1 15.7 + - - +
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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
------------------------------------------------------------
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