Contacts of the helix formed by residues 283 - 304 (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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.4 5.1 - - + +
26B SER* 2.9 29.2 + - - +
235B SER* 3.7 30.5 - - - +
236B GLU* 4.4 7.4 - - + -
237B ALA* 3.8 19.1 - - + +
256B TYR* 4.7 3.1 - - - -
281B THR 3.5 5.5 + - - +
282B ILE* 1.3 85.5 - - - +
284B ALA* 1.3 64.6 + - - +
285B TRP* 3.1 11.6 + - - +
286B ALA* 3.0 21.1 + - - +
287B GLU* 3.2 10.2 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B SER* 5.5 1.4 - - - -
236B GLU* 5.1 4.2 + - - +
254B ALA* 3.7 20.4 - - + -
255B PRO* 4.1 8.9 - - + +
256B TYR* 3.4 29.5 + - - +
257B PHE* 6.1 0.2 - - + -
283B THR* 1.3 75.9 - - - +
285B TRP* 1.3 77.1 + - + +
287B GLU* 3.3 13.3 - - - +
288B ALA* 3.1 20.4 + - - +
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Residues in contact with TRP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.8 16.8 - - + -
27B GLN* 3.5 34.0 - - + +
83B TYR* 3.7 26.9 + + - -
105B PRO 3.6 15.2 - - - +
107B PRO* 3.6 29.8 - - + +
121B GLY* 4.3 5.6 - - - -
122B PRO* 3.7 29.6 - - + -
127B ASN* 5.7 0.7 - - - -
232B LEU 5.8 3.1 - - - -
233B THR 5.2 3.8 + - - -
235B SER* 4.8 9.3 - - - -
253B VAL 5.1 2.5 - - - -
254B ALA* 4.5 7.2 - - + -
255B PRO* 3.5 30.7 - - + -
283B THR* 3.1 11.1 + - - +
284B ALA* 1.3 86.5 - - + +
286B ALA* 1.4 60.8 + - - +
287B GLU 3.2 0.9 - - - -
288B ALA* 3.8 8.9 - - + +
289B ALA* 3.0 27.2 + - - +
500B BMD 5.7 0.2 - - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 3.1 42.1 + - - +
27B GLN* 4.1 2.5 - - - +
30B GLY* 3.6 6.4 - - - -
268B PHE* 4.1 6.7 - - + -
276B PHE* 4.0 18.2 - - + -
282B ILE* 4.9 0.7 - - - -
283B THR* 3.0 16.2 + - - +
285B TRP* 1.4 75.8 - - - +
287B GLU* 1.3 60.6 + - - +
289B ALA* 3.3 0.3 + - - +
290B TYR* 2.9 31.2 + - - +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PRO* 5.3 0.7 - - - +
256B TYR* 3.8 28.6 - - + +
268B PHE* 3.7 12.7 - - + -
283B THR 3.2 5.8 + - - +
284B ALA 3.3 13.0 - - - +
286B ALA* 1.3 77.4 - - - +
288B ALA* 1.3 60.1 + - - +
290B TYR* 3.3 3.6 - - - +
291B TRP* 3.0 28.8 + - - +
322B ALA* 3.4 4.3 - - - +
323B PRO* 3.2 33.2 - - + +
324B GLN* 2.8 58.3 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PRO* 3.6 26.5 - - + +
120B GLY 3.8 21.3 - - - +
255B PRO* 6.4 0.2 - - + -
284B ALA 3.1 11.8 + - - +
285B TRP* 4.1 7.9 - - + +
286B ALA 3.3 0.2 - - - -
287B GLU* 1.3 79.5 + - - +
289B ALA* 1.3 64.8 + - - +
291B TRP* 3.5 13.0 - - - +
292B GLN* 3.0 29.6 + - - +
324B GLN* 5.7 0.2 - - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 3.2 31.2 - - + +
31B ALA* 3.9 10.8 - - + +
80B VAL* 4.8 4.3 - - + -
105B PRO* 3.6 19.0 - - + +
285B TRP 3.0 19.0 + - - +
286B ALA 3.3 3.3 + - - +
288B ALA* 1.3 75.7 - - - +
290B TYR* 1.3 62.9 + - - +
292B GLN* 4.2 1.3 - - - +
293B THR* 2.7 32.2 + - - -
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Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 3.3 21.9 + - - +
33B LEU* 3.8 21.3 - - + -
34B ALA* 3.5 22.2 - - + +
37B GLN* 2.6 36.7 + - - -
268B PHE* 3.7 17.5 - + + -
271B ALA* 6.4 0.2 - - + -
286B ALA 2.9 18.0 + - - +
287B GLU 3.3 4.3 - - - +
289B ALA* 1.3 78.0 - - - +
291B TRP* 1.3 65.7 + - - +
294B LEU* 2.9 43.1 + - + +
321B ASP 5.9 0.9 - - - -
322B ALA* 5.6 0.2 - - - -
323B PRO* 3.7 38.4 - - + -
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Residues in contact with TRP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.8 19.1 + - - -
287B GLU* 3.0 47.4 + - - +
288B ALA* 3.5 14.4 - - - +
290B TYR* 1.3 78.2 - - + +
292B GLN* 1.3 72.7 + - + +
294B LEU* 3.3 8.8 + - + +
295B LEU* 2.8 56.3 + - + +
320B ILE* 4.0 9.7 - - + +
322B ALA* 3.7 24.7 - - + -
324B GLN* 3.7 15.5 - - - +
327B VAL* 3.6 25.4 - - + -
328B ARG* 5.1 1.1 - - - -
329B VAL* 4.0 9.6 - - + -
336B SER* 3.4 32.8 - - - -
338B LEU* 4.2 5.1 - - + +
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 5.8 0.7 - - + -
103B CYS* 3.5 25.9 - - + +
104B TYR 3.4 1.6 - - - -
105B PRO* 3.2 33.7 - - + +
118B VAL* 3.1 44.5 + - - +
120B GLY* 3.2 18.7 - - - +
288B ALA 3.0 18.8 + - - +
289B ALA* 4.2 2.7 - - - +
291B TRP* 1.3 102.9 - - + +
293B THR* 1.3 58.1 + - - +
295B LEU* 3.0 6.1 + - - +
296B LEU* 2.9 29.6 + - - +
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Residues in contact with THR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.8 26.9 - - + +
12B LEU* 5.9 0.7 - - + -
31B ALA* 3.5 33.7 - - + +
34B ALA* 3.6 13.9 - - + -
35B VAL* 3.9 7.4 - - + +
38B LEU* 3.5 7.1 - - + +
80B VAL* 3.7 16.0 - - + +
289B ALA 2.7 23.2 + - - -
292B GLN* 1.3 74.4 - - - +
294B LEU* 1.3 60.4 + - - +
296B LEU* 3.3 11.1 - - - +
297B GLY 3.2 17.2 + - - -
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Residues in contact with LEU 294 (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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34B ALA* 3.7 12.4 - - + +
37B GLN* 3.9 23.8 - - + +
38B LEU* 3.7 27.4 - - + +
290B TYR* 2.9 49.7 + - + +
291B TRP* 3.3 7.6 - - + +
293B THR* 1.3 74.4 - - - +
295B LEU* 1.3 66.1 + - - +
297B GLY* 3.3 2.8 + - - -
298B ARG* 3.1 51.0 + - - +
320B ILE* 4.0 16.8 - - + -
321B ASP 5.7 2.7 - - - +
322B ALA* 6.4 0.4 - - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.3 2.0 - - + -
291B TRP* 2.8 26.4 + - + +
292B GLN* 3.0 10.9 + - - +
294B LEU* 1.3 74.4 - - - +
296B LEU* 1.3 62.8 + - - +
297B GLY 3.2 0.2 + - - -
298B ARG* 3.2 2.3 + - - -
299B ALA* 2.9 25.3 + - - +
315B LEU* 3.5 44.0 - - + +
318B ILE* 3.3 49.6 - - + +
320B ILE* 3.3 17.2 - - + +
328B ARG* 6.1 0.7 - - - -
329B VAL* 3.7 20.9 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.9 11.9 - - + -
78B PHE* 3.7 39.3 - - + -
79B LEU 4.9 1.6 - - - +
80B VAL* 4.3 16.4 - - + -
101B LEU* 3.8 18.4 - - + +
103B CYS* 3.4 30.1 - - - -
292B GLN 2.9 8.5 + - - +
293B THR* 3.3 12.6 - - - +
294B LEU 3.3 0.4 - - - -
295B LEU* 1.3 76.2 - - - +
297B GLY* 1.3 57.8 + - - +
299B ALA* 3.4 2.4 + - - +
300B ALA* 2.9 30.8 + - - +
306B TRP* 4.8 6.7 - - + -
311B VAL* 3.9 15.1 - - + +
315B LEU* 4.5 10.3 - - + +
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 6.0 0.2 - - - +
38B LEU* 3.7 30.9 - - - +
44B VAL* 4.5 0.9 - - - +
49B ILE* 4.4 9.2 - - - -
293B THR 3.2 7.1 + - - -
294B LEU 3.3 0.2 + - - -
295B LEU 3.3 0.4 - - - -
296B LEU* 1.3 79.0 - - - +
298B ARG* 1.3 55.7 + - - +
300B ALA* 3.3 6.9 + - - +
301B GLN* 2.9 33.8 + - - +
306B TRP* 5.2 1.8 - - - -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 3.4 17.2 - - - +
38B LEU* 4.1 1.8 - - - +
41B GLU* 2.5 46.1 + - - +
294B LEU* 3.1 38.4 + - - +
295B LEU* 3.8 4.9 - - - +
297B GLY* 1.3 71.4 - - - +
299B ALA* 1.3 61.4 + - - +
301B GLN* 3.7 18.1 + - - +
302B ALA* 2.9 29.5 + - - +
318B ILE* 4.0 20.0 - - + +
320B ILE* 4.5 11.5 - - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 2.9 17.9 + - + +
296B LEU 3.6 4.0 - - - +
298B ARG* 1.3 76.0 - - - +
300B ALA* 1.3 56.9 + - - +
302B ALA* 3.3 3.7 + - - +
303B ALA* 2.8 29.1 + - - +
311B VAL* 3.7 28.5 - - + +
314B HIS* 3.7 16.7 - - - +
315B LEU* 3.9 13.9 - - + -
318B ILE* 3.7 11.4 - - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.9 10.5 - - + +
296B LEU 2.9 17.8 + - - +
297B GLY 3.5 4.9 - - - +
299B ALA* 1.3 73.6 - - - +
301B GLN* 1.3 55.6 + - - +
303B ALA* 3.0 0.8 + - - +
304B GLY* 2.7 32.4 + - - -
305B ASN 3.5 17.9 + - - +
306B TRP* 3.5 35.0 - - + -
311B VAL* 3.9 10.2 - - + +
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Residues in contact with GLN 301 (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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38B LEU* 3.7 30.3 + - - +
41B GLU* 4.1 20.7 + - - +
43B GLY* 3.0 30.4 + - - +
44B VAL* 4.7 6.3 - - - +
45B GLY 5.3 3.1 - - - +
49B ILE* 5.1 0.4 - - - +
297B GLY* 2.9 25.6 + - - +
298B ARG* 3.7 25.1 + - - +
299B ALA 3.4 0.2 - - - -
300B ALA* 1.3 77.3 - - - +
302B ALA* 1.3 60.8 + - - +
304B GLY* 3.1 12.6 + - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG 2.9 19.0 + - - +
299B ALA* 3.6 5.4 - - - +
301B GLN* 1.3 74.9 - - - +
303B ALA* 1.3 60.3 + - - +
314B HIS* 3.5 30.5 + - + -
318B ILE* 4.6 7.4 - - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA 2.8 16.8 + - - +
300B ALA 3.0 3.8 + - - +
302B ALA* 1.3 75.6 - - - +
304B GLY* 1.3 59.5 + - - +
305B ASN* 3.2 19.8 + - - +
310B ASP* 3.7 27.6 - - + +
311B VAL* 4.2 0.7 - - - +
314B HIS* 3.4 27.3 + - + +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 5.0 6.3 - - - +
45B GLY* 5.1 10.8 - - - -
300B ALA 2.7 9.0 + - - -
301B GLN* 3.1 10.8 + - - -
303B ALA* 1.3 76.7 - - - +
305B ASN* 1.3 61.1 + - - +
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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