Contacts of the helix formed by residues 325 - 350 (chain D) in PDB entry 4OGB
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 PRO 325 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TRP* 4.9 6.5 - - + +
103D GLY* 3.8 29.6 - - - +
323D THR 4.5 1.1 - - - +
324D LYS* 1.3 89.9 - - + +
326D LEU* 1.3 55.8 - - - +
327D GLN* 3.2 26.0 - - - +
328D LEU* 2.8 33.2 + - + +
329D TYR 3.1 4.9 + - - -
398D THR* 4.5 8.3 - - + -
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LYS 3.3 2.7 + - - -
325D PRO* 1.3 70.4 - - - +
327D GLN* 1.3 67.6 + - - +
329D TYR* 3.2 12.0 + - + -
330D ARG* 2.9 48.0 + - + +
398D THR* 5.3 0.4 - - - +
402D ASN* 3.4 33.1 + - + +
405D TRP* 3.7 52.7 - - + +
406D TYR* 5.0 1.1 - - + -
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Residues in contact with GLN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS* 5.5 8.6 - - + +
325D PRO* 3.5 22.9 - - - +
326D LEU* 1.3 83.7 + - - +
328D LEU* 1.3 65.8 + - + +
330D ARG* 4.3 7.3 - - - +
331D GLN* 2.9 35.3 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLY* 3.7 24.2 - - - +
104D LEU 3.5 22.9 - - - +
105D HIS* 4.0 21.3 - - + +
106D VAL* 4.8 4.9 - - + +
107D PHE* 3.8 27.4 - - + -
324D LYS* 4.1 13.7 - - + +
325D PRO* 2.8 24.9 + - + +
327D GLN* 1.3 78.2 - - + +
329D TYR* 1.3 65.1 + - - +
331D GLN* 3.1 13.2 + - - +
332D TRP* 3.1 34.1 + - + +
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Residues in contact with TYR 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ASN* 3.4 32.4 + - + +
322D PRO* 3.5 32.4 - - + +
324D LYS* 4.2 4.9 - - - +
325D PRO 3.1 7.5 + - - +
326D LEU* 3.2 13.2 + - + +
328D LEU* 1.3 79.3 - - - +
330D ARG* 1.3 56.6 + - - +
332D TRP* 3.1 5.6 + - - +
333D THR* 2.8 42.1 + - - -
369D GLN* 2.4 39.3 + - - +
373D ILE* 3.6 20.6 - - + +
402D ASN* 3.7 27.1 - - + -
406D TYR* 3.4 27.1 - + - -
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D LEU* 2.9 33.7 + - + +
327D GLN* 4.3 6.4 - - - +
329D TYR* 1.3 75.5 - - - +
331D GLN* 1.3 60.5 + - + +
333D THR* 3.7 0.7 - - - -
334D ASP* 3.0 46.1 + - - +
405D TRP* 3.3 47.0 - - - -
406D TYR* 3.7 17.4 + - - +
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Residues in contact with GLN 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS* 4.0 13.1 + - - -
107D PHE* 3.5 40.3 - - + +
327D GLN* 2.9 27.7 + - - +
328D LEU* 3.1 16.8 + - - +
330D ARG* 1.3 77.9 - - + +
332D TRP* 1.3 62.1 + - - +
334D ASP* 3.5 8.7 + - - +
335D ARG* 3.1 32.7 + - - +
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Residues in contact with TRP 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D VAL* 3.9 11.2 - - + +
107D PHE* 3.6 34.7 - + - -
159D TYR* 3.6 28.2 - + - -
161D ASN* 5.1 0.4 - - - -
163D ILE* 3.8 19.1 - - + -
164D HIS* 3.8 30.3 - - + -
167D ASP* 3.6 30.8 + - + -
321D ASN* 3.4 43.5 - - + +
324D LYS* 5.2 4.3 - - + +
328D LEU* 3.1 36.1 + - + +
329D TYR* 3.4 7.4 - - + +
331D GLN* 1.3 73.4 - - - +
333D THR* 1.3 61.4 + - - +
335D ARG* 3.3 10.2 + - - -
336D ILE* 2.9 30.5 + - - +
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Residues in contact with THR 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D TYR* 2.8 37.1 + - - -
330D ARG 3.7 2.5 - - - -
331D GLN 3.3 0.2 - - - -
332D TRP* 1.3 75.3 - - - +
334D ASP* 1.3 68.8 + - - +
336D ILE* 3.3 7.5 + - + +
337D MET* 2.9 27.5 + - + +
365D VAL* 3.8 27.4 - - + -
369D GLN* 3.9 18.2 + - + +
406D TYR* 3.1 27.6 + - - +
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Residues in contact with ASP 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ARG* 3.0 32.7 + - - +
331D GLN* 3.7 8.9 - - - +
333D THR* 1.3 79.3 - - - +
335D ARG* 1.3 59.4 + - + +
337D MET* 3.9 4.9 - - - +
338D GLU* 3.0 30.5 + - - +
406D TYR* 5.5 0.5 + - - -
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Residues in contact with ARG 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D PHE* 3.2 39.2 - - - -
158D ALA* 3.0 47.6 + - + +
159D TYR* 3.9 7.8 - - + +
161D ASN* 3.6 14.7 - - - +
163D ILE* 4.1 13.3 - - - +
331D GLN* 3.1 22.8 + - - +
332D TRP* 3.7 15.0 - - - +
333D THR 3.1 0.2 - - - -
334D ASP* 1.3 76.2 - - + +
336D ILE* 1.3 64.0 + - - +
338D GLU* 3.3 6.2 + - - +
339D GLU* 3.0 22.7 + - - +
510D EDO 3.9 9.9 + - - -
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Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D TYR* 3.5 40.6 - - + -
160D HIS* 4.0 7.4 - - + +
332D TRP 2.9 17.4 + - - +
333D THR* 3.4 15.9 - - - +
335D ARG* 1.3 75.5 - - - +
337D MET* 1.3 70.3 + - - +
339D GLU* 3.3 4.8 + - - +
340D PHE* 2.8 55.8 + - + -
369D GLN* 4.8 2.5 - - - +
502D 2SR 3.7 40.6 - - + +
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Residues in contact with MET 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D THR* 2.9 22.6 + - + +
334D ASP* 4.0 4.9 - - - +
336D ILE* 1.3 80.3 - - - +
338D GLU* 1.3 61.8 + - - +
340D PHE* 3.7 14.3 - - + -
341D PHE* 2.8 65.5 + - + -
357D MET* 3.4 40.6 - - + +
363D ALA* 5.8 0.4 - - + -
364D SER 5.8 1.8 - - - +
365D VAL* 3.7 41.7 - - + +
368D SER* 5.5 2.0 - - - +
369D GLN* 5.0 9.6 - - - -
502D 2SR 5.8 0.2 - - - -
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D ALA* 3.6 21.7 - - + +
334D ASP 3.0 18.9 + - - +
335D ARG* 3.3 7.8 + - - +
337D MET* 1.3 77.6 - - - +
339D GLU* 1.3 56.4 + - - +
341D PHE* 4.0 7.0 - - - +
342D ARG* 3.0 32.5 + - + +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D VAL* 3.1 14.9 - - + +
158D ALA* 4.5 5.1 - - + +
159D TYR* 2.8 33.9 + - - +
160D HIS* 2.5 40.2 + - - -
204D HIS* 4.1 1.0 - - - -
206D GLY* 3.4 32.7 - - - +
335D ARG 3.0 12.6 + - - +
336D ILE* 3.6 12.9 - - + +
338D GLU* 1.3 75.6 - - - +
340D PHE* 1.3 67.9 + - + +
342D ARG* 3.4 12.4 + - - +
343D GLN* 3.1 22.0 + - - +
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Residues in contact with PHE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D HIS* 5.6 2.0 - + - -
208D SER* 6.5 1.3 - - - -
336D ILE* 2.8 50.8 + - + +
337D MET* 3.7 15.9 - - - +
339D GLU* 1.3 82.6 - - + +
341D PHE* 1.3 57.4 + - - +
343D GLN* 3.1 9.3 + - - +
344D GLY 2.9 22.7 + - - -
357D MET* 3.9 49.6 - - + +
358D CYS* 3.2 31.3 - - - +
502D 2SR 3.6 34.3 - + + -
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Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D MET* 2.8 49.3 + - + +
338D GLU* 4.0 6.7 - - - +
340D PHE* 1.3 69.4 - - - +
342D ARG* 1.3 61.0 + - - +
344D GLY* 3.0 2.1 + - - -
345D ASP* 2.9 34.7 + - - +
357D MET 3.3 24.7 - - - -
358D CYS 3.5 12.2 - - - +
359D ASP 3.9 5.4 - - - -
360D LYS* 3.8 35.7 - - + -
363D ALA* 3.6 26.0 - - + -
365D VAL* 4.2 7.2 - - + -
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Residues in contact with ARG 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ASP* 3.7 35.1 + - - -
157D VAL* 4.2 17.0 - - - +
158D ALA 4.9 2.6 - - - +
205D PRO 3.9 18.5 + - - -
206D GLY* 4.7 10.8 + - - +
207D VAL* 6.2 0.9 - - + -
338D GLU* 3.0 21.8 + - + +
339D GLU* 4.0 9.3 - - - +
341D PHE* 1.3 76.9 - - - +
343D GLN* 1.3 63.7 + - - +
345D ASP* 3.5 11.6 + - - +
346D ARG* 3.2 47.9 + - + +
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Residues in contact with GLN 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLY 4.2 2.2 - - - +
207D VAL* 3.2 18.1 - - + -
208D SER* 2.8 47.8 + - - -
211D PHE* 3.6 22.0 - - + +
339D GLU 3.1 14.3 + - - +
340D PHE* 3.4 14.2 - - - +
342D ARG* 1.3 77.6 - - - +
344D GLY* 1.3 60.1 + - - +
346D ARG* 3.3 6.2 + - - +
347D GLU* 2.9 50.9 + - - +
355D SER* 3.7 10.9 + - - -
358D CYS* 4.4 8.1 - - - -
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Residues in contact with GLY 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PHE 2.9 10.5 + - - -
341D PHE 3.0 1.0 + - - -
343D GLN* 1.3 75.8 - - - +
345D ASP* 1.3 58.9 + - - +
347D GLU* 3.2 8.8 + - - +
348D ARG* 3.0 34.9 + - - +
354D ILE* 4.0 7.1 - - - +
358D CYS* 3.2 33.1 - - - +
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D PHE* 2.9 19.1 + - - +
342D ARG* 3.7 11.8 - - - +
343D GLN 3.2 0.2 - - - -
344D GLY* 1.3 77.6 - - - +
346D ARG* 1.3 61.6 + - + +
348D ARG* 2.8 32.6 + - - +
349D GLU* 3.1 32.2 + - + +
360D LYS* 3.3 32.0 + - - +
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Residues in contact with ARG 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 4.7 1.3 - - - +
151B ASP* 3.3 46.5 + - - +
152B HIS* 4.7 11.9 - - - -
205D PRO* 4.7 5.3 + - - +
207D VAL* 3.6 24.7 - - - +
211D PHE* 4.1 26.3 - - + -
342D ARG* 3.2 44.2 + - + +
343D GLN* 3.3 4.7 + - - +
345D ASP* 1.3 77.6 - - + +
347D GLU* 1.3 60.7 + - - +
349D GLU* 3.5 16.7 - - - +
350D ARG* 3.0 49.9 + - - +
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Residues in contact with GLU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D PHE* 3.6 22.9 - - + +
214D ASN* 5.7 1.6 + - - -
343D GLN* 2.9 35.6 + - - +
344D GLY* 3.5 7.4 - - - +
345D ASP 3.1 0.2 - - - -
346D ARG* 1.3 78.2 - - - +
348D ARG* 1.3 53.4 + - - +
349D GLU 3.2 1.1 - - - -
350D ARG 3.4 2.3 + - - -
351D GLY 3.1 5.4 + - - -
352D MET* 2.5 50.2 + - + +
353D GLU 3.5 15.7 - - - +
354D ILE* 3.4 11.4 - - - +
355D SER* 2.6 49.7 + - - -
358D CYS* 4.1 1.2 - - - +
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Residues in contact with ARG 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D GLY 3.0 11.6 + - - +
345D ASP* 2.8 35.1 + - - +
347D GLU* 1.3 72.6 - - - +
349D GLU* 1.3 64.8 + - + +
350D ARG 3.3 0.7 - - - -
351D GLY* 3.3 15.6 + - - +
352D MET 4.3 1.3 - - - +
354D ILE* 3.3 28.9 - - + +
358D CYS 4.5 1.2 + - - -
359D ASP* 2.9 34.2 + - - +
360D LYS* 3.7 21.6 - - - +
361D HIS* 3.8 19.2 + - - -
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 2.7 49.3 + - - +
143B ILE* 5.0 3.5 - - - +
144B THR* 5.4 0.3 + - - -
147B MET* 3.3 32.5 - - + +
345D ASP* 3.1 25.9 + - + +
346D ARG* 3.5 17.7 - - - +
347D GLU 3.2 0.2 - - - -
348D ARG* 1.3 80.6 - - + +
350D ARG* 1.3 62.1 + - - +
351D GLY 3.1 2.7 + - - -
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Residues in contact with ARG 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 4.0 29.5 + - + +
147B MET* 4.0 10.2 - - + +
148B THR* 3.0 34.9 + - - +
151B ASP* 3.5 22.0 + - - -
243B GLU* 5.3 2.6 + - - -
244B GLU* 5.6 2.9 - - - -
211D PHE* 4.1 9.2 - - - -
215D THR* 4.1 15.5 - - - +
346D ARG* 3.0 47.9 + - - +
347D GLU 3.4 3.0 + - - +
349D GLU* 1.3 82.1 + - - +
351D GLY* 1.3 64.7 + - - +
352D MET* 3.1 35.6 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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