Contacts of the helix formed by residues 325 - 350 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 4.9 5.4 - - + +
103B GLY* 3.8 29.2 - - - +
323B THR 4.6 1.6 - - - +
324B LYS* 1.3 90.4 - - + +
326B LEU* 1.3 57.8 + - - +
327B GLN* 4.4 7.9 - - + +
328B LEU* 2.8 35.9 + - + +
329B TYR 3.1 5.4 + - - -
398B THR* 4.2 8.4 - - + -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LYS 3.3 2.9 + - - -
325B PRO* 1.3 70.9 - - - +
327B GLN* 1.3 61.9 + - - +
329B TYR* 4.2 12.6 - - + -
330B ARG* 3.0 51.5 + - + +
398B THR* 5.2 0.4 - - - +
402B ASN* 3.5 27.9 + - + +
405B TRP* 3.6 55.0 - - + +
406B TYR* 4.6 0.9 - - + -
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 3.9 21.7 + - + +
325B PRO* 4.5 8.3 - - + +
326B LEU* 1.3 79.7 - - - +
328B LEU* 1.3 63.7 + - + +
330B ARG* 3.9 5.7 + - - +
331B GLN* 3.2 46.8 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLY* 3.7 25.6 - - - +
104B LEU 3.4 23.6 - - - +
105B HIS* 4.0 28.7 - - + +
106B VAL* 4.8 3.1 - - + +
107B PHE* 3.7 28.4 - - + -
324B LYS* 4.0 14.6 - - + -
325B PRO* 2.8 25.0 + - + +
327B GLN* 1.3 74.4 - - + +
329B TYR* 1.3 65.9 + - - +
331B GLN* 2.9 18.3 + - - +
332B TRP* 3.0 23.8 + - + +
509B EDO 4.8 3.4 - - - -
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASN* 3.4 30.0 + - + +
322B PRO* 3.6 30.7 - - + +
324B LYS 4.2 3.8 - - - +
325B PRO 3.1 8.7 + - - +
326B LEU* 3.7 10.3 - - + +
328B LEU* 1.3 76.9 - - - +
330B ARG* 1.3 57.4 + - - +
332B TRP* 3.2 5.9 + - - +
333B THR* 2.8 42.1 + - - -
369B GLN* 2.6 30.6 + - - +
373B ILE* 3.5 21.3 - - + +
402B ASN* 3.7 26.2 - - + -
406B TYR* 3.2 29.2 - + - -
510B DMS 3.9 5.4 - - - -
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.0 45.4 + - + +
327B GLN* 4.3 5.8 + - - +
329B TYR* 1.3 76.4 - - - +
331B GLN* 1.3 58.1 + - + +
333B THR* 3.9 1.2 - - - -
334B ASP* 3.0 36.8 + - - +
405B TRP* 3.1 39.8 - - + -
406B TYR* 3.8 18.6 + - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 3.7 11.3 + - - -
107B PHE* 3.5 38.8 - - + +
327B GLN* 3.2 40.2 + - - +
328B LEU* 2.9 9.9 + - - +
330B ARG* 1.3 76.6 - - + +
332B TRP* 1.3 63.3 + - - +
334B ASP* 3.5 0.6 + - - -
335B ARG* 3.1 30.5 + - - +
505B EDO 3.1 41.4 + - - +
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Residues in contact with TRP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.1 8.7 - - + +
107B PHE* 3.4 30.9 - + - -
159B TYR* 3.6 27.5 - + + -
161B ASN* 5.0 0.9 - - - -
163B ILE* 3.6 25.4 - - + -
164B HIS* 3.7 33.0 - - + -
167B ASP* 3.4 34.9 + - + -
321B ASN* 3.7 40.2 - - + +
324B LYS* 5.3 4.3 - - + +
328B LEU* 3.0 36.3 + - + +
329B TYR* 3.2 6.5 + - - +
331B GLN* 1.3 72.3 - - - +
333B THR* 1.3 61.4 + - - +
335B ARG* 3.1 14.5 + - - +
336B ILE* 2.9 28.1 + - - +
509B EDO 6.1 0.4 - - - -
510B DMS 4.0 2.7 - - - +
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B TYR* 2.8 36.6 + - - -
330B ARG 3.9 2.7 - - - -
332B TRP* 1.3 76.5 - - - +
334B ASP* 1.3 66.2 + - - +
336B ILE* 3.2 3.9 - - - +
337B MET* 3.0 23.2 + - + +
365B VAL* 3.9 21.3 - - + -
369B GLN* 3.8 25.2 - - + +
406B TYR* 3.1 26.4 + - - +
510B DMS 3.5 8.6 + - - -
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.0 22.6 + - - +
331B GLN* 3.7 0.4 - - - +
332B TRP 3.3 0.2 - - - -
333B THR* 1.3 80.2 - - - +
335B ARG* 1.3 58.1 + - - +
337B MET* 3.5 4.1 + - - +
338B GLU* 3.1 30.9 + - - +
365B VAL* 6.1 0.5 - - - +
505B EDO 3.4 25.5 + - - +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.4 24.8 - - - -
158B ALA* 3.0 52.1 + - + +
159B TYR* 3.8 7.8 - - + +
161B ASN* 3.6 13.1 + - - +
163B ILE* 3.9 19.3 - - - +
331B GLN 3.1 13.4 + - - +
332B TRP* 3.1 18.0 + - - +
334B ASP* 1.3 75.4 - - - +
336B ILE* 1.3 64.3 + - - +
338B GLU* 3.5 4.3 + - - +
339B GLU* 3.1 20.1 + - - +
505B EDO 2.8 36.6 + - - -
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 3.7 36.0 - - + -
160B HIS* 3.9 12.6 - - + -
332B TRP 2.9 14.4 + - - +
333B THR* 3.2 17.7 - - - +
335B ARG* 1.3 75.9 - - - +
337B MET* 1.3 71.4 + - + +
339B GLU* 3.4 2.9 + - - +
340B PHE* 2.9 64.1 + - + -
369B GLN* 4.5 2.5 - - - +
501B 2SR 4.1 12.1 - - + +
510B DMS 3.9 25.1 - - + +
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Residues in contact with MET 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B THR* 3.0 22.6 + - + +
334B ASP* 4.1 4.5 - - - +
336B ILE* 1.3 81.7 - - + +
338B GLU* 1.3 60.6 + - - +
340B PHE* 4.1 16.8 - - + -
341B PHE* 2.9 67.7 + - + -
357B MET* 3.5 34.3 - - + +
363B ALA* 4.8 2.9 - - + -
364B SER 5.8 0.2 - - - -
365B VAL* 3.6 42.6 - - + +
368B SER* 5.6 2.7 - - - +
369B GLN* 5.0 7.2 - - - -
501B 2SR 6.0 0.2 - - - -
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA* 3.7 13.6 - - + +
334B ASP 3.1 19.4 + - - +
335B ARG* 3.6 9.0 - - - +
337B MET* 1.3 76.3 - - - +
339B GLU* 1.3 57.3 + - - +
341B PHE* 3.9 7.0 - - - +
342B ARG* 2.4 74.2 + - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.0 21.2 - - + +
158B ALA* 4.3 8.5 - - + +
159B TYR* 2.9 26.4 + - + +
160B HIS* 2.4 37.6 + - - -
204B HIS* 4.0 0.9 - - - -
206B GLY* 3.4 31.4 - - - +
335B ARG 3.1 16.5 + - - +
336B ILE* 3.7 5.6 - - - +
338B GLU* 1.3 74.3 - - - +
340B PHE* 1.3 68.9 + - + +
342B ARG* 3.4 9.8 + - - +
343B GLN* 3.1 21.3 + - - +
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B HIS* 5.4 3.8 - + - -
336B ILE* 2.9 49.2 + - + +
337B MET* 3.8 17.9 - - + +
339B GLU* 1.3 81.3 - - + +
341B PHE* 1.3 57.3 + - - +
343B GLN* 3.1 6.3 + - - +
344B GLY 2.9 23.4 + - - -
357B MET* 3.6 52.0 - - + +
358B CYS* 3.2 23.9 - - - +
501B 2SR 4.0 27.6 - + + -
504B EDO 3.6 27.4 - - - -
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B MET* 2.9 45.2 + - + +
338B GLU* 3.9 6.5 - - - +
340B PHE* 1.3 73.2 - - - +
342B ARG* 1.3 59.8 + - - +
344B GLY* 3.2 1.4 + - - -
345B ASP* 2.8 37.1 + - - +
357B MET 3.4 19.5 - - - -
358B CYS 3.5 16.1 - - - +
359B ASP 3.9 0.4 - - - -
360B LYS* 3.7 37.7 - - + -
363B ALA* 3.5 30.7 - - + -
365B VAL* 4.2 7.6 - - + -
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP 3.4 24.8 + - - -
158B ALA* 4.2 9.1 - - - +
338B GLU* 2.4 58.5 + - - +
339B GLU* 3.5 9.2 - - + +
341B PHE* 1.3 76.3 - - - +
343B GLN* 1.3 61.8 + - - +
345B ASP* 3.3 11.5 + - + +
346B ARG* 3.1 28.9 + - + +
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 4.1 2.1 + - - +
207B VAL* 3.2 26.6 - - + -
208B SER* 2.9 48.5 + - - -
211B PHE* 3.7 11.7 - - + +
339B GLU 3.1 13.5 + - - +
340B PHE* 3.1 12.1 + - - +
342B ARG* 1.3 75.5 - - - +
344B GLY* 1.3 57.8 + - - +
346B ARG* 3.1 9.1 + - - +
347B GLU* 2.8 53.9 + - - +
355B SER* 3.6 10.9 + - - -
358B CYS* 4.4 3.1 - - - -
504B EDO 4.1 11.4 - - - -
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE 2.9 12.1 + - - -
341B PHE 3.2 0.6 + - - -
343B GLN* 1.3 74.9 - - - +
345B ASP* 1.3 59.2 + - - +
347B GLU* 3.3 16.8 + - - +
348B ARG* 2.8 33.6 + - - +
354B ILE* 3.9 8.2 - - - +
358B CYS* 3.2 25.0 - - - +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 2.8 25.7 + - - +
342B ARG* 3.6 9.9 - - + +
344B GLY* 1.3 72.3 - - - +
346B ARG* 1.3 63.1 + - + +
348B ARG* 3.6 18.3 + - - +
349B GLU* 3.0 29.3 + - - +
358B CYS 5.2 0.2 - - - +
360B LYS* 2.8 45.4 + - - +
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Residues in contact with ARG 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 4.0 15.2 + - - +
207B VAL* 3.3 35.2 - - - +
211B PHE* 4.1 26.5 - - + -
342B ARG* 3.1 16.6 + - + +
343B GLN* 3.1 8.2 + - - +
345B ASP* 1.3 74.6 - - + +
347B GLU* 1.3 65.5 + - - +
349B GLU* 3.2 20.2 - - - +
350B ARG* 3.1 30.8 + - - +
116D ARG* 4.6 0.9 - - - +
151D ASP* 2.9 48.7 + - - +
152D HIS* 6.0 0.2 - - - -
501D EDO 4.4 4.9 + - - -
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.8 10.1 - - + -
343B GLN* 2.8 29.1 + - - +
344B GLY* 3.3 18.0 + - - +
346B ARG* 1.3 76.8 - - - +
348B ARG* 1.3 60.4 + - - +
350B ARG* 3.2 2.1 + - - -
351B GLY 3.0 4.3 + - - -
352B MET* 2.8 38.6 + - + +
353B GLU 3.7 11.7 - - - +
354B ILE* 3.3 5.7 - - - +
355B SER* 2.5 49.8 + - - -
358B CYS* 4.1 0.5 - - - +
507B EDO 2.7 30.0 + - - -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLY 2.8 20.2 + - - +
345B ASP* 3.6 26.7 + - - +
347B GLU* 1.3 73.5 - - - +
349B GLU* 1.3 63.4 + - - +
351B GLY* 3.1 12.7 + - - -
352B MET 4.6 2.7 - - - -
354B ILE* 3.2 37.1 - - + +
359B ASP* 3.2 24.2 + - - +
360B LYS* 4.2 7.1 - - - +
361B HIS* 3.4 34.5 + - - +
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASP 3.0 16.8 + - - +
346B ARG* 3.2 31.3 - - - +
348B ARG* 1.3 77.1 - - - +
350B ARG* 1.3 61.4 + - + +
351B GLY 3.6 0.2 + - - -
512B DMS 3.4 18.7 + - - -
116D ARG* 2.6 49.6 + - - +
147D MET* 3.6 31.5 - - + +
151D ASP* 4.9 0.5 - - - +
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 4.0 10.6 - - - -
215B THR* 3.9 19.6 - - - +
346B ARG* 3.1 23.8 + - - +
347B GLU 3.8 3.1 - - - +
348B ARG 3.2 0.2 - - - -
349B GLU* 1.3 83.3 + - + +
351B GLY* 1.3 61.7 + - - +
352B MET* 3.4 26.5 + - + +
512B DMS 3.3 20.1 + - - +
144D THR* 4.5 21.5 + - + +
147D MET* 4.3 12.3 - - + +
148D THR* 3.3 34.2 + - - +
151D ASP* 2.8 29.3 + - - -
243D GLU* 4.9 0.6 + - - -
244D GLU 5.8 0.2 + - - -
246D CYS* 5.6 0.6 - - - -
501D EDO 3.4 21.8 - - - -
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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
------------------------------------------------------------
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