Contacts of the helix formed by residues 301 - 327 (chain B) in PDB entry 1XLB
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 TYR 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL 4.3 6.4 + - - -
18B GLY* 4.9 0.7 - - - -
19B TRP 5.6 0.2 + - - -
20B THR* 4.5 3.8 - - - +
30B ARG* 3.8 23.6 + - + +
31B LYS* 2.8 38.4 + - + -
32B ASN 4.8 1.3 - - - -
33B LEU* 3.2 41.2 + - + +
37B GLU* 6.1 0.4 - - - -
300B GLY* 1.3 70.3 - - - -
302B ASP* 1.3 63.3 + - - +
304B VAL* 3.0 38.9 + - + +
305B TRP* 3.2 39.3 + - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 3.6 16.7 + - - +
300B GLY 3.2 1.0 + - - -
301B TYR* 1.3 78.0 - - - +
303B GLY* 1.3 51.2 + - - +
305B TRP* 3.6 8.5 + - - +
306B ASP* 2.9 43.3 + - - +
309B LYS* 4.9 0.5 + - - -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 3.9 7.2 - - - +
378A ALA* 5.7 1.3 - - - -
380A ILE* 4.3 7.4 - - - +
381A ARG 6.2 0.2 - - - -
295B PRO* 5.0 0.2 - - - -
299B ASP* 4.1 22.7 - - - -
300B GLY 3.0 9.8 + - - -
302B ASP* 1.3 73.9 - - - +
304B VAL* 1.3 54.5 + - - +
306B ASP* 3.5 11.1 + - - +
307B SER* 2.7 39.0 + - - -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.4 42.6 - - + +
30B ARG* 3.5 43.7 - - - +
293B TYR* 3.7 1.7 + - - -
295B PRO* 4.0 9.2 - - + -
300B GLY 3.2 7.7 + - - +
301B TYR* 3.0 27.0 + - + +
303B GLY* 1.3 73.8 - - - +
305B TRP* 1.3 64.1 + - + +
307B SER* 2.6 24.0 + - - -
308B ALA* 3.0 12.8 + - - +
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.9 26.2 - - + -
33B LEU* 3.7 31.9 - - + -
37B GLU* 5.0 7.4 + - - -
38B ALA* 4.4 6.7 - - - -
41B LYS* 3.6 51.3 - - + +
42B LEU* 3.7 25.1 - - + -
45B LEU* 3.8 22.7 - - + +
301B TYR* 3.2 37.7 + + + +
302B ASP* 4.1 8.1 - - - +
304B VAL* 1.3 77.0 - - + +
306B ASP* 1.3 64.1 + - - +
308B ALA* 3.3 3.1 + - + +
309B LYS* 3.0 37.0 + - + +
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 5.5 1.4 + - - -
378A ALA* 5.7 2.8 - - - +
380A ILE* 5.1 2.0 - - + -
381A ARG* 3.5 45.3 - - + +
302B ASP* 2.9 30.4 + - - +
303B GLY* 3.5 10.1 - - - +
305B TRP* 1.3 74.3 - - - +
307B SER* 1.3 53.6 + - - +
309B LYS* 2.8 30.7 + - - +
310B ALA* 2.8 35.8 + - - +
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ILE* 4.0 28.9 - - - +
258B VAL* 3.8 2.4 - - - +
293B TYR* 2.4 40.0 + - - -
295B PRO* 3.5 6.8 - - - +
303B GLY 2.7 17.7 + - - -
304B VAL 2.6 13.9 + - - -
306B ASP* 1.3 72.8 - - - +
308B ALA* 1.3 53.1 + - - +
310B ALA* 3.2 9.8 + - - +
311B ASN* 2.8 31.9 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.2 39.3 - - + -
17B VAL* 4.1 13.5 - - + -
42B LEU* 4.7 2.9 - - + -
45B LEU* 3.8 18.6 - - + -
293B TYR* 3.5 10.8 - - - +
304B VAL 3.0 11.2 + - - +
305B TRP* 3.3 6.5 + - + +
307B SER* 1.3 81.0 + - - +
309B LYS* 1.3 60.0 + - - +
311B ASN 3.6 5.5 + - - -
312B MET* 3.4 7.6 + - - +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 31.6 - - + +
302B ASP 4.9 0.2 + - - -
305B TRP* 3.0 21.3 + - + +
306B ASP* 2.8 38.9 + - - +
308B ALA* 1.3 70.7 - - - +
310B ALA* 1.4 55.9 - - - +
312B MET* 3.1 15.8 + - + +
313B SER* 2.9 37.7 + - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ILE* 4.8 3.6 - - + -
384A GLN* 3.8 35.9 - - + +
258B VAL* 3.9 12.6 - - + -
261B HIS* 4.6 1.1 - - - +
306B ASP 2.8 21.0 + - - +
307B SER* 3.2 11.9 + - - +
309B LYS* 1.4 69.5 - - - +
311B ASN* 1.3 63.6 + - - +
313B SER* 4.3 3.1 - - - -
314B MET* 2.9 28.8 + - - +
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Residues in contact with ASN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.2 2.0 - - + -
245B LEU 4.7 0.2 - - - +
258B VAL* 3.5 17.0 - - - +
259B PHE* 3.0 26.6 + - - -
291B PHE* 3.4 51.6 - - + +
293B TYR* 3.4 29.3 - - - +
307B SER 2.8 27.5 + - - -
308B ALA* 3.7 8.1 - - - +
309B LYS 3.3 0.4 - - - -
310B ALA* 1.3 74.7 - - - +
312B MET* 1.3 62.4 + - - +
314B MET* 3.8 3.2 - - - +
315B TYR 3.2 15.9 + - - -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 3.9 20.9 - - + -
10B PHE* 3.4 44.6 - - + -
12B PHE* 3.6 29.8 - - + -
45B LEU* 3.7 31.9 - - + +
46B GLY 4.4 9.2 - - - -
47B ALA* 4.5 0.7 - - + +
291B PHE* 4.1 2.7 - - + -
308B ALA 3.4 18.6 + - - +
309B LYS* 3.1 15.2 + - + +
311B ASN* 1.3 74.8 - - - +
313B SER* 1.3 63.0 + - - +
315B TYR* 3.4 2.8 + - - +
316B LEU* 3.1 30.5 + - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 3.9 14.8 - - - -
388A GLU* 4.5 8.2 + - - -
2B VAL* 4.1 19.2 + - - +
4B PRO* 5.9 2.6 - - - +
309B LYS* 2.9 18.3 + - - +
310B ALA* 3.6 9.1 - - - -
312B MET* 1.3 74.6 - - - +
314B MET* 1.3 52.6 + - - +
316B LEU* 3.1 6.5 + - - +
317B LEU* 2.8 40.5 + - - +
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Residues in contact with MET 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 3.5 31.0 - - - +
387A ILE* 3.5 33.2 - - + -
388A GLU* 5.7 0.2 - - - -
391A LEU* 3.8 19.7 - - + -
258B VAL* 4.4 0.2 - - + -
259B PHE* 3.1 30.3 - - + +
260B GLY* 4.2 4.5 - - - -
261B HIS* 4.3 5.4 - - + -
264B LEU* 4.1 15.7 - - + -
310B ALA 2.9 22.1 + - - +
311B ASN 3.8 2.0 - - - +
313B SER* 1.3 72.3 - - - +
315B TYR* 1.3 56.5 + - - +
317B LEU* 3.4 6.4 + - - +
318B LEU* 3.0 44.1 + - + +
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 5.8 0.2 - - - -
10B PHE* 3.7 28.7 - + + -
245B LEU* 3.9 18.6 - - + -
259B PHE* 3.8 25.7 - + + -
271B VAL* 3.9 18.2 - - + +
274B LEU* 3.6 21.1 - - + +
275B GLU* 2.5 39.9 + - + +
289B ARG* 3.4 28.5 + - + +
291B PHE* 4.1 7.2 - + + -
311B ASN 3.2 14.8 + - - +
312B MET 3.9 4.0 - - - +
314B MET* 1.3 78.2 - - - +
316B LEU* 1.3 56.9 + - + +
318B LEU* 3.6 3.4 + - - +
319B LYS* 3.0 28.4 + - + +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.9 30.3 - - + +
3B GLN 3.9 7.4 - - - +
4B PRO* 3.7 39.3 - - + -
8B ASP* 4.0 24.2 - - - +
10B PHE* 4.1 10.8 - - + -
312B MET 3.1 20.2 + - - +
313B SER 3.1 6.6 + - - +
315B TYR* 1.3 72.1 - - + +
317B LEU* 1.3 64.9 + - - +
319B LYS* 3.4 21.3 + - + +
320B GLU* 3.1 25.3 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 4.8 3.4 - - - +
388A GLU* 3.7 28.7 - - + +
391A LEU* 3.8 25.4 - - + -
393A SER* 3.2 28.5 - - - +
2B VAL* 3.6 27.1 - - + -
313B SER* 2.8 24.4 + - - +
314B MET* 3.8 6.5 - - - +
316B LEU* 1.3 76.3 - - - +
318B LEU* 1.3 63.3 + - - +
320B GLU* 3.2 7.7 + - - +
321B ARG* 3.2 39.3 + - - +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU* 4.6 6.1 - - + -
259B PHE* 4.1 17.3 - - + -
260B GLY* 4.9 0.9 - - - -
264B LEU* 4.2 11.0 - - + -
267B ALA* 4.0 28.5 - - + -
268B PHE* 3.8 17.9 - - + +
271B VAL* 4.0 15.9 - - + -
314B MET* 3.0 37.7 + - + +
315B TYR 3.9 4.3 - - - +
317B LEU* 1.3 74.8 - - - +
319B LYS* 1.3 54.8 + - - +
321B ARG* 3.5 4.2 + - - +
322B ALA* 2.9 32.1 + - - +
390B LEU* 3.6 31.4 - - + -
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 4.6 11.9 + - - +
271B VAL* 3.7 10.4 - - + +
275B GLU* 3.1 43.1 + - + +
315B TYR* 3.0 23.6 + - + +
316B LEU* 3.5 23.7 - - + +
318B LEU* 1.3 72.6 - - - +
320B GLU* 1.4 60.2 + - - +
322B ALA* 3.5 3.0 + - - +
323B LEU* 2.9 55.6 + - + +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.8 20.8 - - + +
316B LEU 3.1 22.6 + - - +
317B LEU* 3.4 12.7 - - - +
319B LYS* 1.4 71.7 - - - +
321B ARG* 1.3 78.5 + - + +
323B LEU* 3.1 11.4 + - + +
324B ALA* 2.7 37.3 + - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU* 2.7 45.5 + - - +
392A GLY 3.3 19.8 + - - -
393A SER* 3.6 9.6 + - - +
268B PHE* 3.8 15.2 - - + -
317B LEU* 3.2 37.6 + - - +
318B LEU* 3.8 4.3 - - - +
320B GLU* 1.3 101.8 + - + +
322B ALA* 1.3 55.4 + - - +
324B ALA* 3.4 6.4 + - - +
325B PHE* 3.1 29.5 + - - +
389B HIS* 3.6 21.5 - - - +
390B LEU* 3.3 19.0 + - - +
392B GLY* 4.1 7.9 - - - -
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.5 20.8 - - + +
271B VAL* 4.8 1.1 - - + +
272B ASP* 3.9 34.8 - - + +
275B GLU* 5.9 1.1 - - + -
276B ASN* 3.3 15.5 + - - +
318B LEU 2.9 23.1 + - - +
319B LYS* 3.9 5.2 - - - +
321B ARG* 1.3 66.9 - - - +
323B LEU* 1.3 62.3 + - - +
325B PHE* 3.6 1.6 - - - +
326B ARG* 3.2 20.1 + - - +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 4.9 9.0 - - + +
276B ASN* 3.0 30.7 - - - +
319B LYS* 2.9 50.8 + - + +
320B GLU* 3.6 7.6 - - - +
322B ALA* 1.3 70.3 - - - +
324B ALA* 1.3 68.3 + - - +
325B PHE 3.2 0.2 + - - -
326B ARG* 3.3 3.8 + - - +
327B ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLU 2.7 21.5 + - - +
321B ARG* 3.7 7.2 - - - +
322B ALA 3.4 0.2 - - - -
323B LEU* 1.3 76.3 - - - +
325B PHE* 1.3 54.4 + - - +
327B ALA* 3.2 6.6 + - - +
328B ASP* 2.9 31.9 + - - +
389B HIS* 3.7 14.9 - - + +
394B ARG 5.8 1.3 - - - +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.8 16.8 - + + -
269B PHE* 4.3 12.3 - + - -
272B ASP* 4.6 4.0 - - - -
321B ARG 3.1 17.8 + - - +
322B ALA* 3.6 6.3 - - - +
324B ALA* 1.3 75.7 - - - +
326B ARG* 1.3 107.7 + - + +
328B ASP 3.5 2.3 + - - -
331B VAL* 3.2 58.9 - - + +
382B LEU* 4.9 11.0 - - + -
385B LEU* 4.9 0.2 - - + -
386B ALA* 3.5 37.7 - - + -
389B HIS* 3.6 25.3 + + + -
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 4.6 9.1 - - - -
272B ASP* 2.7 34.5 + - - +
276B ASN* 3.4 30.9 - - + +
279B PRO* 4.6 16.9 - - - +
322B ALA 3.2 8.2 + - - +
323B LEU* 4.2 2.2 - - - +
325B PHE* 1.3 109.8 - - + +
327B ALA* 1.3 59.4 + - - +
331B VAL* 4.8 1.1 - - - +
332B GLN* 2.9 29.5 + - - +
335B MET* 3.3 42.3 - - - +
340B VAL* 5.9 0.2 - - - +
382B LEU* 5.7 1.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU 3.0 17.3 + - - +
324B ALA* 3.7 6.7 - - - +
326B ARG* 1.3 75.0 - - - +
328B ASP* 1.3 64.4 + - - +
329B PRO* 3.2 9.4 - - - +
332B GLN* 3.2 14.4 + - - +
----------------------------------------------------------
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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