Contacts of the helix formed by residues 284 - 309 (chain B) in PDB entry 3LKB
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 SER 284 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO* 3.7 15.7 - - - +
236B PRO* 5.0 2.5 - - - -
237B ASP* 2.6 31.7 + - - -
268B GLN* 3.5 1.2 - - - +
280B ASN 3.4 13.9 + - - -
281B PHE* 3.2 15.4 + - - -
283B GLU* 1.3 79.0 - - - +
285B VAL* 1.3 58.9 + - - +
286B ASN* 3.0 16.1 + - - +
287B TYR* 3.2 18.4 + - - +
288B THR* 3.3 12.1 + - - -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B HIS* 4.0 9.2 - - - +
234B GLY 4.0 10.5 - - - +
235B GLY* 4.3 4.5 - - - -
236B PRO* 4.6 4.8 - - + +
237B ASP* 4.4 2.2 + - - +
251B TRP* 3.8 36.6 - - + -
253B THR* 4.6 0.4 - - + -
255B PHE* 3.6 37.7 - - + -
256B TYR 4.6 1.8 - - - +
257B MET* 4.3 7.0 - - + -
283B GLU 3.3 3.2 + - - -
284B SER* 1.3 72.2 + - - +
286B ASN* 1.3 75.6 + - - +
287B TYR 3.3 0.2 - - - -
288B THR* 3.3 9.6 - - - -
289B ASN* 2.8 24.8 + - - +
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Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 5.1 0.4 + - - -
23B ALA* 3.8 28.8 - - - +
26B PRO* 4.3 2.5 - - + -
27B TYR* 3.3 18.1 - - + +
231B HIS* 2.8 30.1 - - - -
232B TYR* 3.2 32.5 + - + +
234B GLY 5.1 3.0 + - - -
237B ASP* 4.3 9.9 + - - -
284B SER* 3.0 8.0 + - - +
285B VAL* 1.3 90.1 - - - +
287B TYR* 1.3 58.4 + - - +
289B ASN* 3.2 6.5 + - + +
290B GLY 3.0 21.8 + - - -
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Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO* 3.4 24.2 - - + +
29B ALA* 3.9 8.1 - - + -
30B ALA* 3.1 25.5 - - + +
33B ASP* 2.6 35.1 + - - +
268B GLN* 3.7 39.3 - - + -
271B ILE* 3.7 2.4 - - - +
272B GLY* 3.3 23.1 + - - -
277B ARG* 4.4 8.7 - - + -
281B PHE* 2.9 31.0 - - + +
282B ILE* 3.8 8.5 - - - -
284B SER* 3.2 10.9 + - - +
286B ASN* 1.3 74.6 - - - +
288B THR* 1.3 62.4 + - - +
291B MET* 3.1 35.4 + - + +
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 3.5 25.6 - - + -
256B TYR 4.7 1.8 + - - +
258B ALA* 5.9 1.2 + - - -
265B ILE* 4.0 10.7 - - + +
268B GLN* 2.6 36.0 + - - +
283B GLU 5.4 0.2 + - - -
284B SER 3.3 6.8 + - - -
285B VAL* 3.3 16.5 + - - +
287B TYR* 1.3 75.9 - - - +
289B ASN* 1.3 57.6 + - - +
291B MET* 3.3 5.2 + - - +
292B LEU* 3.0 28.1 + - - +
333B PHE* 3.9 22.7 - - + +
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.5 13.9 + - + -
104B ALA* 5.3 1.0 - - - +
106B MET* 3.7 7.1 - - - +
122B PRO* 5.6 5.2 - - - +
123B THR* 4.9 1.7 - - - +
231B HIS* 3.5 4.9 - - - -
232B TYR* 2.9 31.9 + - - -
255B PHE* 3.1 31.5 - - + -
285B VAL 2.8 17.3 + - - +
286B ASN* 3.2 25.1 + - - +
287B TYR 3.2 0.2 - - - -
288B THR* 1.3 76.3 - - - +
290B GLY* 1.3 62.0 + - - +
292B LEU* 3.4 4.7 + - - +
293B ALA* 3.1 20.4 + - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.6 38.3 - - - -
30B ALA* 3.6 7.0 - - - -
31B VAL* 4.0 4.6 - - - +
286B ASN 3.0 13.4 + - - -
289B ASN* 1.3 78.1 - - - +
291B MET* 1.3 55.5 + - - +
293B ALA* 3.2 2.4 + - - +
294B ALA* 3.0 29.1 + - - +
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.4 17.8 - - + +
34B TYR* 3.6 19.2 - - + -
267B LEU* 4.5 1.3 - - - -
268B GLN* 3.6 28.3 - - + -
271B ILE* 3.9 41.1 - - + -
287B TYR* 3.1 39.5 + - + +
288B THR* 3.7 5.2 - - - +
289B ASN 3.3 0.2 - - - -
290B GLY* 1.3 72.6 - - - +
292B LEU* 1.3 57.3 + - - +
294B ALA* 3.7 4.5 - - - +
295B ALA* 2.7 36.7 + - - +
333B PHE* 3.6 23.8 - - + -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 4.0 21.1 - - + -
123B THR* 4.1 9.2 - - + -
255B PHE* 3.8 22.7 - - + -
288B THR 3.0 13.9 + - - +
289B ASN 3.6 7.9 - - - +
291B MET* 1.3 76.8 - - - +
293B ALA* 1.3 63.5 + - - +
295B ALA* 3.2 0.7 + - + -
296B ILE* 2.9 44.7 + - + +
331B PRO* 4.1 13.0 - - + -
333B PHE* 3.8 29.3 - - + -
334B ALA* 4.4 8.7 - - + -
342B GLU* 4.6 0.9 - - - +
343B ILE* 4.1 20.2 - - + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.1 31.0 - - + +
31B VAL* 5.5 0.2 - - + -
80B LEU* 4.2 14.7 - - + +
102B ILE* 4.3 22.3 - - + +
122B PRO* 4.8 7.0 - - + -
289B ASN 3.1 9.1 + - - +
290B GLY 3.6 7.0 - - - +
291B MET 3.2 0.2 - - - -
292B LEU* 1.3 79.5 - - - +
294B ALA* 1.3 64.1 + - - +
296B ILE* 3.3 4.6 + - - +
297B ALA* 3.0 21.7 + - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.5 4.9 - - + +
31B VAL* 4.1 23.1 - - + +
34B TYR* 3.8 27.6 - - + -
80B LEU* 4.3 11.7 - - + +
290B GLY 3.0 16.4 + - - +
291B MET* 3.8 3.1 - - - +
293B ALA* 1.3 77.8 - - - +
295B ALA* 1.3 56.5 + - - +
297B ALA* 3.2 3.6 + - - +
298B VAL* 2.9 32.6 + - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.5 30.2 + - + +
291B MET 2.7 22.1 + - - +
292B LEU* 3.2 3.8 + - - +
294B ALA* 1.3 69.2 - - - +
296B ILE* 1.3 60.3 + - - +
298B VAL* 3.3 0.5 + - - +
299B GLU* 2.8 32.6 + - - +
329B PHE* 3.8 18.1 - - + -
331B PRO* 4.8 1.1 - - + -
333B PHE* 4.0 18.2 - - + -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.5 21.1 - - + -
122B PRO* 4.1 22.7 - - + -
292B LEU* 2.9 46.9 + - + +
293B ALA* 3.7 5.4 - - - +
295B ALA* 1.3 73.6 - - - +
297B ALA* 1.3 62.9 + - - +
299B GLU* 3.8 1.2 - - - +
300B ALA* 3.0 22.9 + - - +
320B ILE* 4.9 5.6 - - + -
323B MET* 4.3 11.1 - - + +
329B PHE* 3.9 20.4 - - + -
343B ILE* 3.9 20.0 - - + -
345B PHE* 4.4 19.1 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.1 20.2 - - + -
78B VAL* 4.3 13.3 - - + +
80B LEU* 3.9 21.3 - - + -
102B ILE* 4.1 7.1 - - + +
293B ALA 3.0 13.6 + - - +
294B ALA* 3.2 10.3 + - - +
296B ILE* 1.3 76.1 - - - +
298B VAL* 1.3 57.4 + - - +
300B ALA* 3.3 5.1 + - - +
301B ILE* 3.1 33.5 + - - +
316B VAL* 5.3 0.8 - - - +
320B ILE* 6.1 0.4 - - - -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.8 22.2 - - + -
34B TYR* 3.8 27.8 - - + +
35B CYS* 5.8 0.9 - - - -
38B ALA* 4.5 4.9 - - + -
43B LEU* 4.2 20.2 - - + -
44B VAL* 4.2 8.4 - - + +
49B PHE* 4.1 28.3 - - + -
294B ALA 2.9 18.8 + - - +
295B ALA 3.9 0.7 - - - +
297B ALA* 1.3 73.1 - - - +
299B GLU* 1.3 61.0 + - - +
301B ILE* 3.2 7.4 + - - +
302B ARG* 2.8 28.1 + - + +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 2.8 21.5 + - - +
296B ILE 3.9 3.1 - - - +
298B VAL* 1.3 75.5 - - - +
300B ALA* 1.3 57.5 + - - +
302B ARG* 2.5 44.8 + - - +
303B ARG* 2.6 65.6 + - - +
323B MET* 4.1 5.8 - - + -
329B PHE* 3.7 39.8 - - + -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE 3.0 18.4 + - - +
297B ALA* 3.6 5.2 - - - +
299B GLU* 1.3 73.2 - - - +
301B ILE* 1.3 67.6 + - - +
303B ARG* 3.2 0.9 + - - -
304B ALA* 2.9 25.3 + - - +
316B VAL* 4.0 18.8 - - + +
319B ALA* 3.5 9.8 - - + +
320B ILE* 3.7 29.2 - - + -
323B MET* 4.1 8.9 - - + +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.2 12.1 - - + -
10B LEU* 4.0 26.0 - - + -
44B VAL* 4.5 5.4 - - + -
49B PHE* 4.2 28.5 - - + -
77B PRO* 4.7 2.2 - - + -
78B VAL* 4.0 12.3 - - + -
297B ALA 3.1 19.6 + - - +
298B VAL* 3.2 4.9 + - - +
300B ALA* 1.3 76.4 - - - +
302B ARG* 1.3 62.8 + - - +
304B ALA* 3.2 1.9 + - - +
305B GLN* 3.0 22.9 + - - +
311B ILE* 3.8 32.2 - - + +
316B VAL* 3.9 25.1 - - + -
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 28.7 - - + +
44B VAL* 3.9 20.4 - - + +
45B PRO* 5.2 3.4 - - + -
298B VAL* 2.8 17.9 + - + +
299B GLU* 2.5 49.6 + - - +
301B ILE* 1.3 77.8 - - - +
303B ARG* 1.3 74.6 + - - +
305B GLN* 3.4 4.3 - - - +
306B GLU* 3.2 40.2 + - - +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 2.6 50.5 + - - +
300B ALA 3.9 2.9 - - - +
302B ARG* 1.3 88.0 - - - +
304B ALA* 1.3 52.0 + - - +
306B GLU* 3.2 13.4 + - - +
307B ARG* 2.7 56.2 + - - +
319B ALA* 3.9 18.5 + - + -
322B GLY 4.4 1.4 + - - -
323B MET* 3.6 23.6 - - - +
327B ASN* 2.6 49.1 + - - +
328B ALA 3.7 10.1 + - - -
329B PHE* 4.0 14.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA 2.9 12.6 + - - +
301B ILE* 3.4 11.2 - - - +
303B ARG* 1.3 73.3 - - - +
305B GLN* 1.3 57.1 + - - +
308B PHE* 2.7 43.8 + - - +
309B LYS 3.5 0.9 + - - -
310B ARG 3.5 5.6 - - - +
311B ILE* 4.9 2.7 - - + -
315B THR* 3.6 42.2 - - - +
316B VAL* 4.1 5.4 - - + +
319B ALA* 3.9 2.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 4.8 6.7 + - - -
44B VAL* 4.0 12.3 - - + -
45B PRO* 3.5 30.3 + - + +
47B VAL* 4.4 4.0 - - + +
301B ILE 3.0 9.0 + - - +
302B ARG* 3.4 13.0 - - - +
304B ALA* 1.3 73.8 - - - +
306B GLU* 1.3 60.1 + - + +
309B LYS* 2.9 57.8 + - - +
310B ARG* 4.2 1.8 + - - -
311B ILE* 3.3 34.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ARG* 3.2 32.0 + - + +
303B ARG* 3.6 21.7 - - - +
305B GLN* 1.3 80.6 - - - +
307B ARG* 1.3 76.1 + - - +
309B LYS* 3.6 19.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG* 2.7 49.3 + - - +
306B GLU* 1.3 86.2 + - - +
308B PHE* 1.3 95.6 + - + +
309B LYS* 5.3 2.7 + - - +
318B GLN 4.9 4.2 + - - -
319B ALA* 4.2 17.0 + - - +
322B GLY* 5.5 8.3 + - - -
327B ASN* 4.9 11.9 + - - -
----------------------------------------------------------
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 2.7 22.2 + - - +
307B ARG* 1.3 114.1 - - + +
309B LYS* 1.3 64.9 + - - +
310B ARG* 2.9 26.3 + - + +
315B THR* 3.7 39.9 - - + -
318B GLN* 3.9 33.9 - - + -
319B ALA 5.1 0.4 - - - -
----------------------------------------------------------
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 5.9 1.0 + - - -
304B ALA 3.5 0.4 + - - -
305B GLN* 2.9 49.2 + - - +
306B GLU* 3.6 19.2 + - - +
307B ARG 5.3 1.9 + - - +
308B PHE* 1.3 77.9 - - - +
310B ARG* 1.3 66.6 + - - +
----------------------------------------------------------
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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