Contacts of the helix formed by residues 284 - 309 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 3.9 18.2 - - - +
236A PRO* 4.9 2.5 - - - -
237A ASP* 2.7 34.2 + - - -
268A GLN* 3.5 1.2 - - - +
280A ASN 3.5 12.0 + - - -
281A PHE 3.0 13.8 + - - -
283A GLU* 1.3 78.6 - - - +
285A VAL* 1.3 63.1 + - - +
286A ASN* 3.2 11.4 + - - +
287A TYR* 3.3 15.6 + - - +
288A THR* 3.3 12.8 + - - -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A HIS* 3.8 15.9 - - + +
234A GLY 4.2 9.4 - - - +
235A GLY* 4.8 0.2 - - - -
236A PRO* 4.4 6.7 - - + +
237A ASP* 3.9 4.4 + - - +
251A TRP* 3.7 39.9 - - + -
253A THR* 5.4 0.2 - - + -
255A PHE* 3.6 33.0 - - + -
256A TYR 4.4 8.3 - - - +
257A MET* 5.4 3.1 - - - -
283A GLU 3.4 3.4 + - - -
284A SER* 1.3 73.7 + - - +
286A ASN* 1.3 72.3 + - - +
288A THR* 3.2 12.2 - - - +
289A ASN* 2.9 24.8 + - - +
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP 4.7 2.0 + - - -
23A ALA* 3.6 38.4 - - - +
26A PRO* 4.0 3.6 - - + -
27A TYR* 3.4 14.2 - - + -
231A HIS* 3.0 29.0 - - - -
232A TYR* 3.1 26.5 + - - +
234A GLY 5.3 1.6 + - - -
237A ASP* 4.4 6.9 + - - -
284A SER* 3.0 12.3 + - - +
285A VAL* 1.3 85.7 - - - +
287A TYR* 1.3 59.1 + - - +
288A THR 3.3 0.9 - - - -
289A ASN* 3.4 6.0 + - + +
290A GLY 2.8 25.3 + - - -
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 3.4 27.0 - - + +
29A ALA* 3.9 8.3 - - + -
30A ALA* 3.1 28.5 - - + +
33A ASP* 2.7 33.3 + - - +
268A GLN* 3.7 38.4 - - + -
271A ILE* 3.9 1.9 - - - +
272A GLY* 3.6 21.2 + - - -
277A ARG* 4.0 8.0 - - + +
281A PHE* 3.1 31.9 - - + +
282A ILE* 3.9 7.0 - - + -
284A SER* 3.3 9.4 + - - +
286A ASN* 1.3 75.3 - - - +
288A THR* 1.3 63.4 + - - +
291A MET* 3.1 36.1 + - + +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.8 19.5 - - + -
256A TYR 4.7 5.0 + - - +
265A ILE* 3.9 14.8 - - + +
268A GLN* 2.6 36.9 + - - +
284A SER 3.3 6.9 + - - -
285A VAL* 3.2 16.4 + - - +
287A TYR* 1.3 77.9 - - - +
289A ASN* 1.3 56.1 + - - +
291A MET* 3.2 4.8 + - - +
292A LEU* 2.9 28.9 + - - +
333A PHE* 3.7 22.6 - - + +
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.5 14.1 + - + -
104A ALA* 5.2 1.9 - - - -
106A MET* 3.6 7.9 - - - +
122A PRO* 5.5 7.4 - - - +
231A HIS* 3.5 7.1 - - - -
232A TYR* 2.9 31.9 + - - -
255A PHE* 3.3 31.5 - - + -
285A VAL 2.9 13.8 + - - +
286A ASN* 3.4 26.0 + - - +
288A THR* 1.3 75.0 - - - +
290A GLY* 1.3 62.2 + - - +
292A LEU* 3.3 4.9 + - - +
293A ALA* 3.2 19.8 + - - +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.5 38.4 - - - -
30A ALA* 3.8 6.1 - - - -
31A VAL* 3.9 5.6 - - - +
286A ASN 2.8 17.8 + - - -
289A ASN* 1.3 70.0 - - - +
291A MET* 1.3 60.8 + - - +
293A ALA* 3.3 1.9 + - - +
294A ALA* 2.9 30.0 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.5 16.5 - - + +
34A TYR* 3.6 23.1 - - + -
267A LEU* 4.6 0.9 - - - -
268A GLN* 3.6 29.2 - - + -
271A ILE* 4.2 24.2 - - + -
287A TYR* 3.1 49.1 + - + +
288A THR* 3.2 5.8 + - - +
290A GLY* 1.3 73.4 - - - +
292A LEU* 1.3 61.8 + - - +
294A ALA* 4.0 4.2 - - - +
295A ALA* 2.7 33.2 + - - +
333A PHE* 3.5 26.5 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 3.9 22.4 - - + -
123A THR* 3.9 11.4 - - + -
255A PHE* 3.7 22.0 - - + -
288A THR 2.9 13.5 + - - +
289A ASN 3.7 7.4 - - - +
290A GLY 3.3 0.4 - - - -
291A MET* 1.3 78.1 - - - +
293A ALA* 1.3 57.1 + - - +
295A ALA* 3.2 1.7 + - - +
296A ILE* 2.8 48.1 + - + +
329A PHE* 5.1 0.4 - - + -
331A PRO* 3.9 23.3 - - + -
333A PHE* 3.8 19.8 - - + -
334A ALA* 4.5 6.5 - - + -
342A GLU* 4.5 0.4 - - - +
343A ILE* 3.8 29.2 - - + -
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.3 30.1 - - + +
31A VAL* 5.4 0.2 - - + -
80A LEU* 3.7 19.4 - - + +
102A ILE* 4.1 24.2 - - + +
122A PRO* 4.8 5.6 - - + +
289A ASN 3.2 9.1 + - - +
290A GLY 3.3 6.9 + - - +
292A LEU* 1.3 77.3 - - - +
294A ALA* 1.3 60.8 + - - +
296A ILE* 3.3 5.6 + - - +
297A ALA 3.2 17.2 + - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.9 5.6 - - + -
31A VAL* 4.0 24.0 - - + +
34A TYR* 3.8 28.3 - - + -
35A CYS 5.2 0.2 - - - +
80A LEU* 4.2 12.5 - - + +
290A GLY 2.9 16.2 + - - +
291A MET 4.0 0.4 - - - +
293A ALA* 1.3 76.3 - - - +
295A ALA* 1.3 53.5 + - - +
297A ALA* 3.3 1.6 + - - +
298A VAL* 2.7 39.2 + - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.5 30.4 + - + +
291A MET 2.7 24.1 + - - +
292A LEU* 3.5 4.3 - - - +
294A ALA* 1.3 69.6 - - - +
296A ILE* 1.3 56.5 + - - +
298A VAL* 3.7 0.7 - - - +
299A GLU* 2.7 36.9 + - - +
329A PHE* 3.7 18.5 - - + -
331A PRO* 5.0 0.2 - - + -
333A PHE* 4.1 16.8 - - + -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 3.9 18.2 - - + -
122A PRO* 4.0 24.0 - - + -
292A LEU* 2.8 47.9 + - + +
293A ALA* 3.7 5.2 - - - +
294A ALA 3.3 0.2 - - - -
295A ALA* 1.3 70.7 - - - +
297A ALA* 1.3 53.2 - - - +
299A GLU* 3.1 3.8 + - - +
300A ALA* 2.8 33.8 + - - +
320A ILE* 5.2 6.5 - - + -
323A MET* 4.3 13.0 - - + +
329A PHE* 4.0 15.3 - - + -
343A ILE* 3.7 21.5 - - + -
345A PHE* 4.1 21.3 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.1 22.9 - - + -
78A VAL* 4.5 12.6 - - + -
80A LEU* 4.1 15.3 - - + -
102A ILE* 4.0 9.8 - - + +
293A ALA 3.2 13.0 + - - +
294A ALA* 3.5 8.3 - - - +
296A ILE* 1.3 72.7 - - - +
298A VAL* 1.3 66.1 + - - +
300A ALA* 3.2 5.3 + - - -
301A ILE* 3.0 31.6 + - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 24.7 - - + -
34A TYR* 4.0 24.9 - - + +
35A CYS* 5.3 0.4 - - - -
38A ALA* 4.3 15.0 - - + -
43A LEU* 4.5 11.4 - - + -
44A VAL* 4.0 19.6 - - + +
49A PHE* 4.1 18.2 - - + -
294A ALA 2.7 22.8 + - - +
295A ALA 4.0 0.7 - - - +
297A ALA* 1.3 73.0 - - - +
299A GLU* 1.3 63.9 + - - +
301A ILE* 3.4 6.7 + - - +
302A ARG* 3.1 20.7 + - + +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 2.7 23.0 + - - +
296A ILE 3.1 3.5 + - - +
298A VAL* 1.3 76.1 - - - +
300A ALA* 1.3 61.2 + - - +
302A ARG* 2.7 40.6 + - - +
303A ARG* 2.4 58.4 + - - +
323A MET* 3.9 5.6 - - + -
329A PHE* 3.6 42.2 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE 2.8 18.5 + - - +
297A ALA* 3.2 6.0 + - - +
299A GLU* 1.3 73.1 - - - +
301A ILE* 1.3 54.2 + - - +
303A ARG 3.4 0.3 + - - -
304A ALA* 2.8 32.6 + - - +
316A VAL* 4.1 12.5 - - + +
319A ALA* 3.3 20.1 - - + +
320A ILE* 3.7 30.3 - - + -
323A MET* 4.2 8.5 - - + +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.8 7.4 - - + -
10A LEU* 5.5 3.8 - - + -
44A VAL* 4.5 7.2 - - + -
47A VAL* 5.0 0.4 - - + -
49A PHE* 3.9 34.1 - - + -
77A PRO* 4.7 2.5 - - + -
78A VAL* 3.7 18.4 - - + -
297A ALA 3.0 18.5 + - - +
298A VAL 3.8 4.0 - - - +
300A ALA* 1.3 74.6 - - - +
302A ARG* 1.3 58.2 + - - +
304A ALA* 3.4 7.6 + - - +
305A GLN* 3.0 25.3 + - - +
311A ILE* 3.7 31.7 - - + +
316A VAL* 3.1 28.3 - - + -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.5 25.8 - - - +
44A VAL* 3.6 23.1 - - + +
45A PRO* 4.8 6.1 - - + -
298A VAL* 3.1 13.4 + - + +
299A GLU* 2.7 45.4 + - - +
300A ALA 3.3 0.2 - - - -
301A ILE* 1.3 76.2 - - - +
303A ARG* 1.3 75.7 + - - +
305A GLN* 3.1 13.5 + - + +
306A GLU* 3.1 34.1 + - + +
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 2.4 54.8 + - - +
300A ALA* 4.7 0.7 - - - +
302A ARG* 1.3 81.5 - - - +
304A ALA* 1.3 66.7 + - - +
306A GLU* 3.4 20.4 + - - +
307A ARG* 3.0 35.5 + - - +
319A ALA* 3.8 20.1 + - + -
323A MET* 3.7 26.4 - - - +
327A ASN* 3.1 52.0 + - - +
328A ALA 3.8 15.0 + - - -
329A PHE* 4.3 4.4 - - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 2.8 18.8 + - - +
301A ILE* 3.5 9.0 - - - +
303A ARG* 1.3 77.6 - - - +
305A GLN* 1.3 56.5 + - - +
308A PHE* 2.9 35.0 + - - +
309A LYS 3.4 3.5 + - - -
310A ARG 3.6 10.4 - - - +
311A ILE* 4.3 4.0 - - + -
315A THR* 3.5 38.6 - - - +
316A VAL* 4.0 6.1 - - + +
319A ALA* 3.9 2.1 - - - +
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Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.2 23.5 + - - +
44A VAL* 5.6 3.4 - - + -
45A PRO* 3.0 30.8 + - + +
46A GLY* 4.8 2.6 - - - -
47A VAL* 4.4 6.1 - - + +
301A ILE* 3.0 9.5 + - + +
302A ARG* 3.1 10.2 + - - +
304A ALA* 1.3 74.3 - - - +
306A GLU* 1.3 65.1 + - - +
309A LYS* 3.0 54.2 + - - +
310A ARG 4.2 0.4 + - - +
311A ILE* 3.0 32.2 - - + +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 3.1 30.6 + - + +
303A ARG* 3.6 29.2 - - - +
305A GLN* 1.3 81.7 - - - +
307A ARG* 1.3 79.0 + - - +
309A LYS* 4.7 0.9 + - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 3.0 30.2 + - - +
306A GLU* 1.3 98.2 + - - +
308A PHE* 1.3 88.2 + - + +
309A LYS* 5.5 0.2 - - - -
318A GLN* 3.7 24.7 + - - +
319A ALA* 4.0 13.0 + - - +
322A GLY* 4.8 7.5 + - - -
327A ASN* 3.7 23.4 + - - +
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 2.9 18.8 + - - +
307A ARG* 1.3 106.5 - - + +
309A LYS* 1.3 69.9 + - - +
310A ARG* 3.0 32.5 + - + +
315A THR* 3.6 40.2 - - + -
318A GLN* 4.0 35.0 - - + -
319A ALA* 5.2 0.9 - - - -
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.2 34.1 - - - +
6A GLN* 5.1 2.5 + - - +
304A ALA 3.4 1.0 + - - -
305A GLN* 3.0 43.3 + - - +
306A GLU 5.5 0.7 - - - +
307A ARG 3.7 0.8 - - - +
308A PHE* 1.3 79.1 - - - +
310A ARG* 1.3 58.6 + - - +
----------------------------------------------------------
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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