Contacts of the helix formed by residues 283 - 309 (chain A) in PDB entry 2KSB
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 ILE 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.4 19.0 - - + +
8A ASP* 5.5 9.6 - - + +
26A VAL* 6.0 1.8 - - + +
175A PRO* 3.8 4.0 - - - +
281A LYS* 3.3 13.2 + - + +
282A PHE* 1.3 85.2 - - - +
284A GLN* 1.3 81.9 + - + +
285A GLN* 3.0 28.5 - - + +
286A VAL* 3.3 29.3 + - + +
287A TYR* 3.7 10.4 + - - +
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.5 9.0 - - + +
26A VAL* 2.6 54.5 + - + +
27A GLN* 2.7 20.2 - - - +
175A PRO* 2.8 41.0 - - + +
176A SER* 2.8 24.4 + - - +
283A ILE* 1.3 83.1 - - + +
285A GLN* 1.3 105.3 + - - +
288A LEU* 3.1 3.8 - - - +
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Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.4 4.7 + - - -
28A PRO* 5.1 1.4 - - - +
31A GLN* 3.0 36.2 + - - +
35A TRP* 4.7 10.0 - - - -
283A ILE* 3.0 15.4 - - + +
284A GLN* 1.3 115.4 + - - +
286A VAL* 1.3 67.2 + - + +
288A LEU* 3.5 7.8 - - - +
289A ALA* 2.9 24.1 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.4 44.4 - - + -
280A LYS* 6.5 0.2 - - + -
281A LYS* 3.9 28.0 - - - +
283A ILE* 3.3 22.0 - - + +
285A GLN* 1.3 78.3 - - + +
287A TYR* 1.3 65.3 + - + +
288A LEU 3.2 0.5 + - - -
289A ALA* 3.2 5.9 + - - -
290A ILE* 2.7 35.2 - - + +
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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
----------------------------------------------------------
174A MET* 4.3 2.7 - - + -
175A PRO* 3.0 34.7 - - + +
184A TRP* 2.8 67.2 + + - -
264A PHE* 3.4 18.6 - + - -
267A PHE* 3.1 42.3 + + + -
268A PHE* 3.2 7.1 - - - -
271A PRO* 3.8 15.3 - - + -
282A PHE* 4.0 19.5 - + + -
283A ILE 3.7 4.7 + - - +
284A GLN 3.6 0.8 + - - -
285A GLN 3.4 0.4 - - - -
286A VAL* 1.3 81.6 - - + +
288A LEU* 1.3 59.8 + - - +
290A ILE* 3.6 2.6 + - - +
291A MET* 3.2 21.0 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.1 12.6 - - - +
35A TRP* 2.8 50.0 - - + +
175A PRO* 2.8 15.7 - - + +
176A SER* 2.8 34.3 - - - +
177A ARG* 3.7 22.9 - - - +
284A GLN* 3.1 17.3 - - + +
285A GLN* 3.5 7.9 - - - +
287A TYR* 1.3 74.5 - - - +
289A ALA* 1.3 68.0 + - - +
291A MET* 3.3 1.8 + - - -
292A TRP* 3.0 25.8 + - + +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 5.0 8.3 - - + +
285A GLN 2.9 16.9 + - - +
286A VAL* 3.2 6.0 + - - +
288A LEU* 1.3 84.7 - - - +
290A ILE* 1.3 70.9 + - + +
292A TRP* 3.9 1.9 - - - +
293A LEU* 3.0 22.8 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A CYS 4.5 7.2 - - - +
263A PRO* 3.5 27.4 - - + +
264A PHE* 2.8 48.7 - - + +
267A PHE* 4.3 9.4 - - + -
286A VAL* 2.7 43.0 + - + +
287A TYR* 4.2 2.5 - - - +
288A LEU 3.2 0.2 - - - -
289A ALA* 1.3 86.9 - - + +
291A MET* 1.3 63.0 + - - +
293A LEU* 3.0 9.1 + - + +
294A ALA* 3.0 19.8 + - - +
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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
----------------------------------------------------------
112A PRO* 5.2 8.3 - - + -
116A VAL* 6.4 0.4 - - + -
174A MET* 3.2 13.9 - - + +
179A VAL* 3.1 45.1 - - + -
180A CYS 3.8 3.1 - - - +
181A MET* 3.1 48.5 - - + -
261A TRP* 5.6 8.3 - - + -
264A PHE* 3.6 22.6 - - + -
287A TYR 3.2 12.7 + - - +
288A LEU 4.2 2.0 - - - +
290A ILE* 1.3 78.1 - - - +
292A TRP* 1.3 61.9 + - - +
294A ALA* 3.3 19.7 + - + +
295A MET* 3.5 19.1 + - + +
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Residues in contact with TRP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 3.2 54.1 - + + +
38A ALA* 4.7 6.5 - - + -
39A TYR* 2.9 58.8 - + + -
42A ILE* 4.9 3.4 - - + +
89A ASN* 4.0 22.9 - - + -
93A ALA* 4.6 2.2 - - + -
177A ARG* 2.7 45.9 - - - +
179A VAL* 4.6 10.0 - - + +
288A LEU* 3.0 32.3 + - + +
289A ALA 4.0 2.0 - - - +
291A MET* 1.3 77.9 - - - +
293A LEU* 1.3 60.7 + - - +
295A MET* 3.0 26.9 + - + +
296A SER* 3.5 6.1 + - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 4.5 7.0 - - + +
260A CYS* 3.9 31.6 - - - +
263A PRO* 5.1 9.0 - - + -
289A ALA 3.0 14.8 + - - +
290A ILE* 3.0 15.7 + - + +
292A TRP* 1.3 72.1 - - - +
294A ALA* 1.3 65.3 + - - +
296A SER* 3.0 33.7 + - - +
297A SER* 3.8 3.3 + - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 4.5 1.6 - - - +
260A CYS 4.0 10.1 + - - +
261A TRP* 2.9 55.9 - - + -
264A PHE* 5.1 1.1 - - + -
290A ILE 3.0 11.4 + - - +
291A MET* 3.4 12.3 - - - +
292A TRP 3.2 0.2 - - - -
293A LEU* 1.3 76.4 - - - +
295A MET* 1.3 60.6 + - - +
297A SER* 2.6 29.2 + - - -
298A THR 4.4 0.2 + - - -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.8 36.8 - - + +
42A ILE* 4.7 2.1 - - + +
81A MET* 3.2 17.4 - - - +
85A ASN* 3.8 15.5 - - - +
89A ASN* 3.3 23.3 - - - +
112A PRO* 5.1 7.0 - - + -
179A VAL* 3.7 24.0 - - + -
261A TRP* 5.5 3.6 - - + -
291A MET* 3.5 25.8 - - + +
292A TRP* 3.0 19.9 + - + +
294A ALA* 1.3 80.0 - - - +
296A SER* 1.4 49.3 + - - +
297A SER 3.0 0.9 + - - -
298A THR* 2.7 37.4 + - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.8 15.5 - - - +
260A CYS* 4.9 3.8 - - - -
292A TRP 3.8 6.9 + - - -
293A LEU* 3.0 30.1 + - - +
295A MET* 1.4 72.6 - - - +
297A SER* 1.3 65.8 + - - +
298A THR* 3.0 5.1 + - - -
299A MET* 3.0 20.9 + - - +
300A TYR* 3.6 5.1 + - - +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 4.9 0.8 - - - +
81A MET* 5.7 1.6 - - - -
257A PHE* 5.5 0.4 - - - -
260A CYS* 2.9 25.8 - - - +
261A TRP* 3.6 14.5 + - - -
293A LEU 3.8 0.8 + - - -
294A ALA 2.6 21.6 + - - -
295A MET 3.0 0.2 - - - -
296A SER* 1.3 79.1 - - - +
298A THR* 1.3 64.4 + - - +
300A TYR* 2.7 58.0 + - - -
301A ASN* 3.9 2.1 + - - +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.0 9.4 - - + -
46A SER* 2.8 33.8 - - - +
50A ASN* 3.0 16.5 - - - +
78A GLU* 3.1 47.9 + - - +
81A MET* 3.2 26.2 - - + +
82A ALA* 5.9 0.2 - - - -
295A MET 2.7 23.0 + - - +
296A SER 4.2 0.9 - - - +
297A SER* 1.3 79.2 - - - +
299A MET* 1.3 56.7 + - - +
301A ASN* 3.3 6.8 - - - +
302A PRO* 4.1 0.2 - - - +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 5.2 3.1 - - + -
45A THR* 2.8 50.9 - - + +
46A SER* 4.1 8.5 - - - +
50A ASN* 5.0 0.2 - - - -
296A SER* 3.0 11.1 + - - +
298A THR* 1.3 82.1 - - + +
300A TYR* 1.3 65.3 + - - +
301A ASN 3.3 0.9 - - - -
302A PRO* 3.2 15.5 - - - +
303A ILE* 4.0 23.7 + - + +
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Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 6.6 0.2 - - - -
123A MET* 5.9 0.2 - - - -
253A VAL* 3.9 12.0 + - + +
256A THR* 2.9 46.6 - - + +
257A PHE* 3.4 33.5 - - - +
260A CYS* 4.1 8.7 - - - -
296A SER 3.6 4.2 + - - +
297A SER* 2.7 60.2 + - - -
299A MET* 1.3 75.7 - - - +
301A ASN* 1.3 92.0 + - + -
303A ILE* 2.7 40.8 - - + +
304A ILE* 3.1 10.7 + - + +
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 3.4 12.6 + - - +
53A VAL* 5.0 0.4 - - - +
74A LEU* 4.8 6.2 - - + +
75A ALA* 4.5 7.9 - - - +
78A GLU* 3.3 26.7 + - - +
253A VAL* 5.0 5.2 - - + -
297A SER 4.3 1.2 - - - +
298A THR 3.3 13.7 - - - +
300A TYR* 1.3 98.5 - - + +
302A PRO* 1.3 79.3 - - - +
304A ILE* 2.7 34.0 - - + +
305A TYR* 2.9 38.2 + - + +
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Residues in contact with PRO 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR 5.7 0.2 - - - +
46A SER* 6.2 0.2 - - - -
49A GLY* 3.4 44.9 - - - +
50A ASN* 3.7 14.6 - - - +
53A VAL* 4.1 7.2 - - + -
298A THR 4.1 0.2 - - - +
299A MET* 3.2 14.8 - - - +
301A ASN* 1.3 107.1 - - - +
303A ILE* 1.3 62.4 + - + +
305A TYR* 3.4 12.0 + - + +
306A CYS* 3.3 27.6 + - - -
316A PHE* 5.6 0.3 - - - -
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 4.2 29.4 - - + +
300A TYR* 2.7 36.6 + - + +
302A PRO* 1.3 76.8 - - + +
304A ILE* 1.3 72.6 + - + +
306A CYS* 3.1 7.9 + - - +
307A CYS* 3.1 23.1 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A MET* 3.7 8.5 - - + -
252A VAL* 4.1 19.7 - - + -
253A VAL* 2.9 47.3 - - + -
256A THR* 5.3 4.3 - - + -
300A TYR* 3.7 16.6 - - + +
301A ASN* 2.7 37.9 - - + +
303A ILE* 1.3 89.8 - - + +
305A TYR* 1.3 53.8 + - - +
307A CYS* 3.3 1.3 + - - -
308A LEU* 2.6 55.4 + - + +
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.7 24.9 - - + +
71A LEU* 2.9 56.4 + - + +
74A LEU* 5.0 4.5 - - - +
249A MET* 3.0 33.4 - - + -
301A ASN* 2.9 50.8 + - + +
302A PRO* 3.5 13.0 - - + +
303A ILE 3.2 0.2 - - - -
304A ILE* 1.3 83.1 - - - +
306A CYS* 1.3 57.9 + - - +
309A ASN* 2.8 37.0 + - - +
312A PHE* 3.8 22.2 - + + -
316A PHE* 4.4 14.1 - - + -
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Residues in contact with CYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 3.5 14.6 - - - -
303A ILE* 3.1 10.4 + - - +
305A TYR* 1.3 81.6 - - - +
307A CYS* 1.3 65.1 + - - +
309A ASN 3.7 12.4 - - - +
313A ARG* 4.0 26.1 + - + +
316A PHE* 4.4 23.6 - - - -
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Residues in contact with CYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE 3.1 13.2 + - - +
304A ILE* 4.8 0.4 - - - -
306A CYS* 1.3 80.9 - - - +
308A LEU* 1.3 75.5 + - + +
309A ASN* 4.6 1.0 - - - -
313A ARG* 5.8 1.4 + - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 5.1 4.5 - - - +
248A LYS* 4.4 31.4 + - + +
249A MET* 3.7 47.3 - - + +
252A VAL* 4.0 15.5 - - + -
304A ILE* 2.6 49.5 + - + +
307A CYS* 1.3 87.4 - - + +
309A ASN* 1.3 60.3 + - - +
310A ASP 4.3 0.2 - - - -
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 5.8 8.5 - - + +
246A VAL* 6.4 3.1 - - + -
249A MET* 3.3 32.0 - - + +
305A TYR* 2.8 22.1 + - - +
306A CYS 3.7 3.0 - - - +
307A CYS 3.5 1.7 - - - -
308A LEU* 1.3 77.3 - - + +
310A ASP* 1.3 65.8 + - - +
311A ARG* 4.3 6.1 - - + +
312A PHE* 2.7 52.4 + - - +
313A ARG* 3.0 15.6 + - - +
----------------------------------------------------------
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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