Contacts of the helix formed by residues 287 - 312 (chain A) in PDB entry 2WWB
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 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU 4.4 0.2 + - - -
284A PHE 3.2 11.0 + - - -
286A THR* 1.3 84.7 - - - +
288A ASN* 1.4 61.8 + - - +
289A ILE 3.3 2.2 - - - -
290A PRO* 3.2 17.1 - - - +
291A ILE* 3.2 18.0 - - - +
376A SER* 3.7 9.8 + - - -
421A ALA* 3.5 13.0 + - - +
424A GLY* 3.5 11.6 - - - -
425A GLY* 3.4 30.2 + - - -
428A ILE* 4.8 2.2 - - - -
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 6.4 0.6 - - - -
284A PHE 3.4 5.4 + - - -
285A TYR* 3.3 54.7 + - + +
286A THR 3.3 0.6 - - - -
287A SER* 1.4 78.3 - - - +
289A ILE* 1.4 80.4 + - + +
291A ILE* 3.4 14.4 + - - +
292A ILE* 3.5 20.5 + - - +
428A ILE* 5.4 2.5 - - - -
449A LEU* 4.7 4.7 - - - +
452A THR* 4.0 13.3 - - + +
453A ILE* 3.6 26.7 - - - +
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 5.1 9.9 - - - +
285A TYR 5.3 1.8 - - - +
286A THR 4.7 3.4 - - - +
288A ASN* 1.4 95.1 - - + +
290A PRO* 1.3 69.9 - - + +
291A ILE 3.3 0.7 + - - -
292A ILE* 3.5 22.3 + - + +
293A LEU* 3.5 27.4 + - + +
379A TRP* 3.8 45.1 - - + -
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Residues in contact with PRO 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 4.9 2.2 - - - +
286A THR 3.9 4.0 - - - +
287A SER* 3.2 24.0 - - - +
289A ILE* 1.3 94.0 - - + +
291A ILE* 1.4 58.5 + - + +
293A LEU* 3.5 3.3 + - + +
294A GLN* 3.1 25.8 + - - +
372A CYS* 3.7 21.5 - - - +
375A PHE* 3.6 36.1 - - + +
376A SER* 3.7 19.3 - - - +
379A TRP* 4.4 11.4 - - + -
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER 3.2 19.3 - - - +
288A ASN* 3.4 6.7 + - - +
289A ILE 3.4 0.8 - - - -
290A PRO* 1.4 73.9 - - + +
292A ILE* 1.4 65.3 + - - +
294A GLN* 3.3 7.1 + - + +
295A SER* 3.1 32.8 + - - +
372A CYS* 3.7 36.3 - - + -
425A GLY* 4.0 11.7 - - - +
428A ILE* 3.8 45.1 - - + -
432A SER* 4.4 9.9 - - - +
445A THR* 5.5 1.6 - - + -
449A LEU* 3.9 18.8 - - + -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 5.2 3.1 - - + +
85A VAL* 4.4 20.4 - - + +
180A SER* 5.7 8.3 - - - +
183A ILE* 5.0 20.0 - - + -
288A ASN* 3.5 28.0 - - - +
289A ILE* 3.7 18.2 - - + +
290A PRO 3.4 0.2 - - - -
291A ILE* 1.4 75.9 - - - +
293A LEU* 1.4 61.0 + - + +
295A SER* 3.5 4.2 + - - -
296A ALA* 3.1 24.8 + - - +
449A LEU* 3.9 26.6 - - + +
453A ILE* 3.9 24.9 - - + -
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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
----------------------------------------------------------
85A VAL* 4.3 14.8 - - + +
88A GLY* 3.8 14.6 - - - +
89A LEU* 3.4 47.6 - - + +
92A GLN* 3.7 42.8 - - + +
179A ILE* 6.2 1.8 - - + -
289A ILE* 3.5 23.3 + - + +
290A PRO 3.5 8.0 + - - +
291A ILE 3.3 0.2 - - - -
292A ILE* 1.4 78.2 - - + +
294A GLN* 1.4 59.6 + - - +
296A ALA* 3.5 3.2 + - + +
297A LEU* 3.1 21.5 + - - +
375A PHE* 4.5 6.7 - - + -
379A TRP* 5.9 0.7 - - + -
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PRO 3.1 14.1 + - - +
291A ILE* 3.3 9.3 + - - +
293A LEU* 1.4 74.4 - - - +
295A SER* 1.4 64.3 + - - +
297A LEU* 3.3 19.4 + - + +
298A VAL* 3.5 14.9 + - - +
367A PHE* 5.8 2.6 - - - -
368A MET* 3.4 44.4 - - - +
371A SER* 3.5 34.6 + - - -
372A CYS* 3.4 29.8 - - - +
375A PHE* 3.9 12.7 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 3.7 19.1 - - - -
68A ILE* 3.9 25.3 - - - +
291A ILE* 3.1 18.6 + - - +
292A ILE 3.7 5.2 - - - -
294A GLN* 1.4 77.0 + - - +
296A ALA* 1.4 62.4 + - - +
297A LEU 3.5 0.2 + - - -
298A VAL* 3.6 1.8 + - - -
299A SER* 3.3 23.8 + - - -
368A MET* 5.6 2.0 - - - +
445A THR* 3.4 25.3 - - - +
449A LEU* 3.9 6.5 - - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE 4.9 6.7 + - - +
69A LEU* 5.7 1.9 - - + +
85A VAL* 4.2 34.3 - - + +
86A THR* 5.7 0.2 - - - -
89A LEU* 4.5 6.7 - - + -
292A ILE 3.1 17.5 + - - +
293A LEU* 3.5 11.2 - - - +
294A GLN 3.3 0.2 - - - -
295A SER* 1.4 74.8 - - - +
297A LEU* 1.4 61.4 + - - +
299A SER* 3.4 9.5 + - - -
300A ASN* 2.9 29.8 + - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.9 25.8 - - + +
293A LEU 3.1 14.3 + - - +
294A GLN* 3.3 16.1 + - + +
296A ALA* 1.4 76.0 - - - +
298A VAL* 1.4 66.5 + - + +
300A ASN* 3.2 10.5 + - + +
301A LEU* 3.1 36.0 + - + +
345A LEU* 5.8 2.2 - - + -
367A PHE* 6.3 2.9 - - + -
375A PHE* 5.2 10.8 - - + -
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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
----------------------------------------------------------
64A TRP* 3.5 29.8 - - + -
294A GLN* 3.5 29.5 + - - +
295A SER 3.9 1.1 - - - +
296A ALA 3.4 0.2 - - - -
297A LEU* 1.4 76.4 - - + +
299A SER* 1.4 64.0 + - - +
301A LEU* 3.2 19.8 + - + +
302A TYR* 3.2 24.8 - - + +
345A LEU* 3.5 43.5 - - + +
368A MET* 4.2 12.6 - - + -
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 3.8 9.9 - - - -
65A MET* 3.4 53.2 + - - +
68A ILE* 4.2 8.7 - - - +
69A LEU* 4.4 16.4 - - - -
295A SER 3.3 13.2 + - - -
296A ALA* 3.5 12.6 - - - -
297A LEU 3.3 0.2 - - - -
298A VAL* 1.4 78.4 - - - +
300A ASN* 1.4 60.1 + - - +
302A TYR* 3.5 15.1 + - - +
303A VAL* 4.4 0.3 - - - +
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Residues in contact with ASN 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 5.5 1.6 - - - +
69A LEU* 4.9 8.9 - - - +
86A THR* 3.5 36.2 + - - +
89A LEU* 3.7 20.4 - - + +
127A GLN* 4.8 8.1 + - - +
296A ALA* 2.9 17.9 + - - +
297A LEU* 3.2 11.2 + - + +
299A SER* 1.4 76.3 - - - +
301A LEU* 1.4 63.1 + - - +
302A TYR 3.3 0.7 + - - -
303A VAL* 3.4 14.6 + - - +
304A ILE* 3.5 23.1 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.1 22.3 + - + +
298A VAL* 3.2 16.0 + - + +
300A ASN* 1.4 76.8 - - - +
302A TYR* 1.4 60.5 + - - +
304A ILE* 3.4 21.3 - - + +
305A SER* 2.9 29.5 + - - +
324A TRP* 3.8 37.9 - - + -
341A LEU* 4.8 2.2 - - + -
342A CYS* 3.9 29.8 - - + +
345A LEU* 3.9 28.3 - - + -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.5 1.6 - - + -
64A TRP* 3.6 22.0 - + - -
65A MET* 4.0 15.9 - - + -
298A VAL* 3.2 44.2 - - + +
299A SER* 3.5 15.5 - - - +
300A ASN 3.3 0.2 - - - -
301A LEU* 1.4 77.5 - - - +
303A VAL* 1.4 60.0 + - - +
305A SER* 3.7 6.9 + - - -
306A GLN* 3.4 23.0 + - - +
334A ARG* 3.3 37.1 + - - -
335A ALA 3.6 12.9 - - - +
336A TYR* 3.5 15.3 - - - -
337A PRO* 5.0 0.5 - - - +
342A CYS* 3.5 28.7 - - - -
345A LEU 3.7 2.1 + - - -
346A SER* 3.5 27.9 + - - -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 5.1 0.9 - - + -
65A MET* 3.6 30.7 - - + -
127A GLN* 6.2 1.6 - - - +
130A VAL* 3.8 22.9 - - + -
134A THR* 3.4 26.2 - - + +
136A MET* 3.5 30.5 - - + -
299A SER 4.4 2.9 - - - +
300A ASN* 3.4 7.6 + - - +
301A LEU 3.3 0.4 - - - -
302A TYR* 1.4 73.8 - - + +
304A ILE* 1.4 66.4 + - + +
305A SER 3.3 0.2 + - - -
306A GLN* 3.5 7.7 + - - +
307A MET* 3.3 20.3 + - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 6.2 2.0 - - + -
300A ASN* 3.5 15.5 + - + +
301A LEU* 3.4 35.9 - - + +
303A VAL* 1.4 81.7 - - + +
305A SER* 1.4 56.4 + - - +
307A MET* 4.0 5.2 - - - +
308A LEU* 3.0 33.5 + - + +
324A TRP* 4.0 21.8 - - + +
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 2.9 21.3 + - - +
302A TYR 3.8 6.7 - - - -
303A VAL 3.2 0.6 - - - -
304A ILE* 1.4 77.6 - - - +
306A GLN* 1.4 60.9 + - - +
309A SER* 3.2 17.5 + - - -
324A TRP* 3.3 45.7 + - - -
325A SER* 3.5 7.1 + - - -
328A SER* 3.3 10.1 + - - -
337A PRO* 3.8 13.5 - - - -
342A CYS* 3.8 10.2 - - - +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.8 18.8 - - - -
134A THR* 4.2 17.4 - - + +
136A MET* 4.9 2.0 - - - +
302A TYR 3.4 20.1 + - - +
303A VAL* 3.5 8.6 + - - +
304A ILE 3.5 0.4 - - - -
305A SER* 1.4 77.5 - - - +
307A MET* 1.4 64.4 - - - +
309A SER* 4.1 0.7 - - - -
310A ALA* 3.5 17.0 + - - +
311A ARG* 3.3 21.7 + - - +
328A SER* 4.0 19.0 - - - -
329A SER 4.3 9.5 - - - +
330A GLY* 5.2 0.3 + - - -
335A ALA* 3.4 33.5 + - + +
337A PRO* 5.1 4.0 - - + -
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET* 3.3 55.9 - - + +
134A THR* 3.9 20.6 - - - +
303A VAL* 3.3 15.4 + - + +
304A ILE* 4.1 6.1 - - - +
306A GLN* 1.4 77.5 - - - +
308A LEU* 1.4 62.7 + - - +
311A ARG* 3.3 43.7 + - + +
312A PHE* 3.2 33.3 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
304A ILE* 3.0 19.8 + - + +
305A SER 3.8 0.4 - - - +
307A MET* 1.4 76.9 - - - +
309A SER* 1.4 58.1 + - - +
312A PHE* 3.7 16.6 + - + -
313A SER* 3.0 38.3 + - - +
321A LEU* 3.9 33.9 - - + +
322A GLY* 5.8 0.9 - - - -
324A TRP* 3.9 22.4 - - + +
325A SER* 3.6 22.0 - - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER 3.2 14.6 + - - -
306A GLN 3.6 1.3 + - - -
307A MET 3.4 0.2 - - - -
308A LEU* 1.4 78.3 - - - +
310A ALA* 1.3 61.8 + - - +
313A SER 2.9 19.8 - - - +
314A GLY 3.8 1.9 - - - -
315A ASN* 3.3 20.0 + - - -
318A VAL* 4.0 9.2 - - - +
321A LEU* 3.2 20.1 - - - +
325A SER* 3.4 19.8 + - - -
328A SER* 3.7 20.8 + - - -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN 3.5 4.3 + - - +
309A SER* 1.3 80.8 - - - +
311A ARG* 1.4 94.9 + - + +
312A PHE 3.8 1.3 - - - -
314A GLY 3.6 15.5 - - - +
315A ASN* 3.8 19.0 + - - +
328A SER* 6.3 0.7 - - - -
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A MET 4.7 4.3 - - - -
134A THR 4.0 22.8 + - - -
141A SER* 4.1 20.6 + - - +
306A GLN* 3.3 34.1 + - - +
307A MET* 3.3 42.6 + - + +
310A ALA* 1.4 95.0 - - + +
312A PHE* 1.4 58.0 + - - +
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.2 26.4 + - + +
308A LEU* 3.6 21.7 + - + +
310A ALA 3.8 0.2 - - - -
311A ARG* 1.4 77.2 - - - +
313A SER* 1.3 88.5 + - - +
314A GLY 5.1 0.9 + - - -
----------------------------------------------------------
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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