Contacts of the helix formed by residues 311 - 342 (chain A) in PDB entry 3DC1
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 GLY 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 3.8 8.7 - - - -
307A LEU 2.7 20.6 + - - -
308A HIS* 3.8 8.0 + - - -
309A GLU 3.4 2.4 - - - -
310A TRP* 1.3 79.7 - - - +
312A GLU* 1.3 69.4 + - - +
313A GLU 3.1 2.1 - - - +
315A PHE* 3.2 14.0 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 4.0 15.8 - - + +
89A GLN* 5.2 2.3 + - - +
90A LEU* 6.4 1.6 - - + -
93A LYS* 2.6 47.0 + - - +
94A LEU* 5.0 9.7 - - - +
311A GLY* 1.3 73.0 - - - +
313A GLU* 1.3 74.7 + - + +
315A PHE* 3.2 20.4 - - - +
316A MET* 3.2 21.5 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A TRP 2.3 30.0 - - - +
311A GLY* 3.1 1.4 - - - +
312A GLU* 1.3 91.0 - - + +
314A GLY* 1.3 52.2 + - - +
316A MET* 4.6 7.2 - - + +
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 3.5 28.1 + - - -
312A GLU 3.5 0.4 + - - -
313A GLU* 1.3 72.0 - - - +
315A PHE* 1.3 62.1 + - - +
316A MET 3.2 3.6 - - - +
317A ALA* 3.9 20.1 - - - +
318A HIS* 3.2 21.0 + - - +
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 4.0 13.9 - + + -
90A LEU* 3.7 28.9 - - + -
235A PHE* 3.8 16.6 - + - -
261A PHE* 4.2 16.6 - + - -
264A ILE* 4.0 29.4 - - + -
265A ILE* 4.3 8.5 - - + -
307A LEU* 4.2 16.4 - - + -
310A TRP* 3.7 17.7 - + + +
311A GLY 3.2 16.0 + - - +
312A GLU* 3.2 10.8 - - - +
314A GLY* 1.3 73.2 - - - +
316A MET* 1.3 89.9 + - + +
318A HIS* 3.2 7.9 + - + +
319A VAL* 3.0 36.1 + - + +
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 5.6 0.4 - - - -
94A LEU* 4.6 22.7 - - - -
235A PHE* 4.1 10.3 - - + -
242A ARG* 4.7 14.4 - - - +
312A GLU* 3.2 26.3 + - + +
313A GLU* 4.8 4.7 - - + -
314A GLY 3.2 2.4 - - - +
315A PHE* 1.3 110.5 - - + +
317A ALA* 1.3 67.5 + - - +
319A VAL* 3.0 35.9 + - + +
320A ASP* 2.8 29.0 + - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLY* 3.9 20.4 + - - +
316A MET* 1.3 76.5 - - - +
318A HIS* 1.3 56.0 + - - +
320A ASP* 3.6 7.9 - - - +
321A ARG* 3.0 32.5 + - - +
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Residues in contact with HIS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.3 34.2 - - - +
265A ILE* 5.1 3.6 - - + +
310A TRP* 3.2 39.5 - + + -
314A GLY 3.2 14.7 + - - +
315A PHE* 3.2 12.2 + - - +
316A MET 3.0 0.6 - - - -
317A ALA* 1.3 73.6 - - - +
319A VAL* 1.3 64.2 + - - +
321A ARG* 2.9 48.2 + - - +
322A VAL* 2.9 28.2 - - + +
45B MET 3.1 19.7 + - - -
47B PRO* 4.0 11.5 - - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 3.6 35.5 - - + +
242A ARG* 6.0 3.4 - - - +
264A ILE* 4.9 7.9 - - + -
315A PHE* 3.0 34.1 - - + +
316A MET* 3.0 31.3 + - + +
318A HIS* 1.3 72.9 - - + +
320A ASP* 1.3 65.5 + - - +
322A VAL* 3.8 7.9 - - - +
323A ILE* 2.9 44.5 + - + +
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Residues in contact with ASP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LYS* 4.3 24.8 + - - +
316A MET* 2.8 19.3 + - - +
317A ALA* 3.6 8.2 - - - +
319A VAL* 1.3 77.7 - - - +
321A ARG* 1.3 65.2 + - - +
323A ILE* 3.2 11.9 + - - +
324A ASP* 2.9 35.2 + - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.9 19.8 + - - -
57A ASN* 4.5 16.8 + - - -
317A ALA 3.0 17.0 + - - +
318A HIS* 2.9 52.5 + - - +
320A ASP* 1.3 75.5 - - - +
322A VAL* 1.3 59.1 + - - +
324A ASP* 3.6 9.9 - - - +
325A PHE* 3.2 21.5 + - - +
44B ASN 5.0 2.6 + - - -
45B MET* 4.3 30.3 + - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.5 15.7 - - + -
263A LLP 4.5 2.0 - - - +
264A ILE* 4.2 13.0 - - + -
318A HIS* 2.9 42.6 + - + +
319A VAL* 4.0 6.5 - - - +
321A ARG* 1.3 75.6 - - - +
323A ILE* 1.3 61.3 + - - +
324A ASP 3.1 1.1 - - - -
325A PHE* 3.7 0.2 - - - +
326A TYR* 2.8 51.8 + - + -
45B MET* 3.5 27.8 - - + +
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE 3.1 25.8 - - - +
236A LEU* 4.0 5.2 - - + +
237A GLN* 3.4 40.8 - - + +
238A PHE* 4.0 12.8 - - + +
240A LYS* 4.0 17.5 - - + +
242A ARG* 5.9 5.2 - - + -
319A VAL* 2.9 38.5 + - + +
320A ASP* 3.8 14.4 - - - +
322A VAL* 1.3 76.5 - - - +
324A ASP* 1.3 54.4 + - - +
326A TYR* 4.0 5.3 - - - +
327A SER* 2.7 34.4 + - - -
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LYS* 3.1 27.4 + - - -
320A ASP* 2.9 25.3 + - - +
321A ARG* 3.6 8.7 - - - +
322A VAL 3.1 0.2 - - - -
323A ILE* 1.3 77.3 - - - +
325A PHE* 1.3 64.0 + - - +
327A SER* 3.7 5.4 - - - -
328A ASN* 3.1 32.7 + - - +
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG 3.2 9.9 + - - +
322A VAL 3.7 4.9 - - - +
323A ILE 3.2 0.2 - - - -
324A ASP* 1.3 82.3 - - - +
326A TYR* 1.3 74.6 + + - +
327A SER 3.1 0.7 + - - -
328A ASN* 3.1 8.1 + - + +
329A GLN* 3.0 53.7 + - + +
403A SER 3.6 11.9 - - - -
404A SER* 5.6 0.9 - - - -
42B ASN* 3.2 33.0 - - + -
45B MET* 3.7 38.1 - - + -
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Residues in contact with TYR 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.6 21.1 - - + -
238A PHE* 3.9 15.3 - - + -
263A LLP 4.0 8.0 + - - -
322A VAL* 2.8 49.6 + - + +
323A ILE* 4.0 4.5 - - - +
325A PHE* 1.3 80.9 - + - +
327A SER* 1.3 55.6 + - - +
329A GLN* 3.3 5.2 + - - +
330A LYS* 3.0 24.1 + - - +
353A GLY 4.5 4.0 - - - +
354A MET* 3.4 34.0 - - + +
402A PHE* 3.6 13.2 - + - -
403A SER* 3.6 32.5 - - - -
41B PRO* 3.7 4.9 - - - +
42B ASN* 3.0 32.8 + - + +
45B MET* 4.2 9.0 - - + -
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 3.8 21.5 + - - +
240A LYS* 6.3 0.4 - - - -
323A ILE* 2.7 25.2 + - - -
324A ASP* 3.7 7.4 - - - -
326A TYR* 1.3 70.0 - - - +
328A ASN* 1.3 62.0 + - - +
330A LYS* 3.3 20.1 + - - +
331A ASP* 2.8 36.9 + - - -
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Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASP* 3.1 19.4 + - - +
325A PHE* 3.7 9.9 - - + +
327A SER* 1.3 77.4 - - - +
329A GLN* 1.3 53.2 + - - +
331A ASP* 3.0 18.7 + - - +
332A ALA* 2.7 36.1 + - - +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A PHE* 3.0 53.1 + - + +
326A TYR* 3.5 10.1 - - + +
327A SER 3.3 0.2 - - - -
328A ASN* 1.3 74.8 - - + +
330A LYS* 1.3 59.0 + - - +
332A ALA* 3.1 8.8 + - - +
333A ILE* 2.9 22.3 + - - +
402A PHE* 2.9 36.5 + - + +
403A SER* 5.2 0.2 - - - -
404A SER 3.9 9.6 - - - +
405A ALA 2.9 28.1 + - - +
406A SER* 5.2 0.2 - - - -
407A PRO* 4.9 9.9 - - - +
410A MET* 3.5 15.0 - - - +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 4.3 19.9 - - + +
326A TYR 3.0 7.6 + - - +
327A SER* 3.4 24.9 + - - +
329A GLN* 1.3 73.0 - - - +
331A ASP* 1.3 76.1 + - - +
333A ILE* 3.3 6.1 - - - +
334A LEU* 2.8 58.5 + - + +
349A VAL* 3.8 15.2 - - - +
350A PRO* 4.2 16.1 + - + -
402A PHE* 3.1 38.8 - - + -
28C ARG 3.3 18.9 + - - -
29C GLY* 5.0 4.8 + - - -
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Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A SER* 2.8 21.9 + - - +
328A ASN* 3.0 28.5 + - - +
330A LYS* 1.3 91.6 + - - +
332A ALA* 1.3 59.7 + - - +
334A LEU* 3.2 5.4 + - - +
335A ALA* 3.1 24.7 + - - +
28C ARG* 3.2 47.6 + - - +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASN 2.7 15.5 + - - +
329A GLN* 3.1 12.3 + - - +
331A ASP* 1.3 72.6 - - - +
333A ILE* 1.3 62.5 + - - +
335A ALA* 3.4 8.5 - - - +
336A ALA* 3.3 22.2 + - - +
407A PRO* 4.3 25.9 - - + +
410A MET* 3.9 16.5 - - + +
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN 2.9 12.1 + - - +
330A LYS* 3.3 22.4 - - + +
331A ASP 3.3 0.2 - - - -
332A ALA* 1.3 75.6 - - - +
334A LEU* 1.3 70.2 + - + +
336A ALA* 4.0 2.6 - - - +
337A ALA* 3.2 21.7 + - - +
350A PRO* 5.8 0.2 - - + -
356A LEU* 4.1 18.1 - - + +
400A ALA* 4.3 19.7 - - + -
401A SER 4.4 3.6 - - - +
402A PHE* 3.8 40.8 - - + +
410A MET* 3.7 16.5 - - + -
414A PHE* 3.6 26.2 - - + -
36B LEU* 4.7 6.1 - - + -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS* 2.8 56.6 + - + +
331A ASP* 3.2 3.6 + - - +
333A ILE* 1.3 73.2 - - + +
335A ALA* 1.3 56.6 + - - +
337A ALA* 3.0 4.8 + - - +
338A ASP* 2.7 44.2 + - - +
347A TRP* 3.8 30.3 - - + +
349A VAL* 3.7 19.1 - - + -
350A PRO* 4.2 5.8 - - + -
356A LEU* 3.9 17.0 - - + -
28C ARG* 4.0 22.4 - - + -
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP 3.1 13.6 + - - +
332A ALA* 3.4 14.1 - - - +
334A LEU* 1.3 75.3 - - - +
336A ALA* 1.3 56.4 + - + +
338A ASP* 3.4 10.3 + - - +
339A LYS* 3.1 25.5 + - - +
28C ARG* 6.2 0.6 - - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA 3.3 12.2 + - - +
333A ILE 4.0 1.8 - - - +
334A LEU 3.2 0.6 - - - -
335A ALA* 1.3 75.6 - - - +
337A ALA* 1.3 65.2 + - - +
339A LYS* 3.3 11.1 + - - +
340A TRP* 3.2 28.5 + - + +
407A PRO 5.7 0.4 - - - +
410A MET* 4.1 17.9 - - + +
411A ASP* 4.6 9.2 - - - +
414A PHE* 3.9 23.7 - - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE 3.2 12.6 + - - +
334A LEU* 3.0 9.0 + - - +
336A ALA* 1.3 75.4 - - - +
338A ASP* 1.3 65.9 + - - +
341A LEU* 2.8 45.8 + - + +
347A TRP* 3.6 31.1 - - + +
356A LEU* 4.8 6.1 - - + -
358A ILE* 5.3 0.2 - - + -
414A PHE* 4.4 11.3 - - + -
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 2.7 26.4 + - - +
335A ALA* 3.4 13.2 - - - +
337A ALA* 1.3 71.5 - - - +
339A LYS* 1.3 63.1 + - - +
342A THR* 2.5 28.5 + - - +
347A TRP* 3.4 20.3 + - - -
27C SER* 4.7 10.2 + - - -
28C ARG* 6.0 2.3 - - - +
81C PRO* 3.7 11.3 - - + +
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Residues in contact with LYS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ALA 3.1 14.3 + - - +
336A ALA* 3.5 12.8 - - - +
337A ALA 3.0 1.0 - - - -
338A ASP* 1.3 79.3 - - - +
340A TRP* 1.3 90.5 + - + +
342A THR 5.0 0.2 + - - -
411A ASP* 3.0 31.7 + - - +
81C PRO* 3.8 9.7 - - - +
84C LEU* 5.9 2.8 - - + +
85C SER* 3.1 20.8 + - - -
88C LYS* 3.5 27.5 - - + +
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Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 3.2 20.7 + - - +
339A LYS* 1.3 116.0 - - + +
341A LEU* 1.3 61.1 + - + +
342A THR 3.6 1.5 - - - +
344A LEU* 3.5 9.7 - - - +
411A ASP* 3.5 23.4 + - - -
414A PHE* 3.9 21.1 - - + +
415A GLN* 3.1 44.4 - - + -
418A ALA* 3.2 19.7 - - + +
85C SER* 3.7 48.3 + - - -
88C LYS* 3.9 25.4 - - + -
89C GLN* 4.5 12.8 - - + -
92C ILE* 4.8 8.5 - - + -
109C MET* 6.4 0.7 - - + -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA* 2.8 17.8 + - + +
340A TRP* 1.3 78.6 - - + +
342A THR* 1.3 60.2 + - - +
343A GLY 3.2 0.7 + - - -
344A LEU* 2.9 28.9 + - + +
345A ALA* 3.3 15.2 + - + -
347A TRP* 3.7 15.9 - - + -
358A ILE* 3.9 27.6 - - + -
414A PHE* 3.5 41.1 - - + +
417A LEU* 4.4 4.9 - - + -
418A ALA* 3.8 31.4 - - + +
421A ILE* 4.3 14.6 - - + -
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 3.7 0.8 + - - -
338A ASP* 2.5 34.0 + - - +
339A LYS 5.4 0.4 - - - -
340A TRP 3.6 1.9 - - - +
341A LEU* 1.3 75.6 - - - +
343A GLY* 1.3 62.5 + - - +
344A LEU* 3.2 7.0 + - - +
347A TRP* 4.3 7.1 - - - -
70C ARG* 5.1 3.1 - - - +
81C PRO* 3.8 19.2 - - + +
82C GLU* 3.3 46.8 - - - +
85C SER* 5.2 1.8 + - - -
308C HIS* 4.7 3.8 + - - -
----------------------------------------------------------
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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