Contacts of the helix formed by residues 280 - 304 (chain A) in PDB entry 4WVD
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 ALA 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A SER* 1.3 78.3 - - - +
281A GLU* 1.3 76.4 + - - +
282A GLU 2.8 10.0 + - - -
283A ASN* 2.9 30.3 + - - +
284A PHE* 3.2 5.2 + - - +
351A ARG* 5.4 12.2 - - + +
353A ARG* 6.4 2.0 - - - -
505A IVM 5.7 0.2 - - - +
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Residues in contact with GLU 281 (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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279A SER 4.5 1.4 - - - +
280A ALA* 1.3 91.5 - - - +
282A GLU* 1.3 67.6 + - - +
284A PHE* 3.7 20.6 - - + +
285A LEU* 3.8 10.0 + - - +
353A ARG* 6.4 2.9 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 2.9 55.7 - - + +
279A SER 3.4 13.0 + - - +
280A ALA 2.8 0.4 + - - -
281A GLU* 1.3 80.7 + - - +
283A ASN* 1.3 55.1 + - - +
285A LEU* 2.6 40.6 + - - +
286A ILE* 3.3 7.2 + - - +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 4.6 8.4 - - - +
278A PHE 3.6 4.6 + - - +
279A SER* 4.2 5.8 - - - -
280A ALA 2.9 26.0 + - - +
282A GLU* 1.3 76.7 - - - +
284A PHE* 1.3 62.5 + - - +
286A ILE* 3.5 9.3 + - - +
287A LEU* 3.3 25.6 + - - +
348A LEU* 5.3 1.8 - - - +
351A ARG 4.6 11.7 + - - -
505A IVM 3.0 56.2 + - + +
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Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA 3.2 6.6 + - - +
281A GLU* 3.7 20.4 - - + +
282A GLU 2.8 3.8 + - - -
283A ASN* 1.3 73.5 - - - +
285A LEU* 1.3 64.2 + - + +
286A ILE 2.9 2.1 + - - -
287A LEU* 2.9 17.8 + - - +
288A THR* 2.6 51.4 + - + -
353A ARG* 5.4 10.1 - - + -
354A ASN 3.9 22.9 - - - -
355A SER* 4.1 27.1 - - - -
454A TRP 5.2 3.6 - - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU 3.8 8.9 + - - +
282A GLU* 2.6 19.4 + - - +
284A PHE* 1.3 80.5 - - + +
286A ILE* 1.3 63.1 + - + +
288A THR* 3.4 14.4 + - - +
289A GLU* 3.5 11.6 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 4.6 18.2 - - - +
272A LYS* 5.4 9.9 - - + -
276A GLU* 3.8 24.9 - - - +
278A PHE* 6.3 2.9 - - + -
282A GLU 3.3 7.6 + - - +
283A ASN* 3.9 12.8 - - - +
284A PHE 2.9 1.6 + - - -
285A LEU* 1.3 79.0 - - + +
287A LEU* 1.3 70.9 + - + +
289A GLU* 2.8 17.6 + - + +
290A MET* 2.9 31.2 + - + +
505A IVM 5.6 2.7 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN* 3.3 25.1 + - - +
284A PHE* 2.9 12.4 + - + +
286A ILE* 1.3 74.6 - - + +
288A THR* 1.3 68.5 + - - +
289A GLU 2.7 1.6 + - - -
290A MET* 2.9 19.6 + - + -
291A ALA* 2.6 26.8 + - - +
505A IVM 3.6 92.0 - - + +
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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
----------------------------------------------------------
284A PHE* 2.6 48.2 + - + -
285A LEU* 3.4 16.2 + - - +
287A LEU* 1.3 74.4 - - - +
289A GLU* 1.3 59.2 + - - +
291A ALA* 3.7 7.1 - - - +
292A THR* 2.9 27.1 + - - -
355A SER* 5.9 0.7 - - - +
454A TRP* 3.6 38.1 - - + +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU 3.5 11.6 + - - +
286A ILE* 2.8 15.6 + - + +
287A LEU 2.7 2.6 + - - -
288A THR* 1.3 75.7 - - - +
290A MET* 1.3 55.9 + - + +
291A ALA 2.9 1.6 + - - -
292A THR* 3.0 7.5 - - - -
293A ASN* 2.8 35.2 + - + +
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Residues in contact with MET 290 (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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268A GLU* 6.1 1.1 - - - +
272A LYS* 4.6 14.6 - - + -
286A ILE* 2.9 25.7 + - + +
287A LEU* 2.9 22.1 + - + +
289A GLU* 1.3 75.6 - - + +
291A ALA* 1.3 61.0 + - - +
293A ASN* 3.2 8.5 + - - +
505A IVM 2.7 110.5 - - + +
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Residues in contact with ALA 291 (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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287A LEU 2.6 20.1 + - - +
288A THR* 3.7 7.4 - - - +
289A GLU 2.9 1.2 + - - -
290A MET* 1.3 68.1 - - - +
292A THR* 1.3 54.5 + - - +
294A HIS* 2.5 40.2 + - - +
295A VAL* 3.4 3.4 + - - -
328A MET* 5.0 10.3 - - - -
450A MET* 3.7 27.1 - - + -
454A TRP 6.0 2.9 - - - +
505A IVM 3.6 15.8 - - + +
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR 2.9 14.7 + - - -
289A GLU* 3.0 13.4 - - - +
291A ALA* 1.3 75.6 - - - +
293A ASN* 1.3 58.2 + - + +
294A HIS 3.0 4.5 + - - -
295A VAL* 3.6 13.2 + - - +
296A GLN* 2.6 34.9 - - - +
450A MET* 4.7 3.2 - - - +
454A TRP* 3.2 40.7 + - + +
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Residues in contact with ASN 293 (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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289A GLU* 2.8 20.9 + - + +
290A MET* 3.4 12.7 - - - +
291A ALA 2.8 1.6 + - - -
292A THR* 1.3 73.9 - - + +
294A HIS* 1.3 55.4 + - - +
296A GLN* 4.5 11.2 - - - +
297A VAL* 3.4 16.9 - - - +
505A IVM 2.6 41.5 + - - +
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Residues in contact with HIS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A MET 3.4 8.5 - - - +
291A ALA* 2.5 21.1 + - - +
293A ASN* 1.3 71.6 - - - +
295A VAL* 1.3 63.5 + - + +
296A GLN 3.4 1.1 - - - -
297A VAL* 3.2 6.4 + - - +
298A LEU* 2.7 44.6 + - + +
324A ALA* 3.0 27.8 + - + -
327A ALA* 3.9 9.0 - - + -
328A MET* 3.3 45.5 - - + +
331A ARG* 5.1 9.4 - - + +
450A MET* 5.5 4.0 - - + -
505A IVM 3.6 27.9 + - - +
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Residues in contact with VAL 295 (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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291A ALA 3.4 4.0 + - - +
292A THR* 3.8 13.0 - - - +
294A HIS* 1.3 85.2 - - + +
296A GLN* 1.3 80.5 + - - +
298A LEU* 4.1 7.0 - - + -
299A VAL* 2.9 38.0 + - + +
324A ALA* 4.8 15.0 - - + -
450A MET* 5.1 12.3 - - + -
2263C LEU* 6.0 4.7 - - + -
2266C ILE* 4.5 20.9 - - + -
2267C ILE* 5.0 7.9 - - + -
2270C ALA* 4.7 3.6 - - + -
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 2.6 37.3 + - - +
293A ASN* 4.6 10.0 - - - +
294A HIS 3.4 0.8 - - - +
295A VAL* 1.3 83.7 - - - +
297A VAL* 1.3 56.3 - - + +
299A VAL* 3.8 3.9 + - - +
300A GLU* 3.2 26.7 + - - +
2266C ILE* 5.3 6.7 + - - +
2270C ALA* 4.0 20.7 - - + +
2274C SER* 3.8 20.6 + - - +
2275C PHE 4.6 21.3 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLN* 3.2 49.1 - - + +
293A ASN* 3.4 22.9 - - - +
294A HIS* 3.2 7.8 + - - +
295A VAL 3.2 0.4 - - - -
296A GLN* 1.3 75.1 - - + +
298A LEU* 1.3 68.9 + - - +
300A GLU* 3.0 14.5 + - - +
301A PHE* 2.9 22.0 + - - +
331A ARG* 4.4 4.9 - - - +
505A IVM 4.3 21.1 - - + +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLN* 5.8 0.2 - - - -
294A HIS* 2.7 31.0 + - + +
295A VAL* 3.6 8.3 - - - +
297A VAL* 1.3 76.3 - - - +
299A VAL* 1.3 56.0 - - + +
301A PHE* 3.1 11.7 + - + +
302A THR* 2.6 37.2 + - - +
320A LEU* 4.4 12.6 - - + +
323A SER* 4.2 9.4 - - - -
324A ALA* 3.5 38.8 - - + +
327A ALA* 4.2 18.6 - - + -
386A THR* 5.2 2.2 - - + -
390A ILE* 3.7 25.8 - - + -
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Residues in contact with VAL 299 (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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295A VAL* 2.9 28.0 + - + +
296A GLN 4.2 3.1 - - - +
298A LEU* 1.3 75.9 - - + +
300A GLU* 1.3 63.0 + - - +
302A THR* 3.8 6.0 - - - -
303A LYS* 3.1 27.1 + - + +
320A LEU* 4.0 25.8 - - + -
2267C ILE* 4.7 6.5 - - + +
2270C ALA* 3.8 39.5 - - + +
2271C LEU* 4.0 24.9 - - + +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER* 3.9 11.1 - - - +
262A LYS* 4.4 17.2 - - - +
263A GLN* 3.1 25.9 + - - +
296A GLN 3.2 18.5 + - - +
297A VAL* 3.0 22.7 + - - +
299A VAL* 1.3 76.4 - - - +
301A PHE* 1.3 66.4 + - - +
302A THR 3.4 0.3 + - - -
303A LYS* 3.7 9.2 + - - +
304A LYS* 3.6 20.1 + - - +
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Residues in contact with PHE 301 (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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256A ILE* 4.0 21.1 - - + -
259A SER* 3.9 11.4 - - - -
260A TYR* 3.7 43.3 - + + -
263A GLN* 4.0 13.5 - - - +
297A VAL 2.9 13.6 + - - +
298A LEU* 3.4 12.8 - - + +
300A GLU* 1.3 83.0 + - - +
302A THR* 1.3 60.4 + - - +
304A LYS* 3.6 10.6 + - - +
305A LEU* 3.1 44.6 + - + +
383A ALA 4.4 9.4 - - - -
386A THR* 3.9 25.1 - - + -
387A ALA* 4.2 7.0 - - + -
390A ILE* 3.9 20.9 - - + -
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Residues in contact with THR 302 (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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298A LEU* 2.6 21.9 + - - +
299A VAL* 3.8 4.3 - - - -
300A GLU 3.2 0.4 - - - -
301A PHE* 1.3 74.9 - - - +
303A LYS* 1.3 67.1 + - - +
304A LYS 3.1 1.3 - - - -
305A LEU* 2.9 22.6 + - + +
308A PHE* 3.3 55.8 - - + +
320A LEU* 3.4 24.0 - - + +
390A ILE* 3.4 27.8 - - + +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.1 25.0 + - + +
300A GLU* 4.0 8.3 - - - +
301A PHE 3.6 0.2 - - - -
302A THR* 1.3 77.4 - - - +
304A LYS* 1.3 56.6 + - + +
305A LEU 3.4 4.3 + - - +
308A PHE* 4.1 12.1 - - + +
309A GLN* 3.5 51.9 + - - +
2270C ALA 4.9 1.7 + - - +
2271C LEU* 2.5 52.3 + - + +
2272C MET* 4.1 9.3 - - - +
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 2.6 47.5 - - + -
259A SER* 4.9 12.2 + - - +
300A GLU* 3.6 15.3 + - - +
301A PHE* 3.6 6.3 + - - +
302A THR 3.1 1.4 - - - -
303A LYS* 1.3 76.3 - - + +
305A LEU* 1.3 60.0 + - - +
306A PRO* 3.4 0.3 - - - +
309A GLN* 5.5 0.2 - - - +
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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