Contacts of the helix formed by residues 275 - 296 (chain A) in PDB entry 3DAN
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 PHE 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.3 32.3 - + - -
93A THR* 4.8 4.0 - - + -
111A TYR* 5.0 1.8 - - - -
201A TRP* 4.0 19.3 - + + -
202A VAL* 4.3 19.7 - - + -
205A ASN* 4.2 22.4 - - + -
206A LEU* 3.9 31.4 - - + -
271A PHE* 2.8 56.1 + + + +
274A CYS* 1.3 74.2 - - - +
276A ASN* 1.3 67.9 + - - +
279A GLY* 3.3 20.1 + - - -
280A GLY 4.2 0.3 + - - -
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Residues in contact with ASN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.5 17.4 - - - -
110A SER* 3.4 19.8 + - - -
271A PHE* 3.2 24.0 + - - -
272A ALA* 3.2 32.0 - - - +
275A PHE* 1.3 83.4 - - - +
277A THR* 1.3 66.2 + - - +
280A GLY* 3.3 11.6 + - - -
600A HEM 3.7 55.9 + - + +
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.3 37.2 - - + -
180A TYR* 3.1 11.7 + - - +
272A ALA 2.8 21.9 + - - -
273A VAL* 3.3 12.6 - - - -
275A PHE 3.7 0.2 - - - -
276A ASN* 1.3 70.2 - - - +
278A PHE* 1.3 67.7 + - - +
280A GLY* 3.1 2.9 + - - -
281A VAL* 3.0 33.0 + - + +
431A PHE* 4.5 3.1 - - + -
600A HEM 2.8 40.2 - - + +
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 3.4 52.0 - - + -
172A ALA* 4.3 14.4 - - + -
173A PHE* 4.3 19.7 - + + -
176A LEU* 4.1 10.1 - - + -
195A PRO* 4.0 20.6 - - + -
198A ILE* 3.7 37.7 - - + -
199A SER* 4.9 2.2 - - - -
273A VAL 2.8 21.0 + - - +
274A CYS* 3.4 7.8 + - - +
276A ASN 3.8 0.2 - - - -
277A THR* 1.3 73.3 - - - +
279A GLY* 1.3 62.4 + - - +
281A VAL* 3.3 3.9 + - - +
282A LYS* 2.9 47.5 + - + +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A CYS 3.5 4.0 + - - -
275A PHE 3.3 19.2 + - - -
277A THR 3.3 0.8 - - - -
278A PHE* 1.3 83.4 - - - +
280A GLY* 1.3 60.3 + - - +
282A LYS* 3.6 19.0 + - - +
283A ILE* 3.6 19.1 - - - +
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Residues in contact with GLY 280 (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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275A PHE 4.2 0.2 + - - -
276A ASN 3.3 9.3 + - - -
277A THR 3.1 6.7 + - - -
279A GLY* 1.3 75.7 - - - +
281A VAL* 1.3 59.9 + - - +
283A ILE* 3.2 7.9 + - - +
284A LEU* 2.9 29.8 + - - +
343A PRO* 4.5 3.4 - - - +
344A VAL* 5.7 3.6 - - - -
600A HEM 3.7 30.4 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 4.6 0.2 - - - +
172A ALA* 4.0 25.1 - - + -
176A LEU* 5.6 3.1 - - + -
277A THR* 3.0 25.6 + - + +
278A PHE* 3.9 5.2 - - - +
280A GLY* 1.3 71.6 - - - +
282A LYS* 1.3 65.3 + - - +
283A ILE 3.0 2.9 + - - -
284A LEU* 4.3 6.1 - - - +
285A PHE* 3.2 55.9 + - + +
286A PRO* 3.7 0.5 - - - +
435A ILE* 3.8 25.4 - - + -
600A HEM 4.8 9.9 - - + -
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 4.7 3.1 - - - +
169A GLU* 3.0 49.4 + - + +
172A ALA* 6.1 1.1 - - - -
199A SER* 3.0 30.7 + - - +
278A PHE* 2.9 31.4 + - + +
279A GLY* 3.6 10.8 - - - +
280A GLY 3.2 0.2 - - - -
281A VAL* 1.3 78.3 - - - +
283A ILE* 1.3 60.6 + - + +
286A PRO* 3.3 20.4 - - - +
459A LEU* 4.8 28.3 - - - +
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Residues in contact with ILE 283 (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 GLY 3.6 15.7 - - - +
280A GLY* 3.2 7.7 + - - +
281A VAL 3.0 0.6 - - - -
282A LYS* 1.3 84.5 - - + +
284A LEU* 1.3 65.2 + - - +
285A PHE 3.6 0.4 - - - -
286A PRO* 3.4 3.7 - - - +
287A ASN* 3.3 40.9 + - - +
343A PRO* 3.6 36.6 - - + +
344A VAL* 5.8 2.5 - - + -
459A LEU* 4.9 15.5 - - + +
460A GLY* 5.1 10.5 - - - -
461A ALA 5.8 0.3 + - - -
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Residues in contact with LEU 284 (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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280A GLY 2.9 21.5 + - - +
281A VAL* 4.4 1.3 - - - +
283A ILE* 1.3 74.0 - - - +
285A PHE* 1.3 66.0 + - + +
287A ASN* 3.4 5.0 + - + +
288A THR* 2.8 48.4 + - - +
337A SER* 4.0 10.1 - - - +
338A LEU* 3.6 34.3 - - + +
341A GLU 5.5 1.6 - - - +
343A PRO* 3.9 13.9 - - + -
432A VAL* 4.8 2.2 - - + -
436A THR* 3.2 31.2 - - + +
600A HEM 3.5 24.7 - - + -
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Residues in contact with PHE 285 (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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141A PHE* 4.0 6.5 - + - -
145A TYR* 3.4 35.7 - + - -
164A PHE* 4.3 9.4 - + + -
168A GLY 6.1 0.2 - - - -
172A ALA* 5.9 0.2 - - + -
175A PHE* 6.4 0.2 - + - -
281A VAL* 3.2 31.3 + - + +
284A LEU* 1.3 82.3 - - + +
286A PRO* 1.3 72.3 - - + +
288A THR* 3.3 1.6 + - - -
289A LEU* 2.9 24.3 + - - +
435A ILE* 3.7 35.9 - - + -
436A THR* 3.7 28.9 - - + -
439A PHE* 3.6 44.1 - + + -
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Residues in contact with PRO 286 (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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164A PHE* 3.9 24.5 - - + -
165A ASN* 3.7 16.2 - - - +
281A VAL 3.7 1.8 - - - +
282A LYS* 3.3 28.3 - - - +
283A ILE* 3.4 7.4 - - - +
285A PHE* 1.3 95.9 - - + +
287A ASN* 1.3 57.3 + - - +
289A LEU* 3.3 4.4 + - + +
290A LYS* 2.9 28.2 + - - +
461A ALA 3.8 22.0 - - - +
463A VAL* 3.5 14.2 - - + +
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Residues in contact with ASN 287 (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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283A ILE* 3.3 38.2 + - - +
284A LEU* 3.8 7.5 - - + +
286A PRO* 1.3 80.2 - - - +
288A THR* 1.3 61.4 + - - +
290A LYS* 3.2 7.3 + - - +
291A TRP* 3.0 33.4 + - + -
337A SER* 4.9 3.4 - - - +
341A GLU* 3.4 47.9 + - + +
343A PRO* 5.4 0.8 - - - +
460A GLY* 4.7 2.0 - - - -
461A ALA* 3.3 29.8 + - - +
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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
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284A LEU* 2.8 33.6 + - - +
285A PHE* 3.7 5.8 - - - -
287A ASN* 1.3 73.4 - - - +
289A LEU* 1.3 66.8 + - - +
291A TRP* 3.3 2.4 + - - +
292A ILE* 3.1 38.5 + - + +
333A VAL* 5.1 2.9 - - + +
334A VAL* 5.5 0.9 - - + -
337A SER* 2.9 30.3 + - - +
436A THR* 4.0 14.5 - - + +
439A PHE* 4.7 6.7 - - + -
440A VAL* 4.1 26.2 - - + -
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Residues in contact with LEU 289 (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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164A PHE* 3.9 34.5 - - + -
285A PHE 2.9 16.4 + - - +
286A PRO 3.5 4.9 - - - +
288A THR* 1.3 76.9 - - - +
290A LYS* 1.3 57.4 + - - +
292A ILE* 4.8 2.7 - - - -
293A GLY* 2.9 27.2 + - - -
439A PHE* 4.3 14.8 - - + -
443A LEU* 3.9 23.3 - - + -
450A PHE* 3.7 35.2 - - + -
452A ILE* 4.0 1.7 - - + +
463A VAL* 3.7 24.7 - - + -
465A LEU* 4.4 14.4 - - + -
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Residues in contact with LYS 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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286A PRO 2.9 13.0 + - - +
287A ASN* 3.3 15.8 + - - +
288A THR 3.2 0.2 - - - -
289A LEU* 1.3 76.7 - - - +
291A TRP* 1.3 81.8 + - - +
293A GLY* 3.2 1.7 + - - -
294A LEU* 2.9 43.6 + - + +
341A GLU* 3.0 35.5 + - - -
452A ILE* 3.6 11.0 - - - +
454A LEU* 3.7 43.3 - - + -
461A ALA* 4.1 13.3 - - + +
463A VAL* 4.2 3.7 - - + +
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Residues in contact with TRP 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 ASN* 3.0 31.8 + - + +
288A THR* 3.3 3.8 + - - +
290A LYS* 1.3 89.5 - - - +
292A ILE* 1.3 63.0 + - - +
294A LEU* 3.4 22.8 + - + +
295A ALA* 3.1 22.2 + - - +
337A SER* 4.1 12.8 - - - +
340A ILE* 3.6 44.4 - - + +
341A GLU* 3.0 30.7 + - + +
390A GLU 5.5 3.1 - - - -
392A TYR* 3.6 50.0 - + + +
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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
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288A THR* 3.1 26.8 + - + +
289A LEU* 4.0 3.4 - - - +
291A TRP* 1.3 75.5 - - - +
293A GLY* 1.3 62.9 + - - +
295A ALA* 3.2 12.9 + - - +
299A LEU* 3.8 18.6 - - + -
300A HIS* 2.8 37.2 - - + +
303A LEU* 4.4 2.9 - - + -
333A VAL* 3.1 35.9 - - + -
392A TYR* 3.2 14.8 - - + +
440A VAL* 5.1 4.9 - - + -
443A LEU* 5.2 2.7 - - + -
444A PHE* 3.8 25.4 - - + -
450A PHE* 3.9 8.7 - - + -
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Residues in contact with GLY 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 LEU 2.9 13.8 + - - -
290A LYS 3.2 1.1 + - - -
292A ILE* 1.3 79.5 - - - +
294A LEU* 1.3 60.2 + - - +
295A ALA 3.3 0.9 + - - -
296A GLY* 3.5 9.2 + - - -
300A HIS* 4.1 7.3 + - - -
450A PHE* 3.5 29.2 - - - +
451A GLU* 5.9 0.9 - - - -
452A ILE* 4.1 13.2 - - - -
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Residues in contact with LEU 294 (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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290A LYS* 2.9 38.7 + - + +
291A TRP* 3.9 25.4 - - + +
293A GLY* 1.3 75.7 - - - +
295A ALA* 1.3 62.3 + - - +
296A GLY* 3.3 1.3 + - - -
452A ILE* 4.8 9.6 - - + +
454A LEU* 4.3 18.8 - - + -
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Residues in contact with ALA 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 TRP 3.1 12.1 + - - +
292A ILE 3.4 7.0 - - - +
293A GLY 3.2 0.8 - - - -
294A LEU* 1.3 79.5 - - - +
296A GLY* 1.3 59.8 + - - +
298A ASN* 5.2 2.9 + - - +
299A LEU* 3.4 40.6 + - + +
392A TYR* 4.7 4.7 - - + -
394A PRO* 4.6 9.9 - - + -
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Residues in contact with GLY 296 (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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292A ILE 3.8 1.4 + - - -
293A GLY 3.5 10.1 + - - -
294A LEU 3.3 4.2 - - - -
295A ALA* 1.3 79.1 - - - +
297A GLU* 1.3 66.4 + - - -
298A ASN* 3.2 3.8 - - - -
299A LEU* 3.2 9.7 + - - +
300A HIS* 3.1 23.4 + - - -
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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) + - + + + + + -
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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