Contacts of the helix formed by residues 313 - 333 (chain D) in PDB entry 3HYW
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 THR 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311D PRO* 4.4 9.9 - - + -
312D LYS* 1.3 74.7 - - - +
314D GLY* 1.3 65.2 + - - +
315D MET 4.0 1.4 + - - -
316D MET* 3.1 20.7 + - - +
317D ILE* 2.9 24.0 + - - +
345D ALA* 3.1 25.9 - - + +
346D ILE 5.2 0.6 + - - -
347D CSS 3.6 24.7 - - - -
363D VAL* 5.9 1.1 - - + -
441D FAD 3.2 18.4 - - - +
800D PS9 3.8 22.4 - - - -
802D PS9 4.3 1.1 - - - -
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Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.5 10.3 - - - +
313D THR* 1.3 69.7 - - - +
315D MET* 1.3 54.9 + - - +
317D ILE* 3.2 5.3 + - - +
318D GLU* 2.8 35.0 + - - +
441D FAD 2.7 32.1 + - - -
500D DCQ 3.3 17.9 - - - -
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Residues in contact with MET 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D THR* 3.3 1.2 + - - -
314D GLY* 1.3 73.7 - - - +
316D MET* 1.3 63.5 + - - +
318D GLU* 3.3 5.2 + - + +
319D GLN* 3.0 41.8 + - + +
344D SER* 3.4 22.4 - - - +
345D ALA* 3.8 16.8 - - + -
346D ILE* 3.5 49.1 - - + +
359D PHE* 4.8 4.3 - - - -
407D LEU* 4.1 14.4 - - + -
413D VAL* 4.9 5.4 - - + -
441D FAD 4.4 0.6 + - - -
500D DCQ 2.8 52.0 + - + +
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Residues in contact with MET 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D ILE* 4.9 4.3 - - + -
310D VAL* 4.8 7.4 - - + -
311D PRO 3.3 27.1 - - - +
312D LYS* 4.2 9.2 - - + -
313D THR* 3.1 32.1 + - - +
315D MET* 1.3 76.4 - - - +
317D ILE* 1.3 59.4 + - - +
319D GLN* 3.3 10.0 + - - +
320D MET* 2.9 38.2 + - + +
343D LEU* 3.7 32.6 - - + +
344D SER 3.5 15.9 - - - +
363D VAL* 3.8 33.0 - - + -
364D ILE* 5.0 4.0 - - + -
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.9 8.3 - - + +
13D GLY* 3.5 35.4 - - - +
292D VAL* 4.8 0.6 - - + +
293D GLY* 3.6 27.4 - - - +
294D VAL 4.2 0.4 - - - +
312D LYS* 3.4 32.3 - - + +
313D THR 2.9 19.6 + - - +
314D GLY* 3.7 4.0 - - - +
316D MET* 1.3 72.7 - - - +
318D GLU* 1.3 60.6 + - - +
320D MET* 3.3 9.7 + - - +
321D ALA* 2.9 27.9 + - - +
441D FAD 3.5 31.6 - - - +
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.6 8.1 - - + -
16D ALA* 4.7 3.4 - - + -
20D ASN* 4.5 0.9 + - - -
314D GLY* 2.8 16.8 + - - +
315D MET* 3.6 5.6 - - + +
317D ILE* 1.3 76.3 - - - +
319D GLN* 1.3 57.8 + - + +
321D ALA* 3.5 8.4 + - - +
322D MET* 3.1 43.1 + - + +
385D PHE* 4.2 0.7 - - - -
389D PHE* 3.4 27.6 - - + -
392D LYS* 3.3 21.8 + - - -
398D ILE* 3.6 19.9 - - + +
403D GLU* 3.9 6.6 - - - +
500D DCQ 2.7 35.1 + - + +
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Residues in contact with GLN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D MET* 3.0 30.9 + - + +
316D MET* 3.5 7.1 - - - +
318D GLU* 1.3 73.7 - - - +
320D MET* 1.3 65.4 + - - +
322D MET* 3.1 13.7 + - + +
323D ALA 2.9 18.9 + - - -
341D PRO* 3.5 14.1 - - + +
342D ARG* 4.3 1.3 - - - +
343D LEU* 2.7 33.7 + - - -
344D SER* 2.9 32.8 + - - +
413D VAL* 3.9 16.2 - - - +
415D PRO* 3.6 34.5 - - + +
416D ILE* 3.6 2.6 - - - +
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Residues in contact with MET 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D PHE* 3.6 46.7 - - + -
292D VAL* 4.4 10.8 - - + -
293D GLY* 3.3 28.3 - - - +
296D THR* 4.2 0.9 - - - +
298D ILE* 4.1 6.3 - - + -
312D LYS* 3.9 30.7 - - + -
316D MET* 2.9 25.1 + - + +
317D ILE* 3.4 13.2 - - + +
319D GLN* 1.3 73.7 - - - +
321D ALA* 1.3 57.3 + - - +
323D ALA* 3.3 2.4 + - - +
324D VAL* 2.9 36.2 + - - +
341D PRO* 3.6 9.8 - - - +
343D LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY 4.3 2.0 - - - +
16D ALA* 3.5 25.8 - - + -
17D THR* 3.4 31.0 - - - +
20D ASN* 3.7 6.5 + - - +
292D VAL* 4.4 3.8 - - + +
317D ILE 2.9 17.1 + - - +
318D GLU 3.5 6.7 - - - +
319D GLN 3.2 0.2 - - - -
320D MET* 1.3 75.4 - - - +
322D MET* 1.3 57.9 + - - +
324D VAL* 4.7 0.2 - - - -
325D ALA* 3.0 30.7 + - - +
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Residues in contact with MET 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASN* 3.9 22.7 - - - +
318D GLU* 3.1 39.6 + - + +
319D GLN* 3.1 13.2 + - + +
321D ALA* 1.3 74.4 - - - +
323D ALA* 1.3 64.1 + - - +
325D ALA* 3.9 0.7 - - - +
326D HIS* 3.0 37.0 + - + +
399D ALA* 4.7 17.7 - - + -
404D GLU* 5.7 3.1 - - - +
415D PRO* 3.6 37.7 - - + -
416D ILE* 3.8 13.5 - - + -
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Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D CYS 5.0 2.7 - - - +
281D PHE* 5.9 0.2 - - + -
319D GLN 2.9 15.4 + - - +
320D MET 3.7 3.8 - - - +
322D MET* 1.3 78.1 - - - +
324D VAL* 1.3 56.9 + - + +
326D HIS* 3.3 2.4 + - - +
327D ASN* 2.9 36.4 + - - +
339D TYR* 3.7 20.0 - - - +
340D ALA 4.0 0.4 - - - -
341D PRO* 3.7 30.5 - - + -
416D ILE* 3.6 11.8 - - + +
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 3.8 14.1 - - + -
102D VAL* 4.1 3.4 - - + -
280D CYS 4.1 0.9 - - - +
281D PHE* 3.8 35.0 - - + +
290D PHE* 3.6 24.9 - - + -
292D VAL* 3.6 20.2 - - + -
320D MET 2.9 20.7 + - - +
321D ALA 4.1 2.0 - - - +
323D ALA* 1.3 72.8 - - - +
325D ALA* 1.3 67.6 + - - +
327D ASN* 3.3 8.7 + - - +
328D ILE* 3.0 37.7 + - + +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 4.3 2.7 - - + +
20D ASN* 3.5 27.1 - - + -
21D LEU* 3.7 29.8 - - + +
24D LEU* 4.1 8.1 - - + -
321D ALA 3.0 19.8 + - - +
322D MET 3.9 2.9 - - - +
324D VAL* 1.3 78.2 - - - +
326D HIS* 1.3 57.9 + - + +
328D ILE 3.4 0.9 + - - -
329D VAL* 3.0 33.6 + - - +
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Residues in contact with HIS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASN* 6.3 0.4 - - + -
24D LEU* 3.9 37.7 - - + +
322D MET* 3.0 34.1 + - + +
323D ALA* 3.7 4.3 - - - +
325D ALA* 1.3 76.9 - - + +
327D ASN* 1.3 58.8 + - - +
329D VAL* 4.5 2.9 - - - +
330D ASN* 2.9 39.8 + - - +
339D TYR* 3.7 26.8 - + + -
416D ILE* 3.9 20.5 - - + +
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Residues in contact with ASN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D CYS* 3.1 22.9 - - - +
290D PHE* 3.7 20.7 - - + -
323D ALA 2.9 20.0 + - - +
324D VAL 3.3 4.9 + - - +
326D HIS* 1.3 75.2 - - - +
328D ILE* 1.3 60.7 + - - +
330D ASN* 4.0 3.4 - - - +
331D ASP* 3.1 27.7 + - - +
337D ASP 4.5 0.2 + - - -
338D LYS* 3.4 30.8 + - + +
339D TYR* 2.8 48.7 - - - +
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Residues in contact with ILE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.5 4.7 - - + -
21D LEU* 3.7 26.2 - - + -
28D LEU* 5.1 0.9 - - + -
100D TYR* 3.9 33.4 + - + -
102D VAL* 3.8 20.4 - - + -
290D PHE* 3.6 25.6 - - + -
324D VAL* 3.0 37.5 + - + +
325D ALA 3.8 3.8 - - - +
327D ASN* 1.3 73.9 - - - +
329D VAL* 1.3 61.3 + - - +
331D ASP* 3.1 8.4 + - - +
332D ILE* 3.0 44.2 + - + +
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.2 13.5 - - + -
24D LEU* 4.0 31.6 - - + -
25D MET* 3.6 32.3 - - + -
28D LEU* 5.0 0.2 - - + -
325D ALA 3.0 19.6 + - - +
326D HIS* 4.0 4.3 - - - +
328D ILE* 1.3 75.7 - - - +
330D ASN* 1.3 63.0 + - - +
332D ILE* 3.2 5.6 + - + +
333D ARG* 2.9 60.7 + - - +
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Residues in contact with ASN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D HIS* 2.9 24.4 + - - +
327D ASN 4.0 4.3 - - - +
329D VAL* 1.3 80.6 - - - +
331D ASP* 1.3 59.4 + - - +
333D ARG* 3.4 4.6 + - - +
334D ASN 3.0 8.1 + - - -
335D ASN* 2.7 62.3 + - - +
337D ASP* 2.7 40.8 + - - +
338D LYS* 5.6 0.9 - - - +
339D TYR* 3.8 16.3 + - - -
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Residues in contact with ASP 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR* 2.5 36.0 + - + +
287D LYS 6.1 1.1 - - - -
290D PHE* 6.1 1.8 - - + -
327D ASN 3.1 16.0 + - - +
328D ILE 3.1 8.7 + - - +
330D ASN* 1.3 76.0 - - - +
332D ILE* 1.3 62.1 + - - +
334D ASN* 3.5 10.5 + - - +
335D ASN 4.3 1.8 + - - -
338D LYS* 4.5 14.7 + - - +
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Residues in contact with ILE 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 4.2 24.5 - - + +
25D MET* 3.8 33.7 - - + -
28D LEU* 4.1 17.0 - - + -
100D TYR* 3.5 30.5 - - + +
328D ILE* 3.0 32.6 + - + +
329D VAL* 3.2 6.5 + - - +
331D ASP* 1.3 77.2 - - - +
333D ARG* 1.3 58.6 + - + +
334D ASN* 3.2 5.5 + - - +
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Residues in contact with ARG 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.1 30.7 + - - +
25D MET* 3.3 24.3 - - + +
26D PRO* 5.7 0.6 - - - +
329D VAL* 2.9 36.5 + - - +
330D ASN* 4.2 7.4 + - - +
331D ASP 3.4 0.2 - - - -
332D ILE* 1.3 75.9 - - + +
334D ASN* 1.3 68.6 + - - +
335D ASN* 3.2 8.8 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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