Contacts of the helix formed by residues 317 - 339 (chain D) in PDB entry 1ADO
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 LYS 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D PHE* 4.0 33.4 - - + -
315D GLY 3.3 6.5 + - - +
316D LYS* 1.3 70.5 - - - +
318D GLU* 1.3 72.1 + - - +
319D ASN 3.3 0.6 + - - -
320D LEU* 3.6 18.1 + - + +
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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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316D LYS* 2.9 25.8 - - + +
317D LYS* 1.3 97.4 + - - +
319D ASN* 1.3 65.0 + - - +
320D LEU* 3.3 4.2 + - - +
321D LYS* 4.9 1.7 + - - +
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Residues in contact with ASN 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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312D ALA 3.1 26.1 + - - +
313D TRP* 3.2 20.0 + - - +
314D GLY* 5.0 0.4 - - - -
316D LYS* 3.0 30.7 + - - +
318D GLU* 1.3 85.1 - - - +
320D LEU* 1.3 63.1 + - - +
321D LYS 3.5 1.3 - - - -
322D ALA* 3.1 12.4 + - + +
323D ALA* 2.9 22.8 + - - +
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Residues in contact with LEU 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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57D PHE* 3.9 25.6 - - + -
60D GLN* 6.0 2.7 - - + +
61D LEU* 3.7 44.2 - - + -
313D TRP* 5.0 0.9 - - - -
316D LYS 4.0 2.8 + - - -
317D LYS* 3.6 17.1 + - + +
318D GLU 3.3 3.3 - - - +
319D ASN* 1.3 75.8 - - - +
321D LYS* 1.3 66.7 + - + +
323D ALA* 3.2 2.9 + - - +
324D GLN* 3.0 44.9 + - - +
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Residues in contact with LYS 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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318D GLU 4.9 2.0 + - - +
319D ASN 3.5 0.4 - - - -
320D LEU* 1.3 87.1 - - + +
322D ALA* 1.3 62.3 + - - +
324D GLN* 3.6 18.1 + - - +
325D GLU* 3.1 23.7 + - - +
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Residues in contact with ALA 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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312D ALA* 4.4 9.2 - - + +
319D ASN* 3.1 17.9 + - + +
321D LYS* 1.3 73.7 - - - +
323D ALA* 1.3 66.9 + - - +
325D GLU* 3.0 21.9 + - - +
326D GLU* 3.2 12.9 + - - +
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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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61D LEU* 3.8 12.6 - - + -
309D ALA* 3.2 43.6 - - - +
312D ALA* 3.7 11.8 - - - +
313D TRP* 3.5 22.9 - - + +
319D ASN 2.9 10.5 + - - +
320D LEU 3.5 7.9 - - - +
322D ALA* 1.3 77.8 - - - +
324D GLN* 1.3 60.9 + - - +
326D GLU 3.3 9.2 + - - -
327D TYR 3.4 1.0 + - - -
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Residues in contact with GLN 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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61D LEU* 2.8 44.1 + - + +
64D THR* 3.5 31.1 + - - -
65D ALA* 3.5 12.6 - - + +
66D ASP 5.5 0.7 - - - -
320D LEU* 3.0 36.4 + - - +
321D LYS* 3.8 22.2 + - - +
322D ALA 3.2 0.2 - - - -
323D ALA* 1.3 75.6 - - - +
325D GLU* 1.3 57.6 + - - +
327D TYR* 3.2 8.1 + - - +
328D VAL* 2.9 34.4 + - + +
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Residues in contact with GLU 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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68D ARG* 2.9 44.8 + - - -
321D LYS 3.1 15.0 + - - +
322D ALA* 3.0 14.1 + - - +
324D GLN* 1.3 73.8 - - - +
326D GLU* 1.3 60.4 + - + +
328D VAL* 3.2 5.7 + - - +
329D LYS* 2.9 54.6 + - + +
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Residues in contact with GLU 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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308D SER* 3.5 42.5 + - - +
309D ALA 3.7 5.4 - - - +
312D ALA* 3.8 12.0 - - + +
322D ALA 3.2 13.2 + - - +
323D ALA 3.5 6.5 - - - +
324D GLN 3.3 0.4 - - - -
325D GLU* 1.3 76.2 - - - +
327D TYR* 1.3 63.3 + - - +
329D LYS* 3.3 30.5 + - - +
330D ARG* 3.1 28.0 + - - +
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Residues in contact with TYR 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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30D LEU* 3.5 38.2 - - + +
61D LEU 5.2 0.7 - - - -
62D LEU* 3.3 37.8 + - + -
65D ALA* 3.7 24.7 - - + -
69D VAL* 4.1 15.3 - - + +
73D ILE* 3.6 25.2 - - + +
305D LEU* 3.4 34.3 - - + -
309D ALA* 4.1 12.7 - - + +
323D ALA 3.4 7.7 + - - +
324D GLN* 3.2 9.6 + - - +
325D GLU 3.2 0.2 - - - -
326D GLU* 1.3 77.8 - - - +
328D VAL* 1.3 65.2 + - - +
330D ARG* 3.0 3.3 + - - +
331D ALA* 3.0 28.1 + - + +
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Residues in contact with VAL 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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65D ALA* 4.1 13.9 - - + -
66D ASP* 4.3 15.5 - - - +
68D ARG* 3.5 43.5 - - + +
69D VAL* 3.5 27.1 - - + -
324D GLN* 2.9 21.8 + - + +
325D GLU* 3.2 9.2 + - - +
327D TYR* 1.3 74.5 - - - +
329D LYS* 1.3 58.3 + - - +
331D ALA* 3.4 2.1 + - - +
332D LEU* 3.0 41.2 + - + +
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Residues in contact with LYS 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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68D ARG* 5.9 0.2 - - - +
325D GLU* 2.9 43.8 + - + +
326D GLU* 3.5 32.7 + - - +
327D TYR 3.1 0.2 - - - -
328D VAL* 1.3 77.0 - - - +
330D ARG* 1.3 64.8 + - - +
332D LEU* 3.5 11.2 + - + +
333D ALA* 3.1 27.0 + - - +
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Residues in contact with ARG 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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276D GLU* 3.3 54.9 + - - +
277D GLU* 3.3 25.9 + - - +
280D SER* 2.7 31.9 + - - -
304D ALA 4.1 6.8 + - - +
305D LEU* 3.8 23.8 - - + +
308D SER* 5.4 3.4 - - - -
326D GLU* 3.1 17.1 + - - +
327D TYR 3.0 7.6 + - - +
329D LYS* 1.3 79.8 + - - +
331D ALA* 1.3 65.3 + - - +
333D ALA* 3.3 17.7 + - - +
334D ASN* 2.8 31.2 + - - +
342D TYR* 3.9 5.3 + - - -
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Residues in contact with ALA 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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69D VAL* 4.2 16.6 - - + -
72D CYS* 3.8 21.3 - - + +
73D ILE* 4.5 13.5 - - + -
299D PHE* 4.5 3.8 - - - -
305D LEU* 3.8 12.2 - - + +
327D TYR* 3.0 20.0 + - + +
328D VAL 3.7 4.5 - - - +
330D ARG* 1.3 77.8 - - - +
332D LEU* 1.3 55.9 + - - +
334D ASN* 3.4 3.4 + - - +
335D SER* 2.9 29.3 + - - -
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Residues in contact with LEU 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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68D ARG* 3.9 26.7 - - + +
69D VAL* 5.9 0.2 - - - -
72D CYS* 3.6 24.5 - - - -
328D VAL* 3.0 39.5 + - + +
329D LYS* 3.8 10.5 - - + +
331D ALA* 1.3 75.2 - - - +
333D ALA* 1.3 63.5 + - - +
335D SER* 3.2 3.4 + - - -
336D LEU* 3.1 31.3 + - + +
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Residues in contact with ALA 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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280D SER* 4.1 0.9 - - - +
329D LYS 3.1 17.9 + - - +
330D ARG* 3.6 29.8 - - - +
331D ALA 3.3 0.2 - - - -
332D LEU* 1.3 76.5 - - - +
334D ASN* 1.3 58.6 + - - +
336D LEU* 3.3 3.9 + - - -
337D ALA* 2.9 26.0 + - - +
342D TYR* 3.5 38.0 - - + +
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Residues in contact with ASN 334 (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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276D GLU 5.3 0.4 + - - -
280D SER* 2.7 35.6 + - - -
283D LEU* 4.2 3.3 - - + +
299D PHE* 3.6 27.0 - - + -
301D TYR* 3.5 25.4 - - - -
304D ALA 4.3 6.3 + - - -
305D LEU* 3.4 19.6 - - - +
330D ARG* 2.8 24.2 + - - +
331D ALA 4.0 0.4 - - - +
333D ALA* 1.3 72.4 - - - +
335D SER* 1.3 61.3 - - - +
337D ALA* 3.6 4.5 - - - +
338D CYS* 2.8 32.1 + - - +
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Residues in contact with SER 335 (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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26D GLY* 2.8 29.8 + - - -
71D PRO* 4.4 2.4 + - - +
72D CYS* 3.7 22.0 - - - -
299D PHE* 4.0 3.3 - - - -
331D ALA 2.9 18.5 + - - -
332D LEU* 3.2 6.5 + - - -
334D ASN* 1.3 74.9 - - - +
336D LEU* 1.3 64.9 + - - +
338D CYS* 3.1 21.5 + - - -
339D GLN* 3.2 17.8 + - - +
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Residues in contact with LEU 336 (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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332D LEU* 3.1 17.6 + - + +
333D ALA* 3.5 7.2 - - - +
335D SER* 1.3 83.0 - - - +
337D ALA* 1.3 60.4 + - - +
339D GLN* 3.1 17.4 + - - +
341D LYS* 2.8 58.5 + - + +
342D TYR* 3.8 17.5 - - + +
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Residues in contact with ALA 337 (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 SER 3.4 29.2 - - - +
283D LEU* 4.2 8.5 - - + -
284D ASN* 3.4 21.4 - - - +
287D ASN* 3.4 5.9 + - - -
333D ALA 2.9 17.5 + - - +
334D ASN* 3.2 11.0 + - - +
336D LEU* 1.3 73.1 - - - +
338D CYS* 1.3 57.2 + - - +
339D GLN 3.0 5.2 - - - -
340D GLY 3.0 13.9 + - - -
342D TYR* 3.6 14.7 - - + +
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Residues in contact with CYS 338 (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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26D GLY* 3.5 34.6 + - - -
27D LYS 4.0 1.6 - - - -
283D LEU* 4.2 6.0 - - + +
287D ASN* 3.3 25.1 - - - +
297D LEU 3.7 12.1 + - - +
298D THR* 3.5 29.4 - - - +
299D PHE* 4.4 1.8 - - + -
334D ASN 2.8 18.3 + - - +
335D SER* 3.1 22.0 - - - -
336D LEU 3.3 0.6 - - - -
337D ALA* 1.3 70.9 - - - +
339D GLN* 1.3 57.9 + - - +
340D GLY 3.5 0.2 - - - -
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Residues in contact with GLN 339 (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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25D PRO* 4.3 10.9 - - + +
26D GLY* 3.5 30.6 + - - +
287D ASN* 4.3 4.9 - - - +
335D SER* 3.2 27.5 + - - +
336D LEU* 3.1 14.7 + - - +
337D ALA 3.0 0.6 - - - -
338D CYS* 1.3 80.8 - - - +
340D GLY* 1.3 63.4 + - - +
341D LYS* 3.2 39.6 + - + +
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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