Contacts of the helix formed by residues 305 - 328 (chain D) in PDB entry 3U1K
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 ASP 305 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PHE* 4.3 1.0 - - - -
303D GLU 3.6 2.7 + - - +
304D HIS* 1.3 73.5 - - - +
306D LYS* 1.3 66.3 + - - +
307D VAL* 3.0 24.0 + - - +
308D SER* 2.7 40.4 + - - -
309D ARG* 3.0 28.0 + - - +
390D GLN* 3.2 27.6 + - - +
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Residues in contact with LYS 306 (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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66B PHE* 3.7 20.8 - - + -
305D ASP* 1.3 73.5 - - - +
307D VAL* 1.3 68.1 + - + +
309D ARG* 3.8 15.2 + - - +
310D ASP* 3.2 42.0 + - - +
390D GLN* 2.7 25.0 + - - +
434D THR* 3.9 29.9 + - - +
479D SER 3.0 23.4 + - - +
480D ASN* 3.4 29.4 - - - +
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Residues in contact with VAL 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.8 30.1 - - + -
305D ASP* 3.0 11.2 + - - +
306D LYS* 1.3 83.4 - - + +
308D SER* 1.3 66.5 + - - +
310D ASP* 3.1 6.9 + - - +
311D GLU* 2.9 51.5 + - + +
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D GLU 4.7 0.2 + - - -
304D HIS* 2.7 31.8 + - - -
305D ASP* 2.7 40.5 + - - -
307D VAL* 1.3 73.4 - - - +
309D ARG* 1.3 54.8 + - - +
311D GLU* 3.5 11.3 + - - +
312D ALA* 3.0 29.1 + - - +
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Residues in contact with ARG 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D VAL* 4.0 19.1 - - + -
299D PHE* 4.2 21.1 - - + -
301D ASP 5.1 0.2 + - - -
302D TYR* 6.2 0.2 - - - +
304D HIS* 3.7 41.5 + - + +
305D ASP* 3.0 16.0 + - - +
306D LYS* 3.8 23.2 + - - +
308D SER* 1.3 81.9 + - - +
310D ASP* 1.3 65.5 + - - +
312D ALA* 3.1 2.9 + - - +
313D VAL* 3.0 28.0 + - + +
359D CYS* 3.8 41.1 + - - -
360D ASP* 4.6 7.3 - - - +
480D ASN* 4.9 2.8 + - - +
534D LEU* 4.2 22.6 - - - +
536D ILE* 4.3 17.4 - - + +
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Residues in contact with ASP 310 (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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306D LYS* 3.2 34.4 + - - +
307D VAL* 3.1 7.0 + - - +
309D ARG* 1.3 80.4 + - - +
311D GLU* 1.3 59.3 + - + +
313D VAL* 3.4 9.1 + - - +
314D ASN* 2.9 29.3 + - - +
317D ARG* 5.2 1.6 + - - -
536D ILE* 4.6 9.7 - - - +
539D TYR* 3.3 22.8 + - - -
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Residues in contact with GLU 311 (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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307D VAL* 2.9 47.1 + - + +
308D SER* 3.7 9.3 - - - +
310D ASP* 1.3 74.8 - - + +
312D ALA* 1.3 58.2 + - - +
314D ASN* 3.3 7.2 + - - +
315D LYS* 2.9 29.7 + - - +
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Residues in contact with ALA 312 (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 VAL* 3.8 23.1 - - + +
304D HIS* 3.8 16.6 - - + +
308D SER 3.0 18.1 + - - +
309D ARG 3.5 4.5 - - - +
311D GLU* 1.3 72.9 - - - +
313D VAL* 1.3 68.0 + - - +
315D LYS* 3.4 13.5 + - - +
316D ILE* 3.3 24.9 + - - +
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Residues in contact with VAL 313 (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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295D LEU* 4.4 8.3 - - + -
298D VAL* 4.1 7.0 - - + -
299D PHE* 3.8 32.5 - - + -
309D ARG* 3.0 21.4 + - + +
310D ASP* 3.6 11.9 - - - +
312D ALA* 1.3 75.9 - - - +
314D ASN* 1.3 58.7 + - - +
316D ILE* 2.9 13.8 + - - +
317D ARG* 2.9 42.8 + - - +
340D PHE* 4.0 16.8 - - + -
344D ALA* 4.9 6.7 - - + -
536D ILE* 5.4 2.7 - - + -
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Residues in contact with ASN 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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310D ASP 2.9 18.6 + - - +
311D GLU* 3.7 7.6 - - - +
313D VAL* 1.3 77.6 - - - +
315D LYS* 1.3 62.4 - - - +
317D ARG* 2.9 38.1 + - - +
318D LEU* 2.9 42.1 + - - +
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Residues in contact with LYS 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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294D ARG* 5.1 6.7 - - - +
311D GLU 2.9 14.5 + - - +
312D ALA* 3.6 13.2 - - - +
313D VAL 3.2 0.4 - - - -
314D ASN* 1.3 77.6 - - - +
316D ILE* 1.3 63.3 + - + +
318D LEU* 3.5 5.5 + - - +
319D ASP* 2.7 38.6 + - - +
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Residues in contact with ILE 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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291D ALA* 3.9 15.9 - - + -
294D ARG* 3.5 63.9 - - + +
295D LEU* 3.6 17.3 - - + +
298D VAL* 3.9 10.5 - - + -
312D ALA 3.3 15.9 - - - +
313D VAL* 2.9 5.8 + - - +
315D LYS* 1.3 76.5 - - + +
317D ARG* 1.3 67.0 + - - +
319D ASP* 3.0 10.4 + - - +
320D THR* 2.9 36.9 + - + +
340D PHE* 4.0 6.5 - - + -
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Residues in contact with ARG 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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310D ASP 5.2 1.2 + - - -
313D VAL* 2.9 29.1 + - - +
314D ASN* 2.9 33.6 + - - +
316D ILE* 1.3 74.9 - - - +
318D LEU* 1.3 64.2 + - - +
321D GLU* 2.9 60.7 + - - +
337D ILE* 5.2 6.2 - - - +
340D PHE* 3.4 46.2 - - + +
341D ASN* 2.9 28.1 + - - +
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Residues in contact with LEU 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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314D ASN* 2.9 37.0 + - - +
315D LYS* 3.6 4.7 - - - +
316D ILE 3.2 0.2 - - - -
317D ARG* 1.3 77.4 - - - +
319D ASP* 1.3 71.1 + - - +
321D GLU* 4.0 5.5 - - - +
322D GLU* 3.3 22.9 + - - +
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Residues in contact with ASP 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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294D ARG* 3.2 28.3 + - - +
315D LYS* 2.7 24.5 - - - +
316D ILE 3.0 5.0 + - - +
318D LEU* 1.3 82.1 - - - +
320D THR* 1.3 67.9 + - - +
321D GLU 3.0 2.6 + - - -
322D GLU* 3.0 13.5 + - - +
323D GLN* 3.1 33.4 + - - +
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Residues in contact with THR 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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287D THR* 4.7 2.0 - - - +
290D LEU* 3.9 22.0 - - + +
291D ALA* 3.7 19.3 - - + -
294D ARG* 4.4 9.6 - - - +
316D ILE* 2.9 37.7 - - + +
317D ARG 3.5 1.6 + - - -
319D ASP* 1.3 74.8 - - - +
321D GLU* 1.3 56.3 + - - +
323D GLN* 3.5 4.0 + - - -
324D LEU* 2.7 46.0 + - - +
340D PHE* 3.3 22.4 - - + -
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Residues in contact with GLU 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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317D ARG* 2.9 52.6 + - + +
318D LEU* 4.0 5.0 - - - +
320D THR* 1.3 84.3 + - - +
322D GLU* 1.3 65.2 + - - +
324D LEU* 3.1 16.1 + - + +
325D LYS* 3.1 24.4 + - - +
336D ILE* 3.5 23.0 - - + +
337D ILE* 3.3 35.2 - - - +
340D PHE* 4.1 7.0 - - + +
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Residues in contact with GLU 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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318D LEU 3.3 15.6 + - - +
319D ASP* 3.0 6.7 + - - +
321D GLU* 1.3 79.0 - - - +
323D GLN* 1.3 60.2 + - + +
325D LYS* 3.0 38.5 - - - +
326D GLU* 3.1 32.6 - - - +
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Residues in contact with GLN 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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286D TYR* 4.5 5.4 + - - +
290D LEU* 3.8 28.1 - - + +
294D ARG* 5.6 3.0 + - - +
319D ASP* 3.1 31.7 + - - +
320D THR* 3.6 4.0 - - - +
322D GLU* 1.3 82.1 - - + +
324D LEU* 1.3 63.5 + - - +
325D LYS 3.3 0.7 - - - -
326D GLU* 3.3 23.8 + - + +
327D LYS* 3.5 8.5 + - - +
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Residues in contact with LEU 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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283D ILE* 4.5 5.6 - - + +
286D TYR* 3.4 31.2 - - + -
287D THR* 3.1 36.8 - - + +
290D LEU* 3.9 9.9 - - + -
320D THR* 2.7 29.1 + - - +
321D GLU* 3.1 7.6 + - + +
323D GLN* 1.3 74.7 - - - +
325D LYS* 1.3 56.3 + - - +
326D GLU 3.0 5.2 - - - -
327D LYS 3.3 1.3 + - - +
328D PHE* 3.1 45.8 + - + +
336D ILE* 3.9 38.5 - - + +
340D PHE* 5.2 0.9 - - + +
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Residues in contact with LYS 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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321D GLU* 3.1 19.5 + - - +
322D GLU* 3.0 45.8 - - - +
324D LEU* 1.3 76.8 - - - +
326D GLU* 1.3 61.4 + - - +
328D PHE 3.9 11.2 - - - +
329D PRO* 3.2 27.7 - - + +
331D ALA 5.9 0.9 - - - +
333D PRO* 4.7 16.6 - - - +
336D ILE* 4.5 22.2 - - + +
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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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322D GLU* 3.1 37.0 - - - +
323D GLN* 3.4 15.7 - - + +
324D LEU 3.0 0.4 - - - -
325D LYS* 1.3 82.0 - - - +
327D LYS* 1.3 64.4 + - - +
328D PHE 3.2 1.5 + - - -
329D PRO* 3.5 15.1 - - - +
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Residues in contact with LYS 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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286D TYR* 3.6 50.1 + - + +
323D GLN 3.5 2.5 + - - +
324D LEU 3.3 2.5 + - - +
326D GLU* 1.3 79.4 - - - +
328D PHE* 1.3 92.7 + - + +
329D PRO* 3.6 4.5 - - - +
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Residues in contact with PHE 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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282D GLU* 4.4 13.0 - - + -
283D ILE* 3.9 38.4 - - + -
286D TYR* 3.7 31.2 - + + -
324D LEU* 3.1 31.9 + - + +
325D LYS* 3.6 12.7 - - - +
327D LYS* 1.3 110.6 - - + +
329D PRO* 1.3 65.5 - - - +
330D GLU 3.1 4.0 + - - +
331D ALA* 3.2 31.3 + - + +
336D ILE* 4.7 2.1 - - + +
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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
------------------------------------------------------------
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