Contacts of the helix formed by residues 280 - 300 (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 SER 280 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D THR 3.4 1.9 + - - -
279D PRO* 1.3 72.5 - - - +
281D PRO* 1.3 71.4 - - - +
282D GLU* 3.2 22.0 - - - +
283D ILE* 3.1 30.6 + - - +
284D VAL* 3.0 20.1 + - - +
335D GLU* 3.0 21.9 + - - +
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Residues in contact with PRO 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D PRO 3.5 4.7 - - - +
280D SER* 1.3 85.6 - - - +
282D GLU* 1.3 66.6 + - - +
284D VAL* 2.9 26.2 - - + +
285D LYS* 3.0 20.8 + - - +
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D SER* 3.2 28.0 + - - +
281D PRO* 1.3 83.4 - - - +
283D ILE* 1.3 63.6 + - + +
285D LYS* 3.2 20.0 + - + +
286D TYR* 2.9 30.0 + - - +
328D PHE* 4.4 12.7 - - + -
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Residues in contact with ILE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D SER* 3.1 22.7 + - - +
282D GLU* 1.3 75.8 - - + +
284D VAL* 1.3 58.1 + - - +
286D TYR* 3.4 1.7 + - - +
287D THR* 2.7 35.5 + - - +
324D LEU* 4.5 7.7 - - + +
328D PHE* 3.9 39.5 - - + -
331D ALA* 3.7 29.8 - - + -
335D GLU* 3.8 23.6 - - + +
336D ILE* 4.9 6.7 - - + -
339D SER* 3.2 24.0 - - - +
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Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D PRO* 4.7 7.9 - - + +
280D SER 3.0 14.3 + - - +
281D PRO* 2.9 32.1 - - + +
283D ILE* 1.3 74.1 - - - +
285D LYS* 1.3 56.0 + - - +
287D THR* 3.0 3.1 + - - -
288D HIS* 2.7 35.5 + - + +
339D SER* 3.2 13.8 + - - +
342D VAL* 4.2 24.7 - - + -
343D VAL* 3.5 20.2 - - + -
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Residues in contact with LYS 285 (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 PRO* 3.0 16.7 + - - +
282D GLU* 3.3 26.2 + - + +
284D VAL* 1.3 77.0 - - - +
286D TYR* 1.3 62.5 + - + +
288D HIS* 3.1 22.5 + - - +
289D LYS* 3.2 8.3 + - - +
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Residues in contact with TYR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D GLU 2.9 16.0 + - - +
283D ILE 3.8 2.9 - - - +
285D LYS* 1.3 75.5 - - + +
287D THR* 1.3 67.0 + - - +
289D LYS* 3.2 14.4 + - + +
290D LEU* 3.1 50.3 + - + +
323D GLN* 4.5 5.4 + - - +
324D LEU* 3.4 23.3 - - + -
327D LYS* 3.6 47.7 + - + +
328D PHE* 3.7 19.1 - + + -
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Residues in contact with THR 287 (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 2.7 22.0 + - - -
284D VAL 3.3 8.7 - - - -
286D TYR* 1.3 76.2 - - - +
288D HIS* 1.3 62.6 + - - +
290D LEU* 3.3 4.1 + - - +
291D ALA* 3.0 23.4 + - + +
320D THR* 4.7 3.1 - - - +
324D LEU* 3.1 28.6 - - + +
339D SER* 3.1 12.1 + - - -
340D PHE* 3.9 29.8 - - + +
343D VAL* 3.4 26.0 - - + -
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Residues in contact with HIS 288 (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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284D VAL* 2.7 16.7 + - + +
285D LYS* 3.1 14.1 + - - +
287D THR* 1.3 72.9 - - - +
289D LYS* 1.3 61.1 + - + +
292D MET* 2.8 62.5 + - + +
343D VAL* 3.8 22.5 + - + +
346D GLU* 5.6 9.1 - - + +
347D VAL* 4.7 11.9 - - + +
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Residues in contact with LYS 289 (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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285D LYS 3.2 9.2 + - - +
286D TYR* 3.2 19.3 + - + +
288D HIS* 1.3 84.2 - - + +
290D LEU* 1.3 64.3 + - + +
292D MET* 4.2 5.6 + - - +
293D GLU* 5.4 4.5 + - - +
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Residues in contact with LEU 290 (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* 3.1 44.8 + - + +
287D THR 3.6 7.4 - - - +
289D LYS* 1.3 79.1 - - + +
291D ALA* 1.3 59.2 + - - +
293D GLU* 5.3 1.2 + - - +
294D ARG* 4.1 18.9 + - - +
320D THR* 3.9 28.5 - - + +
323D GLN* 3.8 27.6 - - + +
324D LEU* 3.9 18.8 - - + -
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Residues in contact with ALA 291 (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 3.0 15.0 + - - +
290D LEU* 1.3 76.6 - - - +
292D MET* 1.3 66.6 + - - +
293D GLU 3.1 3.6 + - - -
294D ARG* 3.2 6.9 + - - +
295D LEU* 3.0 41.9 + - + +
316D ILE* 3.9 8.1 - - + -
320D THR* 3.7 26.0 - - + -
340D PHE* 4.2 6.7 - - + -
343D VAL* 4.8 2.5 - - + -
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Residues in contact with MET 292 (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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288D HIS* 2.8 51.2 + - + +
289D LYS* 4.2 3.0 + - - +
290D LEU 3.7 1.0 - - - -
291D ALA* 1.3 76.2 - - - +
293D GLU* 1.3 95.4 + - + +
295D LEU* 3.7 2.6 + - - +
296D TYR* 3.0 43.8 + - + +
343D VAL* 5.2 0.4 - - - +
347D VAL* 4.2 18.8 - - + +
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Residues in contact with GLU 293 (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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289D LYS 5.5 4.5 - - - +
290D LEU 5.3 0.8 + - - +
291D ALA 3.2 0.4 - - - -
292D MET* 1.3 111.8 - - + +
294D ARG* 1.3 70.2 + - + +
296D TYR* 3.3 3.9 + - - +
297D ALA* 3.0 23.7 + - - +
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Residues in contact with ARG 294 (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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290D LEU* 4.1 20.5 + - - +
291D ALA* 3.2 4.2 + - - +
293D GLU* 1.3 79.5 - - + +
295D LEU* 1.3 62.2 + - - +
297D ALA* 3.4 7.7 + - - +
298D VAL* 3.1 25.8 + - - +
315D LYS* 4.4 7.3 + - - +
316D ILE* 3.5 39.7 - - + +
319D ASP* 3.2 40.4 + - - +
320D THR* 4.4 10.9 - - - +
323D GLN* 5.6 3.2 + - - +
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Residues in contact with LEU 295 (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* 3.0 36.7 + - + +
292D MET 3.9 3.1 - - - +
294D ARG* 1.3 75.5 - - - +
296D TYR* 1.3 63.9 - - - +
298D VAL* 3.0 6.2 + - + +
299D PHE* 2.9 36.1 + - + -
313D VAL* 4.4 13.2 - - + -
316D ILE* 3.7 20.9 - - + -
340D PHE* 4.0 21.3 - - + -
343D VAL* 3.8 22.9 - - + -
344D ALA* 3.9 23.1 - - + +
347D VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 296 (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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292D MET* 3.0 36.5 + - + +
293D GLU 3.5 5.8 - - - +
295D LEU* 1.3 75.8 - - - +
297D ALA* 1.3 65.5 + - - +
299D PHE 3.3 1.0 + - - -
300D THR* 2.8 54.2 + - + +
347D VAL* 3.8 12.5 - - + +
350D SER* 5.6 1.8 - - - -
351D ILE* 4.2 21.8 - - + -
355D GLU* 2.6 34.2 + - - -
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Residues in contact with ALA 297 (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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293D GLU 3.0 13.0 + - - +
294D ARG* 3.6 10.8 - - - +
295D LEU 3.2 0.2 - - - -
296D TYR* 1.3 81.1 - - + +
298D VAL* 1.3 62.1 + - + +
300D THR* 3.3 8.9 + - - -
301D ASP* 3.2 23.6 + - - +
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Residues in contact with VAL 298 (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 3.1 13.5 + - - +
295D LEU* 3.0 9.9 + - - +
297D ALA* 1.3 77.5 - - + +
299D PHE* 1.3 66.6 + - + +
300D THR 3.1 4.4 + - - -
301D ASP* 3.2 19.6 + - - +
304D HIS* 3.6 26.1 - - + +
309D ARG* 4.0 20.6 - - + -
312D ALA* 3.8 26.5 - - + -
313D VAL* 4.1 10.3 - - + -
316D ILE* 3.9 15.9 - - + -
359D CYS 4.9 0.2 - - - +
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Residues in contact with PHE 299 (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* 2.9 35.4 + - + +
298D VAL* 1.3 82.0 - - + +
300D THR* 1.3 62.2 + - - +
301D ASP 3.5 0.4 - - - -
302D TYR* 4.5 0.2 - - - -
309D ARG* 4.2 11.2 - - + -
313D VAL* 3.8 31.2 - - + -
344D ALA* 3.7 26.9 - - + -
347D VAL* 4.2 6.3 - - + -
348D PHE* 3.7 37.5 - + + -
351D ILE* 3.4 22.2 - - + +
358D ARG 4.4 2.6 - - - +
359D CYS* 3.3 31.5 - - + -
536D ILE* 3.8 21.8 - - + -
540D ASN* 5.0 1.8 - - - -
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Residues in contact with THR 300 (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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296D TYR* 2.8 54.5 + - + +
297D ALA* 3.4 10.9 + - - -
299D PHE* 1.3 80.9 - - - +
301D ASP* 1.3 58.8 + - - +
302D TYR* 3.6 31.3 + - + +
351D ILE* 3.9 17.9 - - + -
355D GLU* 5.0 3.6 - - - +
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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
------------------------------------------------------------
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