Contacts of the helix formed by residues 274 - 294 (chain D) in PDB entry 1KKQ
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 HIS 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D VAL* 5.7 10.3 - - + +
258D LEU* 6.5 0.9 - - + -
263D ILE* 4.8 25.1 - - + +
270D VAL 5.0 0.4 + - - +
271D ARG* 2.7 21.0 + - + +
273D PHE* 1.3 76.1 - - - +
275D CYS* 1.3 61.2 + - - +
276D CYS 2.7 0.2 + - - -
277D GLN* 2.3 49.4 + - + +
278D CYS* 3.8 1.6 + - - -
454D ALA* 5.5 12.6 - - + +
459D LEU* 5.8 6.4 - - + +
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Residues in contact with CYS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D GLU* 3.4 37.0 - - + -
254D LEU* 4.6 6.8 - - + +
255D VAL* 5.9 7.9 - - - -
258D LEU* 6.0 2.9 - - - -
271D ARG* 3.2 21.3 + - - +
272D ILE* 4.6 3.1 - - - -
274D HIS* 1.3 83.6 - - - +
276D CYS* 1.3 55.2 + - - +
277D GLN 3.1 0.4 - - - -
278D CYS* 3.1 29.0 - - - -
279D THR* 3.3 10.2 + - - -
778D 471 4.1 32.8 - - + -
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Residues in contact with CYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ILE* 2.6 25.6 + - - +
273D PHE 3.3 7.2 - - - +
274D HIS 2.7 2.6 + - - -
275D CYS* 1.3 74.0 - - - +
277D GLN* 1.3 56.5 + - - +
279D THR* 4.2 8.6 - - - -
280D SER* 3.1 21.5 + - - -
778D 471 3.1 93.3 + - + +
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Residues in contact with GLN 277 (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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273D PHE* 2.9 27.6 + - + +
274D HIS* 2.3 41.9 + - + +
276D CYS* 1.3 65.8 - - - +
278D CYS* 1.3 66.7 + - - +
279D THR 3.2 1.1 - - - -
280D SER* 2.9 20.3 + - - -
281D VAL* 3.3 10.0 + - - +
455D ALA* 2.9 32.5 + - - +
456D LEU* 4.3 8.1 - - - +
460D LEU* 5.2 5.7 - - - +
778D 471 3.4 38.5 + - - +
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Residues in contact with CYS 278 (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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254D LEU* 6.0 6.7 - - - -
255D VAL* 6.5 1.6 - - - -
274D HIS 4.4 0.7 - - - -
275D CYS* 3.1 31.4 - - - -
277D GLN* 1.3 74.5 - - - +
279D THR* 1.3 61.0 + - - +
280D SER 2.7 12.5 + - - -
281D VAL* 2.9 10.8 + - - +
282D GLU* 2.8 29.1 + - + +
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Residues in contact with THR 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D CYS 3.3 17.7 + - - -
276D CYS* 4.2 10.7 - - - -
278D CYS* 1.3 80.5 - - - +
280D SER* 1.3 56.3 + - - +
282D GLU* 4.1 8.2 - - - +
283D THR* 3.0 28.6 + - + +
333D ALA* 5.6 6.0 + - - +
334D TYR* 6.0 1.1 - - - -
778D 471 3.9 39.8 + - + +
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Residues in contact with SER 280 (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 CYS 3.1 17.3 + - - -
277D GLN 2.9 7.9 + - - -
278D CYS 2.7 5.3 + - - -
279D THR* 1.3 72.0 - - - +
281D VAL* 1.3 57.2 + - - -
282D GLU 3.0 0.9 - - - -
283D THR* 2.5 23.3 + - - -
284D VAL* 2.6 28.1 + - - +
317D ILE* 5.3 1.6 - - - -
778D 471 3.3 55.8 + - - -
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D GLN 4.1 9.9 - - - +
278D CYS* 2.9 10.6 + - - +
280D SER* 1.3 78.6 - - - +
282D GLU* 1.3 56.2 + - - +
284D VAL* 3.5 9.3 + - - +
285D THR* 2.6 37.5 + - - +
464D TYR* 5.0 10.5 - - - +
778D 471 4.4 14.8 - - + -
688H ILE* 4.1 30.7 - - + +
691H LYS* 6.0 4.0 - - - +
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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
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219D ASN* 5.9 1.7 - - - +
278D CYS* 2.8 17.5 + - + +
279D THR* 4.1 9.9 - - - +
281D VAL* 1.3 78.8 - - - +
283D THR* 1.3 58.5 + - + +
285D THR* 3.4 8.6 + - - -
286D GLU* 3.1 34.5 + - - +
334D TYR* 2.9 41.0 + - + +
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Residues in contact with THR 283 (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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218D PHE* 6.3 0.4 - - - -
279D THR* 3.0 23.1 + - + +
280D SER* 2.5 30.2 + - - -
282D GLU* 1.3 70.4 - - + +
284D VAL* 1.3 63.8 + - - -
285D THR 3.0 1.8 - - - -
286D GLU* 3.1 23.1 + - - +
287D LEU* 2.9 29.2 + - - +
317D ILE* 3.4 26.3 - - + +
320D MET* 6.2 4.9 - - + -
778D 471 5.1 2.9 - - + -
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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
----------------------------------------------------------
280D SER* 2.6 34.1 + - - +
281D VAL* 3.9 8.3 - - - +
283D THR* 1.3 75.4 + - - +
285D THR* 1.3 54.9 + - - +
287D LEU* 3.5 6.1 + - - +
288D THR* 2.7 38.6 + - - +
309D LEU* 5.9 0.2 - - + -
313D VAL* 4.0 23.3 - - + -
314D TYR* 6.4 0.7 - - + -
317D ILE* 5.0 4.9 - - + -
778D 471 5.0 4.3 - - + -
685H LEU* 4.3 17.0 - - + -
688H ILE* 4.6 8.5 - - + -
689H ILE* 3.8 37.9 - - + +
692H ALA* 5.7 0.2 - - - -
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Residues in contact with THR 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 VAL* 2.6 25.6 + - - +
282D GLU* 3.4 11.3 - - - -
284D VAL* 1.3 77.5 - - - +
286D GLU* 1.3 59.3 + - - +
288D THR* 3.3 4.5 + - - +
289D GLU* 2.9 40.6 + - + +
688H ILE* 5.0 4.2 - - - +
692H ALA* 4.2 21.1 - - + +
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Residues in contact with GLU 286 (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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217D ASN* 3.3 20.3 - - - +
218D PHE* 3.1 23.9 - - + +
219D ASN* 2.7 39.9 + - - +
220D MET 4.5 1.0 + - - -
282D GLU* 3.1 29.2 + - - +
283D THR* 3.1 30.8 + - - +
285D THR* 1.3 75.9 - - - +
287D LEU* 1.3 53.2 + - - +
289D GLU* 3.4 6.0 + - - +
290D PHE* 2.7 35.2 + - - +
320D MET* 5.9 0.3 - - - +
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Residues in contact with LEU 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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218D PHE* 3.9 24.5 - - + -
283D THR* 2.9 15.4 + - - +
284D VAL* 3.6 5.6 - - - +
286D GLU* 1.3 75.7 - - - +
288D THR* 1.3 59.7 + - - +
290D PHE* 3.6 1.9 - - + +
291D ALA* 2.8 31.4 + - - +
309D LEU* 4.1 10.0 - - + +
313D VAL* 3.5 38.6 - - + +
316D ALA* 3.7 24.7 - - + -
317D ILE* 3.8 15.9 - - + +
320D MET* 4.5 4.9 - - + -
379D VAL* 4.1 6.1 - - + -
383D ILE* 3.7 21.8 - - + -
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Residues in contact with THR 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 27.7 + - - +
285D THR 3.7 3.6 - - - -
287D LEU* 1.3 74.8 - - - +
289D GLU* 1.3 58.7 + - - +
291D ALA* 3.2 2.8 + - - +
292D LYS* 2.9 32.5 + - - +
309D LEU* 3.2 24.2 - - + +
689H ILE* 4.1 12.8 - - - +
692H ALA* 3.7 27.7 - - + +
693H LEU* 3.2 37.5 - - + -
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Residues in contact with GLU 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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217D ASN* 3.1 28.3 + - - +
285D THR* 2.9 28.9 + - + +
286D GLU* 3.7 3.8 - - - +
288D THR* 1.3 78.1 - - - +
290D PHE* 1.3 59.8 + - - +
292D LYS* 3.0 54.6 + - - +
293D ALA* 3.3 5.5 + - - +
692H ALA* 3.3 10.4 - - - +
696H LYS* 3.4 19.0 - - - +
697H TYR 5.5 0.2 + - - -
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Residues in contact with PHE 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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210D ILE* 3.6 30.3 - - + -
213D ALA* 3.6 21.1 - - + -
214D TYR* 3.9 10.5 - + + -
217D ASN* 3.9 12.0 - - + +
218D PHE* 3.4 29.8 - + + -
286D GLU 2.7 21.9 + - - +
287D LEU* 3.6 7.4 - - + +
289D GLU* 1.3 72.1 - - - +
291D ALA* 1.3 65.1 + - - +
293D ALA* 3.2 11.7 + - - +
294D ILE* 3.5 15.1 + - + +
376D SER* 3.5 24.2 - - - -
379D VAL* 3.4 30.3 - - + -
380D ALA* 4.3 11.0 - - + -
383D ILE* 4.6 3.1 - - + -
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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 LEU 2.8 21.5 + - - +
288D THR 3.4 5.8 - - - +
290D PHE* 1.3 71.9 - - - +
292D LYS* 1.3 67.3 + - - +
294D ILE* 2.9 25.4 + - + +
297D PHE* 3.1 46.4 - - + +
309D LEU* 4.2 10.8 - - + -
383D ILE* 4.3 11.0 - - + -
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Residues in contact with LYS 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 THR* 2.9 23.9 + - - +
289D GLU* 3.0 44.6 + - - +
291D ALA* 1.3 77.4 - - - +
293D ALA* 1.3 58.5 + - - +
294D ILE 3.5 4.5 + - - +
297D PHE* 3.8 10.3 - - + -
298D ALA* 4.2 20.3 + - + +
692H ALA 3.2 19.8 + - - -
693H LEU* 3.6 35.8 + - + +
694H MET 4.3 4.4 + - - -
696H LYS* 3.7 15.6 - - - +
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Residues in contact with ALA 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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209D ARG* 2.6 37.8 + - - +
213D ALA* 3.5 27.8 - - + +
216D LYS* 6.4 0.9 - - + -
217D ASN* 4.8 4.9 - - - +
289D GLU 3.3 6.0 + - - +
290D PHE 3.2 5.7 + - - +
291D ALA 3.1 1.0 - - - -
292D LYS* 1.3 78.0 - - - +
294D ILE* 1.3 64.4 + - - +
295D PRO* 2.9 9.1 - - - +
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Residues in contact with ILE 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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206D LEU* 5.7 0.7 - - + -
210D ILE* 4.7 9.2 - - + +
213D ALA* 6.0 0.2 - - - -
290D PHE* 3.5 21.0 + - + +
291D ALA* 2.9 30.5 + - + +
292D LYS 4.1 2.1 - - - +
293D ALA* 1.3 75.4 - - - +
295D PRO* 1.3 61.5 - - + +
296D GLY 2.5 19.6 + - - -
297D PHE* 2.8 21.1 + - + +
298D ALA 4.5 0.2 + - - -
380D ALA* 3.9 26.5 - - + +
383D ILE* 4.7 7.0 - - + -
384D CYS* 3.7 25.6 - - - -
400D MET* 4.6 6.5 - - + -
404D ILE* 3.8 25.6 - - + -
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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
------------------------------------------------------------
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