Contacts of the helix formed by residues 278 - 292 (chain D) in PDB entry 5UQ9
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 VAL 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286C PHE* 3.2 17.9 - - - -
267D THR* 5.1 5.4 - - + +
268D ALA* 5.4 1.4 - - - +
271D ALA* 3.6 25.3 - - + +
276D VAL* 2.8 23.5 + - + -
277D PRO* 1.3 69.6 - - - +
279D THR* 1.3 62.9 + - - +
280D LEU 3.6 0.2 - - - -
281D ILE* 3.6 41.1 - - + -
282D GLY 3.5 8.5 + - - -
337D GLN* 3.6 35.7 - - + +
338D GLY* 5.1 0.9 - - - +
341D LEU* 4.1 11.4 - - + -
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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
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283C GLU* 3.7 11.6 - - + +
286C PHE* 3.6 35.6 - - + -
277D PRO* 3.2 15.9 + - + +
278D VAL* 1.3 71.7 - - - +
280D LEU* 1.3 62.1 + - - +
282D GLY* 3.2 1.9 + - - -
283D GLU* 2.9 32.2 + - - +
337D GLN* 2.9 20.9 + - - +
425D THR* 3.2 31.3 + - - +
429D PHE* 4.1 8.4 - - + +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLY* 3.6 27.6 - - - +
197D LEU* 4.3 7.9 - - + -
279D THR* 1.3 81.4 + - - +
281D ILE* 1.3 57.7 + - - +
283D GLU* 3.1 3.1 + - - +
284D ALA* 2.8 24.9 + - - +
330D SER 3.5 25.1 - - - +
333D ILE 5.1 0.2 - - - -
334D SER* 3.6 27.4 - - - +
337D GLN* 3.2 14.1 + - - +
422D CYS* 3.7 28.8 - - + +
425D THR* 3.7 11.2 - - + -
426D ALA* 3.8 21.3 - - + -
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Residues in contact with ILE 281 (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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186D VAL* 5.3 0.4 - - + -
189D GLY* 3.5 44.0 - - - +
190D ILE* 3.6 18.4 - - + +
192D TYR* 5.3 0.4 - - + -
193D GLY 5.2 0.4 - - - +
264D GLY 4.3 7.2 - - - +
267D THR* 3.8 24.2 - - + -
268D ALA* 4.5 5.8 - - + +
278D VAL* 3.6 28.5 + - + +
280D LEU* 1.3 78.7 - - + +
282D GLY* 1.3 56.8 + - - +
284D ALA* 3.2 7.6 + - - +
285D VAL* 2.9 32.0 + - + +
334D SER* 4.4 17.7 - - - +
337D GLN* 5.5 0.2 - - - +
338D GLY* 5.2 4.7 - - - -
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Residues in contact with GLY 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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272C LEU* 5.0 0.8 - - - +
286C PHE* 4.7 8.5 - - - -
268D ALA* 4.0 20.5 - - - +
278D VAL 3.5 10.6 + - - -
279D THR 3.2 7.0 + - - -
281D ILE* 1.3 80.0 - - - +
283D GLU* 1.3 56.9 + - - +
285D VAL* 3.6 2.2 + - - +
286D PHE* 3.0 42.5 + - - -
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Residues in contact with GLU 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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279C THR* 4.0 19.1 - - - +
283C GLU* 3.2 22.4 - - - +
425C THR* 2.7 30.0 + - - -
428C SER* 6.0 0.2 - - - -
279D THR 2.9 18.5 + - - +
280D LEU 3.6 7.4 - - - +
282D GLY* 1.3 74.0 - - - +
284D ALA* 1.3 56.2 + - - +
286D PHE* 3.4 4.6 + - - +
287D ALA* 2.7 35.2 + - - +
421D PRO* 3.7 31.9 - - + +
422D CYS* 4.3 4.0 - - - -
425D THR* 3.6 24.2 - - + +
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Residues in contact with ALA 284 (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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192D TYR* 3.6 37.9 - - + +
193D GLY* 3.8 8.3 - - - +
196D GLN* 4.0 9.6 - - + +
280D LEU 2.8 16.1 + - - +
281D ILE 3.2 5.6 + - - +
283D GLU* 1.3 78.5 - - - +
285D VAL* 1.3 61.3 + - - +
287D ALA* 3.2 9.4 + - - +
288D ARG* 3.2 25.8 + - - +
422D CYS* 4.0 6.0 - - - -
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 3.7 25.8 - - + +
192D TYR* 3.8 22.0 - - + -
262D GLY* 6.0 3.1 - - - -
264D GLY 3.5 28.7 - - - +
265D LYS* 3.9 17.7 - - + +
268D ALA* 4.8 2.0 - - + -
281D ILE* 2.9 26.4 + - + +
282D GLY* 4.0 4.0 - - - +
284D ALA* 1.3 76.4 - - - +
286D PHE* 1.3 61.9 + - - +
288D ARG* 3.3 6.2 + - - +
289D CYS* 3.2 28.3 + - - -
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Residues in contact with PHE 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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268C ALA* 4.6 4.3 - - + -
271C ALA* 4.4 10.8 - - + -
272C LEU* 3.5 38.4 - - + -
276C VAL 3.3 26.7 - - - -
277C PRO* 3.7 7.5 - - + +
278C VAL 3.6 23.1 - - - -
279C THR* 3.6 36.3 - - + -
282C GLY* 4.9 10.1 - - - -
286C PHE* 6.4 2.5 - + - -
272D LEU* 6.4 0.2 - - + -
282D GLY* 3.0 28.2 + - - +
283D GLU* 3.8 7.2 - - - +
285D VAL* 1.3 76.1 - - - +
287D ALA* 1.3 56.5 + - - +
289D CYS* 3.2 9.8 + - - +
290D LEU* 2.9 29.8 + - - +
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Residues in contact with ALA 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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438C LEU* 5.6 1.0 - - - +
440C ALA* 5.5 0.6 - - - +
196D GLN* 3.5 36.3 - - + +
283D GLU 2.7 21.0 + - - +
284D ALA* 3.3 8.3 - - - +
285D VAL 3.1 0.4 - - - -
286D PHE* 1.3 73.9 - - - +
288D ARG* 1.3 61.6 + - - +
290D LEU* 3.3 8.3 + - - +
291D SER* 3.1 23.7 + - - -
421D PRO* 4.9 10.8 - - + -
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Residues in contact with ARG 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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440C ALA* 5.9 0.2 - - - -
443C ILE* 3.9 27.9 - - + +
447C ARG* 4.1 27.1 - - - +
191D GLU* 5.7 0.2 + - - -
192D TYR* 3.0 61.6 + - + +
195D MET* 3.4 38.0 - - - +
258D ALA* 3.9 15.6 - - + +
259D GLY 3.6 24.3 + - - +
260D GLN* 5.2 0.2 - - - -
284D ALA 3.2 11.9 + - - +
285D VAL* 3.3 7.6 + - + +
287D ALA* 1.3 77.8 - - + +
289D CYS* 1.3 59.6 - - - +
291D SER* 2.7 22.4 + - - -
292D SER* 2.8 17.9 + - - -
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Residues in contact with CYS 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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272C LEU* 6.0 0.9 - - - -
275C GLY* 3.3 42.9 - - - +
276C VAL 4.5 0.2 - - - -
277C PRO* 4.2 12.2 - - + +
260D GLN* 3.9 22.1 - - - +
285D VAL* 3.2 30.2 + - - -
286D PHE* 3.5 15.0 - - - +
287D ALA 3.2 0.2 - - - -
288D ARG* 1.3 75.2 - - - +
290D LEU* 1.3 64.9 + - - +
292D SER* 3.2 15.1 + - - -
293D LEU* 3.6 12.5 + - - +
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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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277C PRO* 4.3 14.3 - - + +
428C SER 4.9 1.1 - - - +
429C PHE* 3.8 38.1 - - + +
432C GLY* 3.7 33.2 - - - +
433C TYR* 3.8 30.1 - - + +
438C LEU* 4.5 6.3 - - + -
286D PHE 2.9 16.7 + - - +
287D ALA* 3.8 8.5 - - - +
289D CYS* 1.3 75.0 - - - +
291D SER* 1.3 62.0 + - - +
293D LEU* 3.2 17.2 + - + +
297D ARG* 3.2 13.4 + - - -
421D PRO* 6.2 4.3 - - + -
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Residues in contact with SER 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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438C LEU* 4.3 8.7 - - - +
440C ALA* 3.5 26.0 - - - -
256D ASP 3.7 6.1 - - - -
257D SER* 3.3 11.4 - - - -
258D ALA* 3.1 21.2 + - - +
287D ALA 3.1 11.4 + - - -
288D ARG 2.7 23.2 + - - -
290D LEU* 1.3 77.6 - - - +
292D SER* 1.3 58.9 + - - +
293D LEU 3.1 0.4 + - - -
294D LYS 3.5 0.7 + - - -
297D ARG* 2.6 31.8 + - - +
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Residues in contact with SER 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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255D ARG* 5.4 1.6 + - - -
257D SER* 4.2 10.3 - - - -
258D ALA 3.0 18.4 + - - -
260D GLN* 3.1 29.4 - - - +
288D ARG 2.8 18.2 + - - -
289D CYS 3.2 11.7 + - - -
291D SER* 1.3 72.2 - - - +
293D LEU* 1.3 61.8 + - - +
294D LYS* 3.1 11.4 + - - +
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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