Contacts of the helix formed by residues 285 - 304 (chain D) in PDB entry 5UHE
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 285 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D VAL 5.1 0.7 - - - +
283D ASN* 3.5 8.2 - - + +
284D GLY* 1.3 70.2 - - - +
286D GLY* 1.3 57.7 + - - +
287D GLN 3.7 1.3 - - - +
288D LYS* 4.3 23.1 - - + +
289D LYS* 3.1 29.8 + - - +
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Residues in contact with GLY 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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284D GLY 3.0 8.1 + - - -
285D LYS* 1.3 69.4 - - - +
287D GLN* 1.3 59.2 + - - +
289D LYS* 3.2 8.8 + - - +
290D LEU* 2.8 37.9 + - - +
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Residues in contact with GLN 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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285D LYS 3.7 0.2 - - - -
286D GLY* 1.3 74.9 - - - +
288D LYS* 1.3 67.0 + - + +
290D LEU* 3.4 15.8 - - + +
291D ARG* 3.3 60.3 + - - +
23H G 5.6 1.0 + - - -
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Residues in contact with LYS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 3.6 17.7 - - + +
285D LYS* 3.8 20.6 + - + +
286D GLY 3.3 0.2 - - - -
287D GLN* 1.3 83.4 - - + +
289D LYS* 1.3 59.7 + - - +
290D LEU 3.4 0.2 - - - -
291D ARG* 4.1 7.2 - - - +
292D ALA* 3.3 24.9 + - - +
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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
----------------------------------------------------------
280D VAL* 4.0 10.5 - - - +
281D ILE* 3.3 38.8 - - + +
283D ASN 3.5 6.1 - - - +
284D GLY* 3.5 21.5 - - - -
285D LYS 3.1 16.9 + - - +
286D GLY* 3.6 7.7 - - - +
288D LYS* 1.3 75.0 - - - +
290D LEU* 1.3 57.0 + - - +
292D ALA* 3.6 2.8 - - - +
293D LEU* 2.7 59.7 + - + +
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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 GLY 2.8 23.8 + - - +
287D GLN* 3.4 16.8 - - + +
288D LYS 3.4 0.2 - - - -
289D LYS* 1.3 77.2 - - - +
291D ARG* 1.3 65.1 + - + +
293D LEU* 3.1 26.0 + - + +
294D LYS* 3.2 27.0 + - - +
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Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TYR* 5.4 0.7 - - - -
287D GLN* 3.3 49.3 + - - +
288D LYS* 3.9 7.4 + - - +
290D LEU* 1.3 77.9 - - + +
292D ALA* 1.3 57.1 + - - +
294D LYS* 4.1 19.2 - - - +
295D ARG* 3.4 30.3 + - - +
22H T 4.5 22.1 + - - +
23H G 4.3 15.2 + - - -
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Residues in contact with ALA 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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277D LEU* 4.0 29.9 - - + +
280D VAL* 3.9 21.8 - - + -
281D ILE* 4.3 8.2 - - + +
288D LYS 3.3 19.1 + - - +
289D LYS* 3.3 6.2 + - - +
290D LEU 3.2 0.4 - - - -
291D ARG* 1.3 75.6 - - - +
293D LEU* 1.3 64.3 + - - +
295D ARG* 3.9 2.0 - - - +
296D LEU* 3.3 22.9 + - - +
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Residues in contact with LEU 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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281D ILE* 3.6 25.8 - - + -
289D LYS* 2.7 42.0 + - + +
290D LEU* 3.1 19.5 + - + +
292D ALA* 1.3 76.0 - - - +
294D LYS* 1.3 66.5 + - + +
296D LEU* 3.4 12.5 + - + +
297D LYS* 3.4 11.8 + - - +
1176D LEU* 5.1 5.2 - - + +
1177D PRO* 3.3 42.8 - - + +
1178D GLY* 5.1 4.5 - - - -
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Residues in contact with LYS 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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111D PRO* 6.0 0.2 - - + -
116D TYR* 3.6 32.6 + - + +
290D LEU* 3.2 23.0 + - - +
291D ARG* 4.2 19.0 - - - +
293D LEU* 1.3 80.7 - - + +
295D ARG* 1.3 62.0 + - - +
297D LYS* 3.2 21.8 + - - +
298D VAL* 3.6 10.4 + - - +
21H A 3.3 59.0 + - - +
22H T 4.5 4.6 + - - -
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Residues in contact with ARG 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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116D TYR* 2.7 38.3 + - + +
117D LEU 3.2 24.7 + - - -
118D LEU 4.2 0.6 - - - -
119D ASP* 3.1 49.2 + - - +
268D PHE* 4.7 0.2 - - - -
273D GLU* 3.4 24.8 + - - -
277D LEU* 3.9 33.7 - - + +
291D ARG 3.4 18.4 + - - +
292D ALA* 4.0 3.4 - - - +
293D LEU 3.3 0.4 - - - -
294D LYS* 1.3 78.6 - - - +
296D LEU* 1.3 62.8 + - - +
298D VAL* 3.0 6.4 + - - +
299D VAL* 3.0 33.8 + - - +
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Residues in contact with LEU 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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274D ALA* 3.9 29.8 - - + +
277D LEU* 4.0 13.2 - - + +
278D ARG* 4.2 27.8 - - + +
281D ILE* 3.9 22.9 - - + -
292D ALA 3.3 15.1 + - - +
293D LEU* 3.8 5.6 - - + +
294D LYS 3.3 0.6 - - - -
295D ARG* 1.3 74.3 - - - +
297D LYS* 1.3 58.9 + - - +
298D VAL 2.9 5.1 + - - -
299D VAL* 4.3 2.0 - - + +
300D ALA* 2.7 53.1 + - + +
1176D LEU* 3.9 24.0 - - + -
1177D PRO* 5.6 0.9 - - + -
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Residues in contact with LYS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D LEU 3.4 8.7 + - - +
294D LYS* 3.2 14.9 + - - +
296D LEU* 1.3 77.9 - - - +
298D VAL* 1.3 63.3 + - + +
300D ALA* 4.6 0.9 - - - -
301D ALA* 3.8 17.1 + - - +
1176D LEU* 3.9 19.7 - - + +
1235D ASP* 3.4 36.0 + - - +
1238D ILE* 5.6 0.5 - - - +
1239D ASN* 4.5 16.8 + - - +
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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
----------------------------------------------------------
111D PRO* 5.9 3.6 - - + -
113D ARG* 3.8 37.9 - - + +
116D TYR* 3.8 29.6 - - + -
117D LEU* 4.3 12.6 - - + +
294D LYS 3.6 9.4 + - - +
295D ARG 3.0 7.3 + - - +
296D LEU 2.9 0.4 - - - -
297D LYS* 1.3 85.9 - - + +
299D VAL* 1.3 65.0 + - + +
300D ALA 3.3 0.4 - - - -
301D ALA* 3.5 9.9 + - - +
302D PHE* 3.2 32.8 + - + -
1238D ILE* 5.4 3.4 - - + -
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Residues in contact with VAL 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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116D TYR 4.3 11.7 - - - +
117D LEU* 4.2 20.4 - - + +
268D PHE* 4.2 14.8 - - + -
270D ILE* 3.6 36.2 - - + +
273D GLU* 4.6 5.8 - - + +
274D ALA* 4.6 7.6 - - + +
277D LEU* 4.0 19.3 - - + -
295D ARG* 3.0 21.8 + - - +
296D LEU* 4.2 3.4 - - + +
298D VAL* 1.3 78.4 - - + +
300D ALA* 1.3 62.7 + - - +
302D PHE* 3.2 3.9 + - - +
303D GLN* 3.1 17.4 + - - +
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Residues in contact with ALA 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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278D ARG* 4.4 12.8 - - - +
296D LEU* 2.7 41.5 + - + +
297D LYS* 5.1 0.4 - - - -
299D VAL* 1.3 73.5 - - - +
301D ALA* 1.3 60.0 + - - +
303D GLN* 3.7 12.3 - - - +
304D GLN* 3.3 28.6 + - - +
1176D LEU* 4.7 11.2 - - + -
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Residues in contact with ALA 301 (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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297D LYS 3.8 15.4 + - - +
298D VAL 3.5 3.2 + - - +
299D VAL 3.2 0.6 - - - -
300D ALA* 1.3 78.9 - - - +
302D PHE* 1.3 58.7 + - - +
304D GLN* 3.6 15.1 + - - +
305D SER* 3.4 18.7 + - - -
307D ASN* 4.9 0.2 + - - -
1238D ILE* 3.4 26.3 - - + +
1239D ASN* 3.2 37.0 - - - +
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Residues in contact with PHE 302 (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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14D LEU* 4.4 7.0 - - + -
117D LEU* 4.2 12.3 - - + -
270D ILE* 4.5 12.7 - - + +
298D VAL* 3.2 33.0 - - + -
299D VAL* 3.2 7.7 + - - +
300D ALA 3.1 0.6 - - - -
301D ALA* 1.3 79.5 - - - +
303D GLN* 1.3 64.4 + - - +
304D GLN 3.3 0.6 + - - -
305D SER* 4.0 5.2 + - - -
306D GLY* 4.1 1.6 + - - -
307D ASN* 2.9 58.9 + - - +
308D SER 4.2 1.1 - - - -
309D PRO* 3.6 33.7 - - + -
312D MET* 3.5 27.1 - - + -
1238D ILE* 3.7 36.8 - - + -
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Residues in contact with GLN 303 (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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270D ILE* 3.8 15.9 - - + +
271D ASP* 3.5 26.2 + - - +
274D ALA* 3.2 27.6 - - - +
275D GLU* 4.6 5.9 + - - -
278D ARG* 3.8 20.2 + - - +
299D VAL 3.1 11.3 + - - +
300D ALA* 3.7 14.0 - - - +
302D PHE* 1.3 79.9 - - - +
304D GLN* 1.3 64.5 + - - +
305D SER 3.5 0.3 + - - -
306D GLY* 4.2 4.5 + - - -
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Residues in contact with GLN 304 (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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300D ALA 3.3 17.7 + - - +
301D ALA* 3.6 17.6 + - - +
303D GLN* 1.3 82.8 - - - +
305D SER* 1.3 68.4 + - - +
306D GLY 3.8 0.3 + - - -
1239D ASN* 3.5 32.0 + - - +
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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