Contacts of the helix formed by residues 276 - 291 (chain D) in PDB entry 3KHU
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 CYS 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D ASN* 3.7 6.3 - - - +
274D GLY 3.2 1.6 - - - -
275D SER* 1.3 84.6 - - - +
277D PHE* 1.3 65.0 + - + +
278D GLN 3.6 0.9 - - - -
279D LYS* 3.5 2.2 + - - +
280D ASP* 2.8 41.0 + - - +
501D UPG 2.0 70.6 + - - +
502D UPG 3.7 21.1 - - - -
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Residues in contact with PHE 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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224D ASN* 3.5 41.7 - - + -
227D LEU* 3.8 17.3 - - + -
228D ALA* 4.1 16.2 - - + -
231D ILE* 3.9 17.9 - - + -
265D PHE* 3.9 6.1 - + - -
272D PHE* 3.8 33.9 - + + -
273D GLY 4.6 5.3 + - - +
274D GLY 4.4 3.0 + - - -
276D CYS* 1.3 81.7 - - + +
278D GLN* 1.3 65.4 + - - +
280D ASP* 3.8 2.5 - - - +
281D VAL* 2.9 31.7 + - - +
501D UPG 3.6 55.0 - - - -
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Residues in contact with GLN 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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272D PHE* 4.1 8.7 - - + -
274D GLY 4.9 3.4 + - - +
276D CYS 3.6 0.2 - - - -
277D PHE* 1.3 77.5 - - - +
279D LYS* 1.3 65.5 + - - +
281D VAL* 4.1 0.3 - - - +
282D LEU* 2.9 47.1 + - + +
304D ILE* 4.0 25.6 - - + +
307D ASN* 5.1 4.3 + - - -
308D ASP* 4.3 13.5 - - - +
311D ARG* 4.4 12.0 + - - -
347D GLU* 3.9 38.8 + - + +
352D TYR* 4.6 4.3 + - - -
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Residues in contact with LYS 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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91D THR* 3.2 37.6 + - - +
92D PRO* 4.2 7.0 - - - -
93D THR* 3.7 26.2 - - - +
102D ARG 4.8 1.9 - - - +
104D ALA* 5.8 2.1 - - - +
131D THR* 4.8 10.3 + - - +
275D SER 3.9 19.4 - - - +
276D CYS 3.5 7.5 + - - +
277D PHE 3.3 0.4 - - - -
278D GLN* 1.3 81.0 - - - +
280D ASP* 1.3 69.6 + - - +
282D LEU* 3.8 5.5 - - - +
283D ASN* 2.9 30.2 + - + +
347D GLU* 6.1 0.4 - - - +
502D UPG 5.7 5.7 + - - -
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Residues in contact with ASP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D THR* 3.8 22.8 + - - +
220D LYS* 4.4 2.8 - - - +
221D LEU* 3.9 31.5 - - + +
224D ASN* 2.8 37.3 + - + +
276D CYS* 2.8 25.9 + - - +
277D PHE 4.0 1.6 - - - +
279D LYS* 1.3 87.5 + - - +
281D VAL* 1.3 60.1 + - - +
283D ASN* 3.2 5.9 + - - +
284D LEU* 2.9 27.9 + - - +
501D UPG 4.1 4.0 + - - -
502D UPG 5.7 2.5 - - - -
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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
----------------------------------------------------------
224D ASN 4.7 1.6 - - - +
225D ALA* 3.9 29.2 - - + +
228D ALA* 4.3 13.9 - - + -
277D PHE 2.9 23.9 + - - +
280D ASP* 1.3 76.5 - - + +
282D LEU* 1.3 59.0 + - - +
284D LEU* 3.1 9.8 + - + +
285D VAL* 2.9 28.9 + - + +
300D TRP* 3.8 33.9 - - + +
303D VAL* 4.5 6.3 - - + -
304D ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 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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101D GLY 3.9 16.8 - - - +
102D ARG* 3.9 32.3 - - + +
278D GLN* 2.9 47.7 + - + +
279D LYS* 3.9 4.5 - - - +
281D VAL* 1.3 75.8 - - - +
283D ASN* 1.3 57.7 + - - +
285D VAL* 3.4 5.6 + - + +
286D TYR* 3.0 26.7 + - - +
301D GLN* 3.8 26.7 - - - +
304D ILE* 4.1 18.2 - - + -
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Residues in contact with ASN 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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102D ARG 3.4 10.8 + - - +
103D ALA* 3.9 2.8 - - - +
104D ALA* 3.3 38.9 - - - +
133D PRO* 3.6 20.7 - - - +
134D VAL 4.7 0.7 + - - -
221D LEU* 3.5 22.6 - - + +
279D LYS* 2.9 20.2 + - + +
280D ASP* 3.2 8.5 + - - +
282D LEU* 1.3 74.1 - - - +
284D LEU* 1.3 59.8 + - - +
286D TYR* 3.3 5.9 + - - +
287D LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 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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237C ILE* 4.7 4.3 - - + -
240C LEU* 3.9 26.7 - - + -
218D LEU* 3.9 18.2 - - + -
221D LEU* 4.4 15.9 - - + +
222D ALA* 4.7 9.0 - - - -
225D ALA* 3.9 27.6 - - + -
280D ASP 2.9 13.0 + - - +
281D VAL* 3.3 9.2 - - - +
283D ASN* 1.3 78.2 + - - +
285D VAL* 1.3 63.5 + - + +
287D LEU* 3.2 12.9 + - + +
288D CYS* 3.0 28.4 + - - -
300D TRP* 4.0 30.5 - - + +
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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
----------------------------------------------------------
102D ARG* 3.8 20.4 - - - +
281D VAL* 2.9 23.2 + - + +
282D LEU* 3.7 7.9 - - + +
283D ASN 3.3 0.2 - - - -
284D LEU* 1.3 74.7 - - - +
286D TYR* 1.3 64.0 + - - +
288D CYS* 3.1 10.1 + - - +
289D GLU* 3.0 30.2 + - - +
297D ALA* 3.8 18.4 - - + +
300D TRP* 4.0 10.3 - - + -
301D GLN* 3.6 50.0 - - + +
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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
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98D MET* 4.6 4.5 + - - +
99D GLY* 3.7 25.9 + - - -
102D ARG* 4.0 33.8 - - + +
103D ALA* 3.7 28.0 - - + +
282D LEU 3.0 17.6 + - - +
283D ASN* 3.7 8.5 - - - +
284D LEU 3.3 0.2 - - - -
285D VAL* 1.3 78.1 - - - +
287D LEU* 1.3 68.2 + - - +
289D GLU* 3.1 9.6 + - + +
290D ALA* 2.9 35.9 + - + +
320F ASP* 4.8 5.9 + - - -
324F ASN* 3.4 21.2 + - - -
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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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240C LEU* 4.2 20.9 - - + -
244C THR* 4.9 2.0 - - + -
134D VAL* 3.8 51.1 - - + +
135D ARG* 6.1 0.9 - - + -
218D LEU* 4.7 1.1 - - + -
221D LEU* 5.1 2.5 - - + -
283D ASN* 2.9 24.5 + - - +
284D LEU* 3.4 16.4 - - + +
286D TYR* 1.3 79.0 - - + +
288D CYS* 1.3 62.2 + - - +
290D ALA* 3.3 7.3 + - + +
291D LEU* 3.0 51.6 + - + +
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Residues in contact with CYS 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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240C LEU* 3.6 27.1 - - - -
284D LEU* 3.0 26.9 + - - -
285D VAL* 3.1 8.7 + - - +
287D LEU* 1.3 74.9 - - - +
289D GLU* 1.3 66.7 + - - +
291D LEU* 3.1 7.9 + - - -
293D LEU* 2.9 44.4 + - + +
296D VAL* 3.6 31.0 - - - -
297D ALA* 3.7 12.6 - - + +
300D TRP* 5.0 1.1 - - - -
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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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102D ARG* 2.9 44.8 + - - +
285D VAL* 3.0 22.5 + - - +
286D TYR* 3.1 8.4 + - + +
288D CYS* 1.3 76.5 - - - +
290D ALA* 1.3 60.4 + - - +
292D ASN* 3.1 19.4 + - - +
293D LEU 4.8 3.1 - - - +
294D PRO* 5.4 5.2 - - + -
297D ALA* 3.8 15.7 - - + +
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Residues in contact with ALA 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* 2.9 32.1 + - + +
287D LEU* 3.6 12.6 - - + +
289D GLU* 1.3 76.0 - - - +
291D LEU* 1.3 65.8 + - + +
292D ASN* 3.3 7.7 + - - +
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Residues in contact with LEU 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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240C LEU* 3.9 14.1 - - + -
243C ALA* 4.0 23.5 - - + +
244C THR* 3.6 31.0 - - + -
287D LEU* 3.0 34.3 + - + +
288D CYS 3.1 4.1 + - - +
290D ALA* 1.3 82.4 - - + +
292D ASN* 1.3 72.9 + - - +
293D LEU* 3.3 15.8 + - + +
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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