Contacts of the helix formed by residues 273 - 290 (chain D) in PDB entry 6BCH
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 273 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LYS* 3.7 34.8 - - + +
60D ASP* 3.0 17.4 + - - +
272D GLY* 1.3 72.1 - - - -
274D LYS* 1.3 56.8 + - - +
275D LEU 3.0 0.2 - - - -
276D GLN* 2.9 29.4 + - + +
277D ASP* 3.6 8.0 + - - +
313D ARG* 4.1 25.4 - - - -
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Residues in contact with LYS 274 (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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60D ASP* 5.3 0.8 + - - -
181D THR 6.1 0.2 - - - +
182D ALA* 4.9 10.8 - - - +
187D PHE* 4.9 7.6 - - + -
270D ILE* 4.0 13.9 - - + -
271D ILE 4.5 4.7 - - - +
272D GLY* 3.1 1.2 + - - -
273D VAL* 1.3 77.0 - - - +
275D LEU* 1.3 51.8 + - - +
277D ASP* 3.0 18.2 + - + +
278D TYR* 2.8 34.0 + - - +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ILE* 3.6 37.4 - - + +
271D ILE 4.6 0.2 - - - -
272D GLY 3.1 14.8 + - - +
273D VAL 3.0 0.6 + - - -
274D LYS* 1.3 77.6 - - - +
276D GLN* 1.3 51.8 + - - +
278D TYR* 3.0 10.1 + - + +
279D ARG* 2.7 40.1 + - + +
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Residues in contact with GLN 276 (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 GLY 4.4 0.2 + - - -
273D VAL* 2.9 15.6 + - + +
275D LEU* 1.3 78.3 - - - +
277D ASP* 1.3 58.6 + - - +
279D ARG* 3.0 11.3 + - - +
280D ASP* 2.8 31.4 + - - -
313D ARG* 4.3 18.2 - - - +
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Residues in contact with ASP 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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187D PHE* 5.1 6.5 - - + +
273D VAL* 3.6 8.2 + - - +
274D LYS* 3.0 22.3 + - - +
276D GLN* 1.3 75.9 - - - +
278D TYR* 1.3 51.6 - - - +
280D ASP* 3.0 5.6 + - - +
281D TRP* 2.6 38.5 + - - +
309D MET* 3.6 7.9 - - + +
310D ASN* 3.1 42.9 + - - +
313D ARG* 2.8 37.9 + - - +
17F A 5.6 0.7 + - - -
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Residues in contact with TYR 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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187D PHE* 3.4 49.4 - + + -
262D ILE* 3.1 35.0 + - + -
265D PHE* 3.3 31.0 - + + +
266D ASN* 3.5 14.4 + - - -
270D ILE* 4.5 11.0 - - + -
274D LYS 2.8 13.7 + - - +
275D LEU* 3.1 16.8 - - + +
277D ASP* 1.3 75.0 - - - +
279D ARG* 1.3 62.2 + - - +
281D TRP* 3.0 16.9 + + - +
282D CYS* 2.7 56.5 + - - -
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Residues in contact with ARG 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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266D ASN* 4.4 15.0 + - - +
275D LEU* 2.7 24.5 + - + +
276D GLN* 3.0 11.6 + - - +
278D TYR* 1.3 81.1 - - - +
280D ASP* 1.3 65.8 + - - +
282D CYS* 3.0 30.2 + - - +
283D LYS* 2.9 21.7 + - - +
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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
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276D GLN* 2.8 15.2 + - - +
277D ASP 3.5 6.7 - - - +
279D ARG* 1.3 76.8 - - - +
281D TRP* 1.3 63.8 + - - +
283D LYS* 3.0 18.1 + - - +
284D VAL* 3.0 17.4 + - - +
305D ILE* 4.3 13.0 - - + +
308D GLY 4.4 1.7 - - - +
309D MET* 3.9 22.1 - - + +
313D ARG* 2.6 29.3 + - - -
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Residues in contact with TRP 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PHE* 3.4 54.3 - + + -
188D TYR* 3.3 10.4 + - - -
189D ILE* 3.6 21.6 - - + +
205D SER* 4.2 6.5 - - - -
206D VAL 3.1 42.3 + - - +
207D PHE* 3.9 9.2 - - + -
257D ILE* 3.7 39.5 - - + -
261D ILE* 4.5 5.4 - - + -
262D ILE* 4.2 9.2 - - + -
277D ASP 2.6 17.4 + - - +
278D TYR* 3.2 25.4 - + - +
280D ASP* 1.3 71.0 - - - +
282D CYS* 1.3 67.4 + - - +
284D VAL* 3.1 7.7 + - - +
285D VAL* 2.9 26.5 + - + +
309D MET* 3.7 11.4 - - + +
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Residues in contact with CYS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ILE* 3.8 26.6 - - + +
266D ASN* 5.0 0.4 - - - -
278D TYR* 2.7 57.5 + - - -
279D ARG* 3.3 26.2 - - - +
281D TRP* 1.3 72.6 - - - +
283D LYS* 1.3 64.4 + - - +
285D VAL* 3.0 11.7 + - - +
286D THR* 2.9 24.8 + - - +
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Residues in contact with LYS 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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279D ARG 2.9 11.4 + - - +
280D ASP* 3.0 13.4 + - - +
282D CYS* 1.3 75.2 - - - +
284D VAL* 1.3 64.5 + - + +
286D THR* 3.0 19.2 + - - -
287D LEU* 3.0 19.8 + - + +
305D ILE* 5.6 7.0 - - + -
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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
----------------------------------------------------------
189D ILE* 3.7 35.0 - - + -
280D ASP 3.0 16.9 + - - +
281D TRP 3.6 6.5 - - - +
283D LYS* 1.3 74.8 - - - +
285D VAL* 1.3 58.1 + - - +
287D LEU* 3.0 9.7 + - - +
288D ILE* 2.8 39.4 + - + +
302D ILE* 4.0 25.8 - - + +
305D ILE* 3.7 39.7 - - + -
306D LYS 5.5 0.2 - - - +
309D MET* 4.9 0.7 - - - -
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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
----------------------------------------------------------
189D ILE* 5.2 0.2 - - + -
205D SER* 3.6 26.7 - - - +
254D LEU* 4.3 15.2 - - + +
257D ILE* 3.9 28.3 - - + -
258D LYS* 5.3 6.5 - - + +
262D ILE* 4.2 10.5 - - + -
281D TRP* 2.9 32.6 + - + +
282D CYS* 3.3 10.1 - - - +
284D VAL* 1.3 75.4 - - - +
286D THR* 1.3 57.9 + - - +
288D ILE* 3.0 10.4 + - - +
289D ASP* 2.8 30.1 + - + +
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Residues in contact with THR 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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282D CYS 2.9 15.0 + - - -
283D LYS* 3.0 11.7 + - - -
285D VAL* 1.3 75.7 - - - +
287D LEU* 1.3 66.0 + - + +
289D ASP* 2.9 19.4 + - + +
290D ASN* 3.0 29.5 + - - +
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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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283D LYS* 3.0 18.5 + - + +
284D VAL* 3.0 12.0 + - - +
286D THR* 1.3 77.9 - - + +
288D ILE* 1.3 62.5 + - - +
290D ASN* 3.3 9.6 + - - +
292D GLU* 3.0 43.3 + - + +
293D HIS 4.7 1.3 - - - -
298D GLY* 5.6 0.4 - - - +
301D LYS* 5.1 8.5 - - + -
302D ILE* 4.3 18.8 - - + -
305D ILE* 3.9 28.0 - - + -
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Residues in contact with ILE 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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203D VAL* 3.7 35.2 - - + +
204D GLN* 4.4 0.9 - - - -
205D SER* 4.1 30.3 - - - +
254D LEU* 3.9 27.4 - - + +
284D VAL* 2.8 33.3 + - + +
285D VAL* 3.4 7.9 - - - +
287D LEU* 1.3 75.0 - - - +
289D ASP* 1.3 59.9 + - - +
291D LYS* 2.9 17.2 + - - -
293D HIS* 3.2 37.5 - - + +
302D ILE* 4.4 1.3 - - + -
5E T 5.3 0.7 - - - +
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Residues in contact with ASP 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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254D LEU* 4.7 15.6 - - + +
258D LYS* 5.0 12.2 - - - +
285D VAL* 2.8 19.2 + - + +
286D THR* 2.9 14.1 + - + +
288D ILE* 1.3 75.0 - - - +
290D ASN* 1.3 64.7 + - - +
291D LYS* 3.5 3.1 + - - +
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Residues in contact with ASN 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 THR* 3.0 31.6 + - - +
287D LEU* 3.3 6.9 + - - +
288D ILE 3.1 0.4 - - - -
289D ASP* 1.3 86.1 - - - +
291D LYS* 1.3 63.0 + - - +
292D GLU* 3.0 15.1 + - + +
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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