Contacts of the helix formed by residues 272 - 294 (chain C) in PDB entry 3D5K
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 ARG 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C LEU* 2.9 29.6 + - + +
271C ARG* 1.3 72.1 - - - +
273C PRO* 1.4 72.6 - - + +
274C ASP* 2.8 38.5 + - - +
275C ILE* 3.2 12.7 + - + +
276C LEU* 3.2 21.5 + - - +
364C THR* 5.2 1.4 - - - +
365C ALA* 3.5 28.3 - - - +
368C GLU* 2.7 31.4 + - - -
444C LYS* 5.1 5.3 - - - +
445C ALA* 3.0 40.2 + - - +
446C LEU 4.6 3.4 - - - +
447C GLY* 4.4 6.1 - - - +
476C NA 3.4 11.4 - - - -
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Residues in contact with PRO 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLN* 3.5 36.7 - - - +
151C ARG* 4.2 15.9 - - + +
152C SER* 3.6 23.1 - - - +
155C THR* 4.5 4.7 - - + +
271C ARG 3.3 10.3 - - - +
272C ARG* 1.4 89.8 - - + +
274C ASP* 1.3 50.7 + - - +
276C LEU* 3.2 2.4 + - + -
277C GLU* 2.7 35.8 + - - +
444C LYS 5.9 0.2 - - - +
447C GLY* 4.1 20.2 - - - +
450C TRP* 5.6 2.2 - - + -
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Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C SER* 3.7 18.9 + - - +
272C ARG* 2.8 44.7 + - - +
273C PRO* 1.3 74.9 - - - +
275C ILE* 1.3 72.5 + - - +
277C GLU* 3.9 20.8 - - - +
278C ALA* 3.3 20.8 + - - +
361C ALA* 4.2 5.2 - - - +
476C NA 3.0 13.9 - - - -
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 3.7 34.8 - - + +
269C LEU* 3.8 28.3 - - + +
272C ARG* 3.2 13.6 + - + +
274C ASP* 1.3 90.5 + - - +
276C LEU* 1.3 58.1 + - - +
278C ALA* 3.3 1.9 + - - +
279C GLU 3.0 21.7 + - - -
358C TYR* 3.6 28.7 - - + -
361C ALA* 3.9 23.1 - - - +
362C ILE* 4.1 16.8 - - + -
365C ALA* 3.9 17.7 - - + -
476C NA 4.2 0.4 - - - -
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 4.7 0.4 - - - +
148C GLN* 3.4 27.6 - - + +
269C LEU 3.5 24.0 - - - +
270C GLN* 3.4 34.3 - - - +
271C ARG 4.5 5.6 - - - +
272C ARG 3.2 13.0 + - - +
273C PRO 3.2 7.0 + - - +
275C ILE* 1.3 75.9 - - - +
277C GLU* 1.3 63.2 + - - +
279C GLU* 3.7 19.5 - - - +
280C HIS* 3.0 40.1 + - + +
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ALA* 3.3 32.1 - - + +
148C GLN* 3.8 12.2 - - + +
149C ALA* 3.6 28.6 - - - +
152C SER* 4.7 2.6 - - - -
273C PRO 2.7 19.5 + - - +
274C ASP* 3.9 21.8 - - - +
275C ILE 3.3 0.2 - - - -
276C LEU* 1.3 74.1 - - - +
278C ALA* 1.3 61.9 + - - +
280C HIS 3.4 0.3 + - - -
281C GLN* 3.2 25.7 + - + +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ASP 3.3 15.3 + - - +
275C ILE 3.3 4.9 + - - +
277C GLU* 1.3 77.0 - - - +
279C GLU* 1.3 60.2 + - - +
281C GLN* 3.4 8.4 + - - +
282C LEU* 3.0 26.0 + - - +
354C ASN* 4.7 3.1 - - - +
357C GLN* 4.6 4.9 - - + +
358C TYR* 3.9 29.9 - - + +
361C ALA* 4.3 8.3 - - + -
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 2.9 32.7 + - + +
9C ARG* 2.8 43.9 + - - +
269C LEU 4.6 1.6 - - - +
275C ILE 3.0 16.9 + - - +
276C LEU* 3.7 21.6 - - - +
277C GLU 3.3 0.2 - - - -
278C ALA* 1.3 74.0 - - - +
280C HIS* 1.3 63.5 + - + +
282C LEU* 3.1 7.7 + - + +
283C MET* 2.9 36.0 + - - +
358C TYR* 3.7 20.2 + - + -
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Residues in contact with HIS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 2.8 42.4 + - - +
144C LEU* 3.6 30.6 - - + +
145C ALA* 3.6 21.5 - - + +
148C GLN* 4.1 19.9 + - + +
276C LEU* 3.0 38.0 + - + +
279C GLU* 1.3 80.4 + - + +
281C GLN* 1.3 55.3 + - - +
283C MET* 3.4 12.1 + - + -
284C ALA* 3.1 19.2 + - - +
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Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C PHE* 6.0 3.0 - - - -
142C GLN* 4.2 28.9 + - - +
145C ALA* 3.8 16.6 - - + +
146C THR* 5.6 1.0 + - - -
277C GLU* 3.2 22.3 + - + +
278C ALA* 3.7 10.5 - - - +
279C GLU 3.2 0.4 - - - -
280C HIS* 1.3 72.7 - - - +
282C LEU* 1.3 64.9 + - - +
284C ALA* 3.3 6.7 + - - +
285C ALA* 3.2 17.2 + - - +
354C ASN* 3.7 22.3 + - - +
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 4.0 20.6 - - + +
8C GLN 5.4 0.2 - - - +
10C PRO* 3.7 36.3 - - + -
278C ALA 3.0 13.4 + - - +
279C GLU* 3.3 8.3 - - - +
281C GLN* 1.3 75.6 - - - +
283C MET* 1.3 57.8 + - - +
285C ALA* 3.5 2.1 + - - +
286C ASN* 3.1 24.8 + - - +
351C LYS* 3.4 38.6 - - + +
354C ASN* 3.7 18.3 + - + +
355C VAL* 3.6 16.8 - - + +
358C TYR* 4.3 12.6 - - + -
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Residues in contact with MET 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 3.9 42.8 - - + -
141C GLU* 3.3 47.3 - - + +
279C GLU* 2.9 26.9 + - - +
280C HIS* 3.6 15.7 - - + +
282C LEU* 1.3 75.4 - - - +
284C ALA* 1.3 62.6 + - - +
286C ASN* 3.5 9.1 + - - +
287C ALA* 3.2 22.2 + - - +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLN* 3.2 47.9 - - + +
141C GLU* 3.7 10.7 - - + +
142C GLN* 3.8 20.0 - - + +
280C HIS 3.1 13.9 + - - +
281C GLN* 3.5 13.7 - - - +
282C LEU 3.2 0.4 - - - -
283C MET* 1.3 74.5 - - - +
285C ALA* 1.3 63.4 + - - +
287C ALA* 3.5 1.2 + - - +
288C SER* 3.3 10.6 + - - -
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLN* 5.3 1.3 - - - +
281C GLN 3.2 3.5 + - - +
282C LEU 3.7 7.6 - - - +
283C MET 3.4 0.2 - - - -
284C ALA* 1.3 74.7 - - - +
286C ASN* 1.3 63.6 + - - +
288C SER* 2.6 26.4 + - - +
289C ILE* 3.4 11.5 + - - +
347C ALA 4.3 1.7 - - - +
350C GLN* 3.8 14.4 - - + +
351C LYS* 3.8 13.7 - - - +
354C ASN* 3.3 29.8 - - - +
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Residues in contact with ASN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.5 11.9 - - - +
5C PRO* 2.8 48.3 + - - +
7C TYR* 3.9 23.3 - - + +
282C LEU 3.1 15.0 + - - +
283C MET* 3.6 12.5 + - - +
284C ALA 3.3 0.2 - - - -
285C ALA* 1.3 76.3 - - - +
287C ALA* 1.3 61.3 + - - +
289C ILE* 3.3 22.4 + - - +
351C LYS* 2.8 38.3 + - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.8 17.1 - - + +
134C SER* 3.3 25.1 - - - +
137C ASP* 4.0 12.1 - - + +
138C GLN* 3.7 27.4 - - - +
141C GLU* 5.7 0.4 - - + -
283C MET 3.2 13.7 + - - +
284C ALA 3.7 7.0 - - - +
285C ALA 3.3 0.2 - - - -
286C ASN* 1.3 76.9 - - - +
288C SER* 1.3 62.1 + - - +
290C GLY* 3.1 11.3 + - - -
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER 5.1 0.2 - - - -
135C LEU* 5.4 1.3 - - - -
138C GLN* 3.4 36.5 - - - +
284C ALA 3.3 4.7 + - - -
285C ALA* 2.6 24.6 + - - +
287C ALA* 1.3 75.3 - - - +
289C ILE* 1.3 63.1 + - - +
291C ALA* 3.3 11.6 + - - +
292C ALA* 3.2 20.4 + - - +
347C ALA* 4.1 15.9 + - - +
350C GLN* 5.4 2.6 - - - +
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.7 20.2 - - + -
285C ALA 3.6 11.9 - - - +
286C ASN* 3.3 9.4 + - - +
287C ALA 3.2 0.2 - - - -
288C SER* 1.3 78.0 + - - +
290C GLY* 1.3 57.3 + - - +
292C ALA* 3.1 3.1 + - - +
293C ARG* 3.0 53.4 + - - +
344C LEU* 4.0 12.8 - - + -
347C ALA* 3.6 30.7 - - + +
348C LYS* 4.1 15.9 - - + +
351C LYS* 3.8 31.6 - - + +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.7 14.0 - - - +
4C ILE* 3.7 27.2 - - - +
129C PHE 4.7 0.5 - - - +
130C GLY 4.1 1.0 - - - +
134C SER* 3.4 13.8 + - - -
286C ASN 3.8 2.0 + - - -
287C ALA 3.1 11.3 + - - -
289C ILE* 1.3 79.2 - - - +
291C ALA* 1.3 56.9 + - - +
293C ARG 4.0 0.2 - - - -
294C ALA* 3.3 24.6 + - - +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ARG* 3.6 39.0 - - + +
134C SER* 3.6 11.6 - - - -
135C LEU* 3.8 25.4 - - + -
287C ALA 4.6 0.2 - - - +
288C SER* 3.3 11.5 + - - +
289C ILE 3.1 0.6 - - - -
290C GLY* 1.3 76.1 - - - +
292C ALA* 1.3 63.3 + - - +
293C ARG 3.2 0.7 - - - -
294C ALA 3.5 1.0 + - - -
295C ALA* 3.4 18.5 + - - +
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C SER 3.2 9.2 + - - +
289C ILE 3.1 8.7 + - - +
291C ALA* 1.3 78.6 - - - +
293C ARG* 1.3 59.5 + - - +
295C ALA* 3.5 16.6 - - - +
296C PHE* 3.7 15.2 - - - -
340C LEU 4.8 2.1 - - - +
343C SER* 3.7 29.0 - - - +
344C LEU* 3.9 15.7 - - + +
347C ALA* 4.1 8.1 - - + -
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 3.0 46.6 + - + +
4C ILE 4.5 0.2 - - - -
5C PRO* 3.5 32.6 - - - +
289C ILE* 3.0 27.8 + - - +
290C GLY 4.1 0.2 - - - +
292C ALA* 1.3 74.1 - - - +
294C ALA* 1.3 57.6 + - - +
295C ALA 3.0 9.4 + - - -
296C PHE* 3.2 20.7 + - + +
297C PHE* 3.3 15.8 - - + -
344C LEU* 3.6 22.1 - - + +
348C LYS* 4.4 16.0 - - - +
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 3.6 8.2 - - + +
129C PHE* 3.4 31.5 - - + +
131C ARG* 3.7 30.1 - - + +
290C GLY 3.3 15.8 + - - +
291C ALA 3.5 1.9 + - - +
293C ARG* 1.3 75.5 - - - +
295C ALA* 1.3 61.5 + - - +
296C PHE 3.3 0.4 - - - -
297C PHE* 3.4 22.8 + - - +
298C PRO 5.2 0.9 - - - +
299C SER* 6.2 0.3 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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