Contacts of the helix formed by residues 267 - 291 (chain C) in PDB entry 2H63
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 SER 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C GLN 4.2 0.2 + - - -
266C PHE* 1.3 72.8 - - - +
268C GLU* 1.3 65.4 + - - +
269C LYS* 3.5 10.1 + - - +
270C GLU* 3.0 40.2 + - - +
271C LEU* 3.0 28.8 + - - +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C SER* 1.3 70.5 - - - +
269C LYS* 1.3 67.6 + - - +
270C GLU 3.0 0.5 + - - -
271C LEU* 3.1 8.5 + - - +
272C ALA* 2.8 27.2 + - - +
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Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C SER* 3.3 10.8 + - - +
268C GLU* 1.3 77.6 - - - +
270C GLU* 1.3 56.9 + - + +
272C ALA* 3.5 6.4 - - - +
273C ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C GLN 4.7 0.3 - - - +
266C PHE* 3.3 28.7 - - + -
267C SER* 3.0 37.5 + - - +
268C GLU 3.1 0.2 - - - -
269C LYS* 1.3 74.9 - - + +
271C LEU* 1.3 65.2 + - - +
273C ALA* 3.2 8.3 + - - +
274C GLU* 3.1 22.6 + - - +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C TRP* 5.4 2.8 - - - -
261C LYS* 3.7 38.1 - - + -
264C GLY* 6.4 0.9 - - - -
266C PHE* 3.9 30.7 - - + +
267C SER 3.0 19.9 + - - +
268C GLU* 3.8 5.6 - - - +
270C GLU* 1.3 73.7 - - - +
272C ALA* 1.3 61.8 + - - +
274C GLU* 3.4 8.9 + - - +
275C LYS* 3.1 22.9 + - - +
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Residues in contact with ALA 272 (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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268C GLU 2.8 19.0 + - - +
269C LYS* 3.5 6.3 - - - +
271C LEU* 1.3 73.6 - - - +
273C ALA* 1.3 68.2 + - - +
274C GLU 3.1 0.3 + - - -
275C LYS* 3.2 6.6 + - - +
276C LYS* 2.9 24.6 + - - +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS 3.0 15.2 + - - +
270C GLU* 3.2 10.3 + - - +
272C ALA* 1.3 75.5 - - - +
274C GLU* 1.3 56.7 + - - +
276C LYS* 3.4 9.9 + - - +
277C ARG* 3.1 27.2 + - - +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C TRP* 5.7 3.9 - - + -
122C HIS* 4.2 8.5 - - - -
123C GLU 4.4 4.9 + - - +
125C HIS* 5.3 0.5 - - - -
257C ILE* 5.4 2.2 - - - +
261C LYS* 2.7 37.9 + - - -
270C GLU 3.1 12.5 + - - +
271C LEU* 3.7 11.8 - - - +
272C ALA 3.1 0.2 - - - -
273C ALA* 1.3 73.6 - - - +
275C LYS* 1.3 66.0 + - - +
277C ARG* 3.1 32.6 + - - +
278C ILE* 2.9 42.8 + - + +
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Residues in contact with LYS 275 (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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111C TRP* 3.9 40.6 - - + -
271C LEU 3.1 14.2 + - - +
272C ALA* 3.7 8.7 - - - +
274C GLU* 1.3 75.1 - - - +
276C LYS* 1.3 64.2 + - - +
278C ILE* 3.1 2.9 + - - +
279C LEU* 3.0 35.3 + - + +
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLU* 3.4 33.3 + - - +
272C ALA 2.9 12.9 + - - +
273C ALA* 3.5 11.9 - - - +
275C LYS* 1.3 76.4 - - - +
277C ARG* 1.3 58.9 - - - +
279C LEU* 3.5 6.9 + - - +
280C HIS* 2.9 27.0 + - - +
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Residues in contact with ARG 277 (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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125C HIS* 3.8 28.5 + - - +
128C LEU* 3.7 21.7 - - - +
174C THR* 3.3 22.0 + - - +
177C VAL* 4.3 19.7 - - + -
178C SER* 3.7 23.0 + - - +
182C GLU* 4.6 3.8 - - - -
273C ALA 3.1 14.0 + - - +
274C GLU* 3.1 37.0 + - - +
276C LYS* 1.3 73.7 - - - +
278C ILE* 1.3 79.6 + - - +
280C HIS* 3.2 8.3 + - - +
281C CYS* 3.1 24.4 + - - -
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Residues in contact with ILE 278 (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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100C MET* 4.3 9.2 - - - -
111C TRP* 3.8 27.6 - - + +
123C GLU* 3.1 46.8 - - + +
125C HIS* 4.2 2.9 - - + +
274C GLU* 2.9 39.1 + - + +
275C LYS* 3.7 4.5 - - - +
277C ARG* 1.3 98.3 - - - +
279C LEU* 1.3 58.4 + - - +
281C CYS* 3.2 5.2 + - - +
282C LEU* 3.0 44.1 + - + +
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Residues in contact with LEU 279 (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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104C LEU* 3.7 21.3 - - + +
107C ALA* 3.8 28.9 - - + -
108C GLN* 4.3 20.9 - - + +
111C TRP* 4.0 24.2 - - + +
275C LYS* 3.0 28.5 + - + +
276C LYS* 3.9 5.2 - - - +
278C ILE* 1.3 72.9 - - - +
280C HIS* 1.3 64.6 + - - +
282C LEU* 4.4 4.0 - - + +
283C GLY* 2.8 23.4 + - - -
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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
----------------------------------------------------------
177C VAL* 4.3 21.1 - - + -
182C GLU* 3.1 54.4 + - + +
183C LEU* 3.0 39.6 + - - -
276C LYS* 2.9 14.8 + - + +
277C ARG* 3.2 6.7 + - - +
279C LEU* 1.3 75.0 - - - +
281C CYS* 1.3 56.4 + - - +
283C GLY* 3.6 1.4 + - - -
284C LEU* 3.1 36.5 + - + +
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Residues in contact with CYS 281 (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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125C HIS* 6.4 0.4 - - + -
170C ILE* 3.7 21.2 - - + +
173C LEU* 3.8 13.2 - - + +
174C THR* 3.8 22.9 - - - +
177C VAL* 3.8 35.4 - - - -
277C ARG* 3.1 22.1 + - - +
278C ILE* 3.5 8.3 - - - +
280C HIS* 1.3 72.8 - - - +
282C LEU* 1.3 66.3 + - - +
283C GLY 3.1 1.3 - - - -
284C LEU* 3.1 3.5 + - - +
285C ALA* 2.9 23.4 + - - +
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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
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99C PRO* 4.6 4.3 - - + -
100C MET* 4.0 8.5 - - + -
101C THR* 4.0 22.7 - - - +
103C SER 5.2 0.4 - - - +
104C LEU* 4.4 16.9 + - + +
107C ALA* 3.4 32.3 - - + -
123C GLU* 4.0 14.8 - - - +
167C PHE* 4.0 9.4 - - + -
170C ILE* 3.7 21.5 - - + +
278C ILE* 3.0 36.8 + - + +
279C LEU* 3.9 8.3 - - + +
281C CYS* 1.3 75.2 - - - +
283C GLY* 1.3 63.5 + - - +
285C ALA* 3.2 5.1 + - - +
286C GLU* 3.0 21.4 + - - +
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Residues in contact with GLY 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.9 19.8 - - - +
279C LEU 2.8 17.6 + - - -
280C HIS 3.8 2.0 - - - -
282C LEU* 1.3 76.0 - - - +
284C LEU* 1.3 56.7 + - - +
286C GLU* 3.1 9.3 + - - +
287C GLU* 2.8 29.5 + - - +
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Residues in contact with LEU 284 (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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173C LEU* 3.8 29.4 - - + -
177C VAL* 4.8 2.0 - - + -
183C LEU* 3.6 42.6 - - + +
184C SER* 4.6 6.7 - - - -
185C LEU* 4.6 13.5 - - + +
205C LEU* 4.4 9.2 - - + -
280C HIS* 3.1 30.6 + - + +
281C CYS 3.1 7.9 + - - +
283C GLY* 1.3 71.7 - - - +
285C ALA* 1.3 57.4 + - - +
287C GLU* 3.2 7.4 + - + +
288C ILE* 2.8 44.7 + - + +
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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
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166C ALA* 3.8 30.1 - - + +
167C PHE* 3.4 34.3 - - + -
170C ILE* 4.2 5.4 - - + -
173C LEU* 4.5 3.2 - - + +
281C CYS 2.9 13.0 + - - +
282C LEU 3.4 9.2 - - - +
284C LEU* 1.3 74.8 - - - +
286C GLU* 1.3 57.0 + - - +
288C ILE* 3.5 3.8 + - - +
289C GLN* 2.9 28.4 + - - +
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Residues in contact with GLU 286 (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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103C SER* 5.7 1.6 - - - -
104C LEU* 5.0 14.1 - - + +
167C PHE* 3.6 12.5 - - + -
282C LEU 3.0 12.9 + - - +
283C GLY* 3.3 10.8 - - - +
285C ALA* 1.3 73.0 - - - +
287C GLU* 1.3 66.7 + - - +
289C GLN* 3.0 6.5 + - - +
290C LYS* 2.9 28.2 + - + +
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Residues in contact with GLU 287 (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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185C LEU* 3.4 26.6 - - + +
283C GLY 2.8 19.3 + - - +
284C LEU* 3.9 9.9 - - + +
286C GLU* 1.3 71.6 - - - +
288C ILE* 1.3 60.5 + - - +
290C LYS* 3.4 15.3 - - + +
291C TYR* 3.2 17.3 + - - +
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Residues in contact with ILE 288 (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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164C PHE* 4.4 7.8 - - + -
166C ALA* 4.4 5.4 - - + -
173C LEU* 5.6 0.2 - - + -
185C LEU* 3.8 22.0 - - + -
188C ALA* 3.6 20.0 - - + +
201C MET* 4.3 14.4 - - + -
203C VAL* 3.4 39.7 - - + -
205C LEU* 4.6 5.2 - - + -
215C TRP* 3.7 22.7 - - + -
284C LEU* 2.8 30.7 + - + +
285C ALA* 3.7 4.9 - - - +
287C GLU* 1.3 69.6 - - - +
289C GLN* 1.3 66.2 + - - +
291C TYR* 3.2 19.1 + - - +
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Residues in contact with GLN 289 (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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102C LEU 4.8 3.5 - - - +
164C PHE* 3.5 49.4 - - + +
167C PHE* 3.0 25.8 - - - -
285C ALA 2.9 16.0 + - - +
286C GLU* 3.0 6.0 + - - +
288C ILE* 1.3 75.4 - - - +
290C LYS* 1.3 66.9 + - - +
291C TYR 4.1 2.6 - - - +
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLU* 2.9 15.2 + - + +
287C GLU* 3.4 17.9 - - + +
289C GLN* 1.3 77.8 - - - +
291C TYR* 1.3 67.7 + - - +
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Residues in contact with TYR 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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185C LEU* 4.7 8.5 - - + -
187C SER* 5.5 2.0 - - - -
188C ALA* 4.0 33.6 - - + +
287C GLU 3.2 10.6 + - - +
288C ILE 3.2 15.7 + - - +
289C GLN 4.1 2.6 - - - +
290C LYS* 1.3 85.1 - - - +
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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
------------------------------------------------------------
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