Contacts of the helix formed by residues 240 - 262 (chain C) in PDB entry 1QK1
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 ASN 240 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLY 3.6 11.0 + - - -
115C TYR* 3.9 35.8 - - + +
118C GLU* 5.3 0.4 - - - +
124C SER* 4.2 1.8 + - - -
236C GLU* 3.8 17.4 + - - +
237C LYS 6.1 0.2 - - - +
238C GLY* 3.8 1.8 - - - -
239C GLY* 1.3 75.2 - - - +
241C MET* 1.3 62.9 + - - +
242C LYS* 3.7 6.5 - - - +
243C ARG* 3.0 54.1 + - - +
244C VAL* 3.1 16.9 + - - +
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLY 3.0 7.4 + - - +
116C PHE* 3.6 21.5 - - + -
124C SER* 4.2 12.1 + - - +
125C ARG 4.2 2.0 - - - +
126C VAL* 3.8 23.6 - - - -
239C GLY 3.0 9.1 + - - -
240C ASN* 1.3 71.6 - - - +
242C LYS* 1.3 57.9 + - - +
244C VAL* 3.1 8.4 + - - +
245C PHE* 2.9 29.0 + - - +
288C ALA* 4.5 3.1 - - + -
289C GLY* 3.5 39.9 - - - +
290C VAL* 4.0 12.3 - - + -
345C VAL* 4.2 13.0 - - + +
348C VAL* 4.4 11.2 - - + -
349C ILE* 4.0 22.9 - - + -
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Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA 3.7 17.0 + - - -
109C SER* 4.7 5.3 + - - +
111C ILE* 3.2 39.1 + - + -
112C ARG* 5.4 0.2 - - - +
113C SER 3.6 17.5 - - - +
114C GLY* 3.0 18.0 + - - +
240C ASN* 3.8 6.7 - - - +
241C MET* 1.3 78.9 - - - +
243C ARG* 1.3 57.6 + - - +
245C PHE* 3.4 4.8 + - - +
246C GLU* 3.0 59.0 + - + +
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Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 5.9 0.8 + - - -
236C GLU* 2.7 40.9 + - - +
237C LYS 5.4 2.0 + - - -
240C ASN* 3.0 35.9 + - - +
242C LYS* 1.3 77.5 - - - +
244C VAL* 1.3 67.0 + - - +
246C GLU* 3.3 15.5 + - + +
247C ARG* 3.1 31.2 + - + +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C SER* 4.0 16.8 - - - +
125C ARG* 4.2 4.5 - - - -
126C VAL* 3.9 19.3 - - + +
234C SER* 2.8 52.8 + - - +
236C GLU* 3.7 33.7 - - + +
240C ASN 3.1 13.2 + - - +
241C MET* 3.4 11.0 - - - +
243C ARG* 1.3 78.3 - - - +
245C PHE* 1.3 57.8 + - - +
247C ARG* 4.1 6.5 - - - +
248C PHE* 3.0 15.6 + - - +
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Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP 4.8 0.2 - - - -
106C LEU* 5.0 0.2 - - + -
108C ALA* 4.0 17.7 - - + -
111C ILE* 3.8 26.9 - - + -
126C VAL* 4.4 10.1 - - + -
241C MET 2.9 15.5 + - - +
242C LYS* 3.8 5.8 - - - +
244C VAL* 1.3 78.2 - - - +
246C GLU* 1.3 63.3 + - - +
248C PHE* 3.3 25.4 + + + +
249C CYS* 3.0 47.7 + - - -
286C LEU* 4.6 1.8 - - + -
341C GLU* 4.0 24.9 - - + -
342C VAL* 4.2 14.1 - - + -
345C VAL* 3.6 36.8 - - + -
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA* 3.7 26.2 - - + +
109C SER* 5.2 2.3 + - - -
242C LYS* 3.0 51.9 + - + +
243C ARG* 3.3 15.9 + - + +
245C PHE* 1.3 75.7 - - - +
247C ARG* 1.3 59.2 + - - +
249C CYS* 3.3 2.4 + - - +
250C ARG* 2.9 37.2 + - - +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASP* 4.5 12.1 + - - -
164C LEU* 4.4 13.9 - - + +
215C ASN* 4.5 7.0 - - - +
217C GLU* 4.3 7.7 + - - -
219C SER* 3.2 39.2 + - - -
220C PHE* 4.2 8.6 - - + -
234C SER* 3.5 11.9 + - - +
235C MET 3.2 26.3 + - - -
236C GLU* 3.1 32.5 + - - +
243C ARG* 3.1 24.4 + - + +
244C VAL* 3.8 6.9 - - - +
246C GLU* 1.3 76.2 - - - +
248C PHE* 1.3 57.4 - - - +
250C ARG* 3.8 17.5 - - - +
251C GLY* 2.8 29.6 + - - -
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Residues in contact with PHE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.3 8.7 - - + -
126C VAL* 3.6 38.6 - - + -
128C THR* 3.5 37.9 - - + -
130C ARG* 5.5 0.7 - - - -
220C PHE* 4.3 5.4 - - - -
232C VAL* 4.1 14.4 - - + -
234C SER* 3.8 14.8 + - - -
244C VAL 3.0 16.1 + - - +
245C PHE* 3.3 31.0 - + - +
247C ARG* 1.3 76.8 - - - +
249C CYS* 1.3 64.5 + - - +
251C GLY* 4.0 0.5 - - - -
252C LEU* 3.1 43.3 + - + +
286C LEU* 3.8 19.1 - - + -
341C GLU* 5.9 0.2 - - - -
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Residues in contact with CYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.3 43.3 - - + +
108C ALA* 4.1 10.1 - - + +
245C PHE* 3.0 55.5 + - - +
246C GLU 3.9 2.9 - - - +
248C PHE* 1.3 75.8 - - - +
250C ARG* 1.3 66.0 + - - +
252C LEU* 3.5 4.8 + - - +
253C LYS* 3.2 32.8 + - - +
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASP* 2.5 44.9 + - - -
164C LEU* 4.3 18.5 - - + +
246C GLU* 2.9 24.3 + - - +
247C ARG* 3.8 24.1 - - - +
249C CYS* 1.3 76.4 - - - +
251C GLY* 1.3 64.2 + - - +
253C LYS* 3.4 7.2 + - - +
254C GLU* 3.1 26.4 + - + +
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Residues in contact with GLY 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LEU* 5.1 0.4 - - - +
164C LEU* 3.8 20.5 - - - +
220C PHE* 3.7 21.8 - - - -
247C ARG 2.8 17.4 + - - -
250C ARG* 1.3 77.6 - - - +
252C LEU* 1.3 55.1 + - - +
254C GLU* 3.4 1.6 + - - +
255C VAL* 3.0 35.3 + - - +
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Residues in contact with LEU 252 (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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106C LEU* 4.6 14.6 - - + -
128C THR* 4.1 2.7 - - + -
130C ARG* 3.6 41.3 - - + +
220C PHE* 4.3 0.4 - - - -
232C VAL* 4.1 33.7 - - + -
248C PHE* 3.1 54.6 + - + +
249C CYS* 4.0 4.7 - - - +
251C GLY* 1.3 76.3 - - - +
253C LYS* 1.3 58.2 + - - +
255C VAL* 3.4 6.7 + - + +
256C GLU* 3.0 30.0 + - - +
266C PHE* 4.6 9.2 - - + -
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Residues in contact with LYS 253 (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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106C LEU* 3.1 49.2 + - + -
107C ASP* 4.4 7.3 + - - +
249C CYS* 3.2 19.9 + - - +
250C ARG* 3.9 5.4 - - - +
251C GLY 3.3 0.2 - - - -
252C LEU* 1.3 72.8 - - - +
254C GLU* 1.3 61.4 + - - +
256C GLU* 3.6 11.1 + - - +
257C ARG* 3.0 28.9 + - - +
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Residues in contact with GLU 254 (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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160C LEU* 3.6 25.4 - - + -
161C LYS 5.9 0.7 - - - +
164C LEU* 4.4 11.4 - - + -
250C ARG* 3.1 18.4 + - + +
251C GLY 3.7 4.7 - - - +
252C LEU 3.2 0.2 - - - -
253C LYS* 1.3 77.9 - - - +
255C VAL* 1.3 64.1 + - - +
257C ARG* 2.3 45.3 + - - +
258C LEU* 3.0 31.6 + - + +
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Residues in contact with VAL 255 (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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153C VAL* 6.2 2.9 - - + -
156C ALA* 4.8 5.2 - - + -
157C LEU* 4.0 28.0 - - + -
160C LEU* 4.3 15.9 - - + -
220C PHE* 5.0 2.5 - - + -
222C ILE* 4.7 11.0 - - + -
232C VAL* 6.5 0.7 - - + -
251C GLY 3.0 22.6 + - - +
252C LEU* 3.8 8.5 - - + +
254C GLU* 1.3 77.3 - - - +
256C GLU* 1.3 62.5 + - - +
258C LEU* 3.3 8.8 + - + +
259C ILE* 3.1 32.6 + - + +
266C PHE* 4.4 16.2 - - + -
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Residues in contact with GLU 256 (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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106C LEU* 6.0 1.9 - - - +
252C LEU 3.0 18.7 + - - +
253C LYS* 3.9 10.4 - - - +
255C VAL* 1.3 74.0 - - - +
257C ARG* 1.3 64.8 + - - +
259C ILE* 3.4 9.3 + - + +
260C GLN* 3.0 55.6 + - + +
266C PHE* 3.6 39.5 + - + +
274C TYR* 4.8 9.9 + - - -
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Residues in contact with ARG 257 (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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159C GLY 5.5 1.6 + - - -
253C LYS 3.0 18.1 + - - +
254C GLU* 2.3 39.2 + - - +
256C GLU* 1.3 76.7 - - - +
258C LEU* 1.3 84.4 + - - +
260C GLN* 3.3 11.1 + - - +
261C GLU* 3.1 49.2 + - - +
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Residues in contact with LEU 258 (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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156C ALA* 3.2 38.5 - - + +
159C GLY* 3.8 27.8 - - - +
160C LEU* 3.9 15.3 - - + -
254C GLU* 3.0 17.8 + - - +
255C VAL* 3.7 5.4 - - - +
256C GLU 3.3 0.2 - - - -
257C ARG* 1.3 107.4 - - - +
259C ILE* 1.3 61.8 + - - +
261C GLU* 3.5 28.2 - - - +
262C ARG* 3.9 10.6 + - - +
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Residues in contact with ILE 259 (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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132C ILE* 4.2 12.8 - - + -
152C VAL* 4.3 18.2 - - + +
153C VAL* 5.3 3.1 - - + -
156C ALA* 3.5 24.5 - - + -
255C VAL* 3.1 14.2 + - + +
256C GLU* 3.4 12.6 - - + +
258C LEU* 1.3 74.2 - - - +
260C GLN* 1.3 67.6 + - + +
261C GLU 3.1 0.7 - - - -
262C ARG* 3.1 13.9 + - - +
263C GLY 3.4 0.2 + - - -
264C TRP* 3.0 43.7 + - + +
265C GLU* 4.2 11.0 - - - -
266C PHE* 3.7 36.3 - - + +
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Residues in contact with GLN 260 (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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15A TYR* 6.0 0.2 - - - -
31A PRO* 5.9 0.9 - - - +
256C GLU* 3.0 43.0 + - + +
257C ARG* 3.3 8.3 + - - +
259C ILE* 1.3 76.8 - - + +
261C GLU* 1.3 63.5 + - - +
263C GLY* 3.1 12.7 + - - -
264C TRP 3.3 17.0 - - - +
265C GLU* 4.3 24.8 + - + +
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Residues in contact with GLU 261 (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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17A ASP* 5.0 1.6 - - - +
19A ARG* 3.4 59.4 + - + +
257C ARG* 3.1 39.8 + - - +
258C LEU* 3.5 26.1 - - - +
259C ILE 3.1 0.2 - - - -
260C GLN* 1.3 79.2 - - - +
262C ARG* 1.3 61.0 + - + +
263C GLY 3.6 0.5 + - - -
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Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 4.7 5.4 - - - +
15A TYR* 5.0 4.7 - - - +
17A ASP* 4.3 18.1 + - - +
19A ARG* 3.8 34.8 - - - +
155C ASP* 5.5 14.5 + - + +
258C LEU 4.0 12.1 - - - +
259C ILE* 3.1 9.6 + - - +
260C GLN 3.1 0.4 - - - -
261C GLU* 1.3 79.6 + - + +
263C GLY* 1.3 57.6 + - - +
264C TRP* 3.4 23.8 + - + +
147E ARG* 5.0 20.7 + - - +
170E ARG* 6.1 1.4 - - - +
208E ASP* 5.6 1.6 + - - -
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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