Contacts of the helix formed by residues 240 - 262 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLY 3.6 9.3 + - - -
115D TYR* 3.9 36.3 + - + +
118D GLU* 5.3 0.9 - - - +
124D SER* 4.2 2.1 + - - -
236D GLU* 3.8 16.7 + - - +
237D LYS 5.3 0.2 + - - -
238D GLY 3.8 1.6 - - - -
239D GLY* 1.3 74.8 - - - +
241D MET* 1.3 63.3 + - - +
242D LYS* 3.7 6.9 - - - +
243D ARG* 3.0 55.3 + - - +
244D VAL* 3.1 17.4 + - - +
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLY 3.0 7.9 + - - +
116D PHE* 3.6 21.5 - - + -
124D SER* 4.1 13.0 + - - +
125D ARG 4.3 1.8 - - - +
126D VAL* 3.8 24.0 - - - -
239D GLY 2.9 8.7 + - - -
240D ASN* 1.3 71.8 - - - +
242D LYS* 1.3 57.7 + - - +
244D VAL* 3.1 8.4 + - - +
245D PHE* 2.8 27.9 + - - +
288D ALA* 4.5 3.1 - - + -
289D GLY* 3.5 39.7 - - - +
290D VAL* 4.0 11.9 - - + -
345D VAL* 4.2 12.8 - - + +
348D VAL* 4.4 11.2 - - + -
349D ILE* 4.0 23.6 - - + -
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA 3.7 16.2 + - - -
109D SER* 4.7 5.8 + - - +
111D ILE* 3.3 38.2 + - + -
113D SER 3.7 11.9 - - - +
114D GLY* 3.0 24.3 + - - +
240D ASN* 3.1 7.4 - - - +
241D MET* 1.3 77.6 - - - +
243D ARG* 1.3 58.7 + - - +
245D PHE* 3.3 6.1 + - - +
246D GLU* 3.0 59.4 + - + +
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TYR* 5.8 1.6 + - - -
236D GLU* 2.8 38.7 + - - +
237D LYS 5.5 1.6 + - - -
240D ASN* 3.0 37.8 + - - +
242D LYS* 1.3 76.2 - - - +
244D VAL* 1.3 66.5 + - - +
246D GLU* 3.2 16.6 + - + +
247D ARG* 3.1 32.2 + - + +
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D SER* 3.9 17.0 - - - +
125D ARG* 4.2 4.3 - - - +
126D VAL* 3.9 20.6 - - + +
234D SER* 2.8 51.0 + - - +
236D GLU* 3.7 35.0 - - + +
240D ASN 3.1 12.9 + - - +
241D MET* 3.4 10.8 - - - +
243D ARG* 1.3 77.9 - - - +
245D PHE* 1.3 57.5 + - - +
247D ARG* 3.5 6.4 + - - +
248D PHE* 3.1 14.9 + - - +
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Residues in contact with PHE 245 (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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105D ASP 4.7 0.2 - - - -
108D ALA* 3.9 17.7 - - + -
111D ILE* 3.7 26.9 - - + -
126D VAL* 4.4 9.0 - - + -
241D MET 2.8 17.4 + - - +
242D LYS* 3.8 6.3 - - - +
244D VAL* 1.3 78.2 - - - +
246D GLU* 1.3 64.2 + - - +
248D PHE* 3.3 32.2 - + + +
249D CYS* 3.0 42.0 + - - -
286D LEU* 4.6 1.6 - - + -
341D GLU* 4.0 24.7 - - + -
342D VAL* 4.2 13.9 - - + -
345D VAL* 3.6 35.7 - - + -
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA* 3.7 26.5 - - + +
109D SER* 5.2 2.1 - - - -
242D LYS* 3.0 51.5 + - + +
243D ARG* 3.2 18.2 + - + +
245D PHE* 1.3 73.0 - - - +
247D ARG* 1.3 60.5 + - - +
249D CYS* 3.4 1.9 + - - +
250D ARG* 2.9 38.4 + - - +
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ASP* 4.5 13.4 + - - -
164D LEU* 4.4 15.0 - - + +
215D ASN* 4.6 7.0 - - - +
217D GLU* 4.3 7.0 + - - -
219D SER* 3.2 38.0 + - - -
220D PHE* 4.2 7.7 - - + -
234D SER* 3.5 12.9 + - - +
235D MET 3.2 25.1 + - - -
236D GLU* 3.1 33.1 + - - +
243D ARG* 3.1 23.6 + - + +
244D VAL* 3.8 7.4 - - - +
246D GLU* 1.3 77.1 - - - +
248D PHE* 1.3 57.6 + - - +
250D ARG* 3.8 17.7 - - - +
251D GLY* 2.8 29.1 + - - -
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 4.3 9.0 - - + -
126D VAL* 3.7 39.3 - - + -
128D THR* 3.4 39.3 - - + -
130D ARG* 5.5 0.7 - - - -
220D PHE* 4.3 5.4 - - - -
232D VAL* 4.0 15.0 - - + -
234D SER* 3.8 15.4 + - - -
244D VAL 3.1 14.4 + - - +
245D PHE* 3.3 32.1 - + - +
247D ARG* 1.3 77.6 - - - +
249D CYS* 1.3 66.7 + - - +
251D GLY* 4.0 0.7 - - - -
252D LEU* 3.1 41.5 + - + +
286D LEU* 3.9 18.6 - - + -
341D GLU* 5.5 0.2 - - + -
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Residues in contact with CYS 249 (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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106D LEU* 3.2 46.2 - - + +
108D ALA* 4.1 9.4 - - + -
245D PHE* 3.0 53.9 + - - +
246D GLU 3.9 3.8 - - - +
248D PHE* 1.3 77.4 - - - +
250D ARG* 1.3 62.9 + - - +
252D LEU* 3.5 4.7 + - - +
253D LYS* 3.2 32.0 + - - +
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Residues in contact with ARG 250 (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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163D ASP* 2.6 44.1 + - - -
164D LEU* 4.3 18.7 - - + +
246D GLU* 2.9 24.2 + - - +
247D ARG* 3.8 23.6 - - - +
249D CYS* 1.3 76.1 - - - +
251D GLY* 1.3 63.7 + - - +
253D LYS* 3.4 7.6 + - - +
254D GLU* 3.1 25.3 + - + +
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Residues in contact with GLY 251 (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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160D LEU* 5.1 0.2 - - - +
164D LEU* 3.8 20.5 - - - +
220D PHE* 3.7 22.0 - - - -
247D ARG 2.8 16.4 + - - -
250D ARG* 1.3 76.6 - - - +
252D LEU* 1.3 57.8 + - - +
254D GLU* 3.3 1.4 + - - +
255D VAL* 2.9 34.4 + - - +
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Residues in contact with LEU 252 (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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106D LEU* 4.6 15.3 - - + -
128D THR* 4.0 2.0 - - + -
130D ARG* 3.6 42.6 - - + +
220D PHE* 4.3 0.4 - - - -
232D VAL* 4.1 33.7 - - + -
248D PHE* 3.1 51.9 + - + +
249D CYS* 4.0 4.3 - - - +
250D ARG 3.3 0.2 - - - -
251D GLY* 1.3 76.6 - - - +
253D LYS* 1.3 57.1 + - - +
255D VAL* 3.4 7.3 + - + +
256D GLU* 3.0 29.5 + - - +
266D PHE* 4.6 8.9 - - + -
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Residues in contact with LYS 253 (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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106D LEU* 3.1 48.0 + - + -
107D ASP* 4.4 7.7 + - - +
108D ALA 5.4 0.2 - - - +
249D CYS* 3.2 19.4 + - - +
250D ARG* 3.9 5.4 - - - +
252D LEU* 1.3 75.7 - - - +
254D GLU* 1.3 60.2 + - - +
256D GLU* 3.9 10.8 - - - +
257D ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 254 (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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159D GLY 5.6 0.5 - - - +
160D LEU* 3.6 25.1 - - + -
161D LYS 6.0 0.9 - - - +
164D LEU* 4.4 9.0 - - + -
250D ARG* 3.1 20.0 + - + +
251D GLY* 3.6 5.8 - - - +
252D LEU 3.3 0.2 - - - -
253D LYS* 1.3 77.4 - - - +
255D VAL* 1.3 62.7 + - - +
257D ARG* 2.3 45.4 + - - +
258D LEU* 3.1 31.0 + - + +
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Residues in contact with VAL 255 (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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153D VAL* 6.3 2.9 - - + -
156D ALA* 4.8 4.7 - - + -
157D LEU* 4.0 28.7 - - + -
160D LEU* 4.3 14.8 - - + -
220D PHE* 5.0 2.9 - - + -
222D ILE* 4.7 11.0 - - + -
251D GLY 2.9 22.2 + - - +
252D LEU* 3.8 8.7 - - + +
254D GLU* 1.3 75.9 - - - +
256D GLU* 1.3 64.4 + - - +
258D LEU* 3.3 9.3 + - + +
259D ILE* 3.1 31.3 + - + +
266D PHE* 4.4 15.9 - - + -
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Residues in contact with GLU 256 (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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106D LEU* 6.0 2.3 - - - +
252D LEU 3.0 18.9 + - - +
253D LYS* 3.9 11.0 - - - +
255D VAL* 1.3 73.3 - - - +
257D ARG* 1.3 65.0 + - - +
259D ILE* 3.4 9.9 + - + +
260D GLN* 2.9 53.7 + - + +
266D PHE* 3.6 39.1 + - + +
274D TYR* 4.9 9.8 + - - -
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Residues in contact with ARG 257 (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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159D GLY 5.5 1.8 + - - -
253D LYS 3.0 17.7 + - - +
254D GLU* 2.3 40.8 + - - +
256D GLU* 1.3 78.4 - - - +
258D LEU* 1.3 82.5 + - - +
260D GLN* 3.3 9.8 + - - +
261D GLU* 3.1 50.1 + - - +
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Residues in contact with LEU 258 (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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156D ALA* 3.3 38.7 - - + +
159D GLY* 3.8 26.9 - - - +
160D LEU* 3.9 15.3 - - + -
254D GLU* 3.1 18.6 + - - +
255D VAL* 3.7 5.8 - - - +
256D GLU 3.2 0.2 - - - -
257D ARG* 1.3 110.1 - - - +
259D ILE* 1.3 60.0 + - - +
261D GLU* 3.5 28.2 - - - +
262D ARG* 3.9 11.3 + - - +
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Residues in contact with ILE 259 (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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132D ILE* 4.2 13.0 - - + -
152D VAL* 4.4 17.7 - - + +
153D VAL* 5.3 3.4 - - + -
156D ALA* 3.5 25.8 - - + -
255D VAL* 3.1 16.4 + - + +
256D GLU* 3.4 13.0 - - + +
258D LEU* 1.3 76.8 - - - +
260D GLN* 1.3 67.7 + - + +
261D GLU 3.1 0.2 - - - -
262D ARG* 3.2 12.4 + - - +
263D GLY 3.4 0.2 + - - -
264D TRP* 3.0 44.2 + - + +
265D GLU* 4.1 11.0 - - - +
266D PHE* 3.7 36.1 - - + +
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Residues in contact with GLN 260 (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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256D GLU* 2.9 48.2 + - + +
257D ARG* 3.3 7.7 + - - +
259D ILE* 1.3 75.3 - - + +
261D GLU* 1.3 65.7 + - - +
263D GLY* 3.1 12.4 + - - -
264D TRP 3.3 16.6 - - - +
265D GLU* 4.3 25.6 + - - +
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Residues in contact with GLU 261 (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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17B ASP* 5.1 0.7 - - - +
19B ARG* 3.6 54.6 + - + +
257D ARG* 3.1 40.0 + - - +
258D LEU* 3.5 25.8 - - - +
259D ILE 3.1 0.2 - - - -
260D GLN* 1.3 79.3 - - - +
262D ARG* 1.3 63.4 + - + +
263D GLY 3.3 0.7 + - - -
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Residues in contact with ARG 262 (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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12B SER 4.7 5.9 - - - +
15B TYR* 5.0 4.7 - - - +
17B ASP* 4.3 17.8 + - - +
19B ARG* 3.9 34.2 - - - +
155D ASP* 5.3 15.4 + - + +
258D LEU 4.0 12.1 - - - +
259D ILE* 3.2 8.9 + - - +
260D GLN 3.1 0.4 - - - -
261D GLU* 1.3 81.2 + - + +
263D GLY* 1.3 57.8 + - - +
264D TRP* 3.4 24.1 + - + +
147F ARG* 5.1 18.0 - - - +
170F ARG* 6.1 1.6 - - - +
208F ASP* 5.6 1.8 + - - -
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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
------------------------------------------------------------
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