Contacts of the helix formed by residues 240 - 261 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLY 3.6 10.8 + - - -
115E TYR* 4.0 36.7 + - + +
118E GLU* 4.4 0.9 + - - +
124E SER* 4.2 1.2 + - - -
236E GLU* 3.8 16.7 + - - +
237E LYS 5.3 0.2 + - - -
238E GLY 3.8 1.2 - - - -
239E GLY* 1.3 74.4 - - - +
241E MET* 1.3 62.6 + - - +
242E LYS* 3.7 6.3 - - - +
243E ARG* 3.0 56.8 + - - +
244E VAL* 3.1 17.0 + - - +
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Residues in contact with MET 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLY 3.0 7.0 + - - +
116E PHE* 3.6 21.5 - - + -
124E SER* 4.2 12.5 + - - +
125E ARG 4.3 1.6 - - - +
126E VAL* 3.8 24.0 - - - -
239E GLY 2.9 9.3 + - - -
240E ASN* 1.3 70.6 - - - +
242E LYS* 1.3 57.7 + - - +
244E VAL* 3.1 8.0 + - - +
245E PHE* 2.8 28.3 + - - +
288E ALA* 4.5 2.7 - - + -
289E GLY* 3.5 37.0 - - - +
290E VAL* 4.0 14.8 - - + -
345E VAL* 4.2 14.6 - - + -
348E VAL* 4.4 11.9 - - + -
349E ILE* 4.0 20.2 - - + -
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Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ALA 3.8 15.5 + - - +
109E SER* 4.6 6.6 + - - +
111E ILE* 3.1 37.4 + - + -
113E SER 3.7 17.7 - - - +
114E GLY* 3.0 16.8 + - - +
240E ASN* 3.8 6.3 - - - +
241E MET* 1.3 78.1 - - - +
243E ARG* 1.3 57.3 + - - +
245E PHE* 3.3 6.4 + - - +
246E GLU* 3.0 60.3 + - + +
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Residues in contact with ARG 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E TYR* 5.8 1.6 + - - -
236E GLU* 2.8 39.7 + - - +
237E LYS 5.5 1.2 + - - -
240E ASN* 3.0 38.7 + - - +
242E LYS* 1.3 75.6 - - - +
244E VAL* 1.3 67.0 + - - +
246E GLU* 3.2 14.6 + - + +
247E ARG* 3.1 32.4 + - + +
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Residues in contact with VAL 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E SER* 4.0 17.0 - - - +
125E ARG* 4.2 4.5 - - - -
126E VAL* 3.9 20.9 - - + +
234E SER* 2.9 50.8 + - - +
236E GLU* 3.7 33.4 - - + +
240E ASN 3.1 13.4 + - - +
241E MET* 3.4 10.8 - - - +
243E ARG* 1.3 77.7 - - - +
245E PHE* 1.3 57.0 + - - +
247E ARG* 3.5 7.1 + - - +
248E PHE* 3.0 15.4 + - - +
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Residues in contact with PHE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ASP 4.7 0.2 - - - -
108E ALA* 4.0 17.9 - - + -
111E ILE* 3.8 26.5 - - + -
126E VAL* 4.4 8.7 - - + -
241E MET 2.8 16.7 + - - +
242E LYS* 3.8 5.8 - - - +
244E VAL* 1.3 77.0 - - - +
246E GLU* 1.3 60.3 + - - +
248E PHE* 3.3 33.1 + + + +
249E CYS* 3.0 47.0 + - - -
286E LEU* 4.6 1.1 - - + -
341E GLU* 4.1 25.6 - - + -
342E VAL* 4.2 13.7 - - + -
345E VAL* 3.6 37.7 - - + -
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Residues in contact with GLU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ALA* 3.7 26.6 - - + +
109E SER* 5.1 1.7 - - - -
242E LYS* 3.0 52.5 + - + +
243E ARG* 3.2 15.6 + - + +
245E PHE* 1.3 75.5 - - - +
247E ARG* 1.3 58.1 + - - +
249E CYS* 3.4 2.4 + - - +
250E ARG* 2.9 37.2 + - - +
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Residues in contact with ARG 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ASP* 4.5 12.9 + - - -
164E LEU* 4.4 15.0 - - + -
215E ASN* 4.6 6.7 - - - +
217E GLU* 4.3 7.5 + - - -
219E SER* 3.3 38.0 + - - -
220E PHE* 4.2 8.4 - - + -
234E SER* 3.5 13.3 + - - +
235E MET 3.2 25.5 + - - -
236E GLU* 3.1 32.7 + - - +
243E ARG* 3.1 23.3 + - + +
244E VAL* 3.8 7.1 - - - +
246E GLU* 1.3 77.1 - - - +
248E PHE* 1.3 58.4 + - - +
250E ARG* 3.8 17.7 - - - +
251E GLY* 2.9 29.1 + - - -
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Residues in contact with PHE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.3 8.5 - - + -
126E VAL* 3.7 39.0 - - + -
128E THR* 3.5 39.7 - - + -
130E ARG* 5.5 0.7 - - - -
220E PHE* 4.3 5.4 - - - -
232E VAL* 4.0 13.7 - - + -
234E SER* 3.9 15.7 + - - -
244E VAL 3.0 14.8 + - - +
245E PHE* 3.3 31.9 - + + +
247E ARG* 1.3 78.0 - - - +
249E CYS* 1.3 64.9 + - - +
251E GLY* 3.9 0.5 - - - -
252E LEU* 3.1 41.9 + - + +
286E LEU* 3.8 19.3 - - + -
341E GLU* 5.9 0.2 - - - -
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Residues in contact with CYS 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 3.3 44.8 - - + +
108E ALA* 4.0 10.8 - - + -
245E PHE* 3.0 54.2 + - - +
246E GLU 3.9 2.9 - - - +
248E PHE* 1.3 75.3 - - - +
250E ARG* 1.3 66.3 + - - +
252E LEU* 3.5 4.4 + - - +
253E LYS* 3.1 32.5 + - - +
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Residues in contact with ARG 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ASP* 2.6 44.1 + - - -
164E LEU* 4.3 19.4 - - + +
246E GLU* 2.9 23.8 + - - +
247E ARG* 3.8 24.4 - - - +
249E CYS* 1.3 76.2 - - - +
251E GLY* 1.3 63.8 + - - +
253E LYS* 3.3 7.9 + - - +
254E GLU* 3.0 26.0 + - + +
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Residues in contact with GLY 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LEU* 5.1 0.4 - - - +
164E LEU* 3.9 20.1 - - - +
220E PHE* 3.7 21.5 - - - -
247E ARG 2.9 16.5 + - - -
250E ARG* 1.3 77.6 - - - +
252E LEU* 1.3 56.0 + - - +
254E GLU* 3.3 1.7 + - - +
255E VAL* 2.9 34.9 + - - +
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.6 15.0 - - + -
128E THR* 4.0 2.9 - - + -
130E ARG* 3.7 40.6 - - + +
220E PHE* 4.3 0.4 - - - -
232E VAL* 4.1 33.4 - - + -
248E PHE* 3.1 53.3 + - + +
249E CYS* 4.0 4.9 - - - +
250E ARG 3.3 0.2 - - - -
251E GLY* 1.3 75.1 - - - +
253E LYS* 1.3 59.1 + - - +
255E VAL* 3.4 7.2 + - + +
256E GLU* 2.9 31.1 + - - +
266E PHE* 4.6 8.2 - - + -
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Residues in contact with LYS 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 3.1 48.8 + - + -
107E ASP* 4.4 6.7 + - - +
108E ALA 5.4 0.2 - - - +
249E CYS* 3.1 19.4 + - - +
250E ARG* 3.8 5.8 - - - +
252E LEU* 1.3 77.4 - - - +
254E GLU* 1.3 58.9 + - - +
256E GLU* 3.5 10.3 + - - +
257E ARG* 3.0 29.3 + - - +
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Residues in contact with GLU 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E GLY 5.6 0.7 - - - +
160E LEU* 3.6 24.5 - - + -
161E LYS 6.0 1.1 - - - +
164E LEU* 4.4 10.1 - - + -
250E ARG* 3.0 18.2 + - + +
251E GLY 3.6 5.2 - - - +
253E LYS* 1.3 77.3 - - - +
255E VAL* 1.3 63.6 + - - +
257E ARG* 2.3 45.9 + - - +
258E LEU* 3.0 31.8 + - + +
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Residues in contact with VAL 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E VAL* 6.2 3.6 - - + -
156E ALA* 4.9 4.9 - - + +
157E LEU* 4.0 29.2 - - + -
160E LEU* 4.3 15.3 - - + -
220E PHE* 5.0 2.9 - - + -
222E ILE* 4.6 10.3 - - + -
251E GLY 2.9 21.7 + - - +
252E LEU* 3.8 10.1 - - + +
254E GLU* 1.3 72.7 - - - +
256E GLU* 1.3 66.6 + - - +
258E LEU* 3.3 8.6 + - - +
259E ILE* 3.1 31.4 + - + +
266E PHE* 4.4 16.6 - - + -
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Residues in contact with GLU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 6.0 2.3 - - - +
252E LEU 2.9 18.1 + - - +
253E LYS* 3.9 10.6 - - - +
255E VAL* 1.3 77.3 - - - +
257E ARG* 1.3 63.4 + - - +
259E ILE* 3.4 7.2 + - + +
260E GLN* 3.0 54.2 + - + +
266E PHE* 3.6 41.4 + - + +
274E TYR* 4.9 9.4 + - - -
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Residues in contact with ARG 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E GLY 5.5 1.8 + - - -
253E LYS 3.0 18.8 + - - +
254E GLU* 2.3 39.8 + - - +
256E GLU* 1.3 79.0 - - - +
258E LEU* 1.3 84.8 + - - +
260E GLN* 3.3 9.9 + - - +
261E GLU* 3.0 47.9 + - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ALA* 3.1 39.2 - - + +
159E GLY* 3.8 26.7 - - - +
160E LEU* 3.9 14.4 - - + -
254E GLU* 3.0 21.8 + - - +
255E VAL* 3.7 6.1 - - - +
256E GLU 3.2 0.2 - - - -
257E ARG* 1.3 107.7 - - - +
259E ILE* 1.3 61.2 + - - +
261E GLU* 3.5 27.8 - - - +
262E ARG* 3.9 10.7 + - - +
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Residues in contact with ILE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ILE* 4.2 13.0 - - + -
152E VAL* 4.5 17.0 - - + +
153E VAL* 5.2 3.6 - - + -
156E ALA* 3.5 24.5 - - + -
255E VAL* 3.1 17.9 + - + +
256E GLU* 3.4 12.1 - - + +
258E LEU* 1.3 74.2 - - - +
260E GLN* 1.3 67.6 + - + +
261E GLU 3.1 0.7 - - - -
262E ARG* 3.1 13.7 + - - +
263E GLY 3.4 0.3 + - - -
264E TRP* 3.0 44.3 + - + +
265E GLU* 4.2 11.0 - - - -
266E PHE* 3.7 35.7 - - + +
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Residues in contact with GLN 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLU* 3.0 43.0 + - + +
257E ARG* 3.3 8.4 + - - +
259E ILE* 1.3 76.5 - - + +
261E GLU* 1.3 63.6 + - - +
263E GLY* 3.1 12.2 + - - -
264E TRP 3.3 15.9 - - - +
265E GLU* 4.3 24.8 + - - +
31G PRO* 5.6 2.4 - - - +
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Residues in contact with GLU 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E ARG* 3.0 39.0 + - - +
258E LEU* 3.5 26.0 - - - +
260E GLN* 1.3 78.4 - - - +
262E ARG* 1.3 67.3 + - + +
263E GLY 3.3 0.8 + - - -
17G ASP* 5.5 0.2 - - - +
19G ARG* 4.0 42.0 + - - +
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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