Contacts of the helix formed by residues 241 - 262 (chain S) in PDB entry 3FKS
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 ALA 241 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77S LEU 3.9 11.0 - - - +
78S PHE* 3.5 31.5 + - - +
79S GLY* 4.3 7.0 - - - +
239S SER 3.7 1.1 + - - -
240S GLU* 1.3 80.6 - - - +
242S ALA* 1.3 67.1 + - - +
243S PRO* 3.6 3.4 - - + -
244S LEU* 3.5 19.1 + - + +
245S GLN* 3.6 8.5 + - - +
287V THR* 4.5 6.3 - - - -
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Residues in contact with ALA 242 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241S ALA* 1.3 69.3 - - - +
243S PRO* 1.3 75.6 - - + +
245S GLN* 3.0 17.0 + - - +
246S TYR* 3.1 9.4 + - - +
279S ALA* 3.8 16.1 - - + +
282S GLN* 3.6 34.0 - - + +
283S LEU* 3.8 21.1 - - + -
287V THR* 4.3 7.1 - - - +
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Residues in contact with PRO 243 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S GLY 5.7 0.7 - - - +
64S MET* 5.1 2.7 - - - -
76S VAL* 3.8 23.1 - - + -
77S LEU 3.5 25.6 - - - +
78S PHE* 3.9 20.4 - - + -
241S ALA* 3.7 3.4 - - + -
242S ALA* 1.3 95.1 - - + +
244S LEU* 1.3 56.6 + - - +
246S TYR* 3.1 4.2 + - + +
247S LEU* 2.9 36.0 + - + +
283S LEU* 3.6 30.5 - - + -
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Residues in contact with LEU 244 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S PHE* 3.4 51.8 - - + +
111S ASP* 5.1 4.7 - - - +
112S ALA* 3.2 32.0 - - + +
113S LEU* 4.6 13.7 - - + -
236S ALA* 3.9 2.7 - - + -
240S GLU* 3.5 40.2 - - + +
241S ALA* 3.6 13.0 - - + +
242S ALA 3.1 0.6 - - - -
243S PRO* 1.3 80.8 - - - +
245S GLN* 1.3 56.7 + - - +
247S LEU* 3.4 0.8 + - - -
248S ALA* 3.0 24.9 + - - +
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Residues in contact with GLN 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208S VAL* 3.7 12.3 - - + +
209S GLY* 3.9 15.1 + - - -
236S ALA* 3.3 29.2 - - + +
237S THR 3.2 17.7 + - - +
238S ALA* 3.8 12.5 + - - +
240S GLU 3.4 13.9 + - - -
241S ALA 3.7 10.1 + - - +
242S ALA* 3.0 7.5 + - - +
244S LEU* 1.3 75.1 - - - +
246S TYR* 1.3 62.9 + - - +
249S PRO* 3.2 18.7 - - - +
275S LYS* 3.7 17.2 - - - +
276S GLN* 3.6 10.0 - - - +
279S ALA* 3.9 15.6 - - + +
286V ALA* 5.1 12.3 + - - +
287V THR* 4.8 7.7 - - - +
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Residues in contact with TYR 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S GLU* 5.0 8.7 + - - -
64S MET* 5.2 6.1 - - + -
66S LEU* 5.1 17.4 - - + +
132S GLN* 3.7 12.7 + - - -
242S ALA 3.1 10.5 + - - +
243S PRO* 3.1 8.4 + - + +
245S GLN* 1.3 78.3 - - - +
247S LEU* 1.3 84.0 + - + +
248S ALA 3.5 0.2 - - - -
249S PRO* 4.0 0.2 - - - -
250S PHE* 3.3 20.8 - + - -
276S GLN* 3.7 13.0 + - - -
279S ALA* 4.5 0.4 - - - +
280S TYR* 3.3 50.0 + + + +
283S LEU* 3.8 21.8 - - + -
303S LEU* 3.7 21.3 - - + -
306S ARG* 3.6 18.2 + - - -
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Residues in contact with LEU 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S GLU* 5.7 2.7 - - - +
64S MET* 3.5 29.4 - - + -
78S PHE* 3.6 27.6 - - + -
97S VAL* 4.1 20.4 - - + -
112S ALA* 4.5 6.7 - - + +
113S LEU* 5.2 2.2 - - + -
131S ALA* 4.3 20.0 - - + -
132S GLN* 4.8 9.4 - - + +
243S PRO 2.9 13.6 + - - +
244S LEU* 4.1 3.4 - - - +
246S TYR* 1.3 98.7 - - + +
248S ALA* 1.3 59.6 + - - +
249S PRO* 3.4 2.0 - - - -
250S PHE* 3.3 3.7 + - + +
251S THR* 2.8 38.9 + - - +
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Residues in contact with ALA 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112S ALA* 3.9 14.3 - - + +
206S VAL* 4.3 7.1 - - + +
208S VAL* 4.2 11.9 - - + -
234S VAL* 4.4 5.3 - - + +
236S ALA* 3.6 22.7 - - + +
244S LEU 3.0 17.6 + - - +
245S GLN 3.8 3.1 - - - +
247S LEU* 1.3 76.9 - - - +
249S PRO* 1.3 65.3 - - + +
251S THR* 3.9 1.0 - - - -
252S ALA* 3.0 32.7 + - - +
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Residues in contact with PRO 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206S VAL* 4.4 5.4 - - + -
208S VAL* 4.3 11.2 - - + -
245S GLN 3.2 14.8 - - - +
246S TYR 3.9 4.9 - - - +
247S LEU 3.6 2.5 - - - -
248S ALA* 1.3 94.6 - - + +
250S PHE* 1.3 56.0 + - - +
252S ALA* 3.9 0.9 - - + +
253S ALA* 3.1 26.7 + - - +
270S TYR* 3.6 18.5 - - + -
273S LEU* 4.6 3.8 - - + -
276S GLN* 3.4 31.2 - - + +
307S LEU* 3.2 30.4 - - + +
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Residues in contact with PHE 250 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131S ALA* 3.1 32.7 - - + +
132S GLN* 3.4 33.9 - - - +
246S TYR* 3.3 22.4 - + - -
247S LEU* 3.3 7.9 + - + +
249S PRO* 1.3 75.1 - - + +
251S THR* 1.3 65.8 + - - +
253S ALA* 3.2 14.7 + - - +
254S SER* 3.6 4.9 + - - -
276S GLN* 3.3 24.0 - - - -
303S LEU* 3.4 36.8 - - + -
306S ARG* 4.0 16.8 - - + -
307S LEU* 3.8 31.4 - - + -
310S ARG* 3.4 10.8 + - - -
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Residues in contact with THR 251 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S VAL* 4.9 5.4 - - - +
98S ASP 5.5 0.9 + - - -
99S VAL* 3.5 36.7 - - + +
111S ASP 5.0 2.7 - - - +
112S ALA* 2.9 32.4 + - - +
113S LEU* 4.5 0.8 - - - -
114S GLY* 5.5 0.2 - - - -
131S ALA* 3.7 19.9 - - - +
234S VAL* 5.2 3.6 - - + -
247S LEU* 2.8 18.3 + - - +
248S ALA 3.9 2.0 - - - -
250S PHE* 1.3 74.0 - - - +
252S ALA* 1.3 58.9 + - - +
253S ALA 2.9 9.3 + - - -
254S SER* 3.0 17.0 + - - -
255S ILE* 3.5 10.9 + - + +
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Residues in contact with ALA 252 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204S VAL* 3.5 14.0 - - + +
206S VAL* 3.7 27.1 - - + -
234S VAL* 3.8 24.0 - - + -
248S ALA 3.0 17.7 + - - +
249S PRO 4.3 0.7 - - - +
251S THR* 1.3 77.2 - - - +
253S ALA* 1.3 59.3 + - - +
254S SER 3.4 0.2 - - - -
255S ILE* 4.0 12.3 - - - +
256S GLY* 3.7 8.7 + - - -
268S ILE* 3.2 15.0 - - + +
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Residues in contact with ALA 253 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249S PRO 3.1 14.5 + - - +
250S PHE 3.2 16.2 - - - +
251S THR 2.9 1.4 - - - -
252S ALA* 1.3 79.2 - - - +
254S SER* 1.3 57.8 + - - +
256S GLY* 4.0 0.3 + - - -
257S GLU* 2.9 28.8 + - - +
268S ILE* 4.0 6.5 - - - -
270S TYR* 3.9 7.0 - - - +
307S LEU* 3.9 12.8 - - + +
310S ARG* 3.6 24.5 - - + +
323S LEU* 4.1 10.1 - - + +
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Residues in contact with SER 254 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99S VAL* 4.3 4.7 - - - -
101S VAL* 3.9 8.4 - - - +
129S SER* 4.0 18.9 + - - -
130S ARG 2.7 27.6 + - - -
131S ALA* 4.2 0.3 - - - -
133S VAL* 4.1 2.6 - - - +
250S PHE 3.7 5.0 + - - -
251S THR 3.0 7.8 + - - -
253S ALA* 1.3 77.9 - - - +
255S ILE* 1.3 66.2 + - - +
257S GLU* 3.3 5.8 - - - +
258S TRP* 2.9 23.7 + - - +
310S ARG* 3.1 15.9 + - - +
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Residues in contact with ILE 255 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99S VAL* 3.6 17.7 - - + -
100S PRO 3.2 27.1 - - - +
101S VAL* 3.6 15.9 - - + +
102S GLY 5.0 2.5 + - - +
105S LEU* 3.7 19.3 - - + -
204S VAL* 4.7 4.9 - - + -
232S ILE* 4.0 32.3 - - + -
234S VAL* 4.9 8.5 - - + -
251S THR* 3.6 13.0 - - + +
252S ALA* 4.0 13.7 - - - +
253S ALA 3.4 0.2 - - - -
254S SER* 1.3 78.5 - - - +
256S GLY* 1.3 64.0 + - - +
258S TRP* 3.2 16.8 + - - +
259S PHE* 3.4 14.5 - - + -
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Residues in contact with GLY 256 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204S VAL* 3.7 23.5 - - - +
252S ALA 3.7 8.1 + - - -
253S ALA 4.1 1.3 - - - -
255S ILE* 1.3 80.2 - - - +
257S GLU* 1.3 60.8 + - - +
259S PHE* 3.3 25.8 + - - +
260S ARG* 3.6 4.7 + - - +
266S ALA* 3.6 14.6 - - - +
268S ILE* 5.9 0.4 - - - -
323S LEU* 4.3 10.7 - - - +
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Residues in contact with GLU 257 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133S VAL* 3.7 21.9 - - - +
134S LYS 4.5 4.0 - - - +
253S ALA* 2.9 17.7 + - - +
254S SER* 3.0 9.8 + - - +
256S GLY* 1.3 75.8 - - - +
258S TRP* 1.3 64.7 + - - +
260S ARG* 3.0 59.6 + - - +
261S ASP* 3.3 15.3 + - - +
310S ARG* 2.8 40.5 + - - +
323S LEU* 4.2 7.4 - - + +
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Residues in contact with TRP 258 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101S VAL* 3.5 30.1 - - + -
102S GLY* 3.8 15.2 - - - +
103S PRO* 3.2 36.3 - - + -
126S ALA* 4.4 12.7 - - + +
127S GLY* 6.1 0.4 - - - -
254S SER 2.9 10.3 + - - +
255S ILE 3.3 12.1 - - - +
256S GLY 3.2 0.4 - - - -
257S GLU* 1.3 77.3 - - - +
259S PHE* 1.3 95.1 + + - +
260S ARG 3.3 0.7 + - - -
261S ASP* 3.5 5.1 + - - +
262S ASN* 3.0 54.1 + - + +
264S LYS* 4.7 13.7 - - + -
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Residues in contact with PHE 259 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S GLY 4.5 7.4 - - - -
103S PRO* 4.5 7.0 - - + -
106S LEU* 3.8 34.5 - - + -
202S TYR* 3.3 45.8 - + + -
204S VAL* 5.3 0.4 - - + -
232S ILE* 4.4 12.8 - - + -
255S ILE* 3.4 22.4 - - + -
256S GLY* 3.4 15.9 - - - +
257S GLU 3.2 0.2 - - - -
258S TRP* 1.3 104.0 - + - +
260S ARG* 1.3 59.8 + - - +
262S ASN* 3.5 5.2 + - - -
263S GLY 3.6 0.2 + - - -
264S LYS* 2.8 45.3 + - + +
266S ALA* 4.2 14.8 - - + +
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Residues in contact with ARG 260 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S LYS 5.5 1.0 + - - -
136S PRO* 3.5 21.1 - - - +
256S GLY 3.6 3.3 + - - +
257S GLU* 3.0 53.3 + - - +
259S PHE* 1.3 81.4 - - - +
261S ASP* 1.3 83.4 + - - +
262S ASN 3.4 0.3 + - - -
263S GLY 3.6 6.6 + - - -
264S LYS 3.8 7.6 - - - -
310S ARG 2.7 30.3 + - - -
312S ALA 4.0 10.8 - - - +
314S LEU* 3.4 32.4 - - + +
319S GLY* 5.1 0.9 - - - -
321S GLY* 3.6 19.7 + - - +
322S SER 3.8 15.5 + - - +
323S LEU* 4.0 16.2 - - + +
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Residues in contact with ASP 261 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257S GLU* 3.3 19.7 + - - +
258S TRP* 3.5 4.8 + - - +
260S ARG* 1.3 107.9 + - - +
262S ASN* 1.3 66.3 + - - +
263S GLY 3.3 3.8 + - - -
314S LEU* 4.1 8.5 - - - +
318S GLU* 4.7 15.7 - - + +
319S GLY* 5.0 2.4 - - - -
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Residues in contact with ASN 262 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S TRP* 3.0 62.5 + - + +
259S PHE 3.5 2.9 + - - +
260S ARG 3.2 0.8 - - - -
261S ASP* 1.3 86.3 - - - +
263S GLY* 1.3 58.8 + - - +
264S LYS* 3.4 13.6 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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