Contacts of the helix formed by residues 241 - 262 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77U LEU 3.7 12.1 - - - +
78U PHE* 3.2 36.7 + - - +
79U GLY* 4.2 4.7 - - - +
239U SER 3.7 1.7 + - - -
240U GLU* 1.3 78.9 - - - +
242U ALA* 1.3 66.5 + - - +
243U PRO* 3.4 2.5 - - + -
244U LEU* 3.1 23.3 + - + +
245U GLN* 3.4 5.0 + - - +
287X THR* 5.7 1.1 - - - -
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Residues in contact with ALA 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240U GLU 3.6 1.3 + - - -
241U ALA* 1.3 71.8 - - - +
243U PRO* 1.3 67.0 - - + +
245U GLN* 2.8 32.4 + - - +
246U TYR* 3.0 9.2 + - - +
279U ALA* 3.9 14.0 - - + +
282U GLN* 3.6 32.5 - - - +
283U LEU* 3.6 16.6 - - + -
287X THR* 4.2 9.8 - - + +
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Residues in contact with PRO 243 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39U GLY* 5.5 2.0 - - - +
76U VAL* 3.7 34.1 - - + +
77U LEU 3.2 24.2 - - - +
78U PHE* 3.9 22.7 - - + -
241U ALA* 3.5 3.8 - - + -
242U ALA* 1.3 96.1 - - + +
244U LEU* 1.3 60.7 + - - +
246U TYR* 3.2 7.0 + - + +
247U LEU* 3.1 31.7 + - + +
283U LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 244 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78U PHE* 3.4 43.7 - - + +
111U ASP* 5.0 3.8 - - - +
112U ALA* 3.5 32.7 - - + +
113U LEU* 4.0 21.1 - - + -
236U ALA* 3.6 3.0 - - + +
240U GLU* 3.7 26.7 - - + +
241U ALA* 3.1 32.0 + - + +
242U ALA 3.0 0.2 - - - -
243U PRO* 1.3 79.1 - - - +
245U GLN* 1.3 55.4 + - - +
247U LEU* 3.4 0.8 + - - -
248U ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208U VAL* 3.8 13.9 - - + +
209U GLY* 3.6 18.6 + - - -
236U ALA* 3.6 28.7 - - + +
237U THR 3.7 9.6 + - - +
238U ALA* 4.0 12.9 + - - +
240U GLU 3.5 18.0 + - - -
241U ALA 3.8 8.0 + - - +
242U ALA* 2.8 8.0 + - - +
244U LEU* 1.3 73.9 - - - +
246U TYR* 1.3 65.0 + - - +
248U ALA* 3.6 2.0 - - - +
249U PRO* 3.2 20.6 - - - +
275U LYS* 3.9 14.4 - - - +
276U GLN* 4.2 3.4 - - - +
279U ALA* 3.7 16.0 - - + +
286X ALA* 5.9 4.4 - - - +
287X THR* 4.3 15.8 - - - +
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Residues in contact with TYR 246 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U GLU* 4.5 11.6 + - - -
64U MET* 4.9 12.9 - - + +
66U LEU* 5.4 10.6 - - + +
132U GLN* 3.5 16.1 + - - -
242U ALA 3.0 10.0 + - - +
243U PRO* 3.2 10.7 + - + +
245U GLN* 1.3 79.3 - - - +
247U LEU* 1.3 85.6 + - + +
249U PRO* 3.9 2.4 - - - +
250U PHE* 3.0 33.7 - + - -
276U GLN* 4.2 8.3 + - - -
279U ALA* 4.5 2.6 - - - +
280U TYR* 3.5 40.6 - + + +
283U LEU* 4.5 16.6 - - + -
303U LEU* 3.5 30.1 - - + -
306U ARG* 3.2 17.8 + - - -
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Residues in contact with LEU 247 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64U MET* 4.5 8.3 - - + -
78U PHE* 3.8 28.3 - - + -
97U VAL* 3.5 34.1 - - + -
112U ALA* 4.4 6.7 - - + +
113U LEU* 4.9 6.1 - - + -
131U ALA* 5.1 7.2 - - + -
132U GLN* 6.3 0.4 - - - +
243U PRO* 3.1 28.2 + - + +
244U LEU 3.4 4.2 + - - +
245U GLN 3.2 0.2 - - - -
246U TYR* 1.3 106.1 - - + +
248U ALA* 1.3 66.8 + - - +
250U PHE* 2.7 20.1 + - + -
251U THR* 2.8 28.4 + - + -
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Residues in contact with ALA 248 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112U ALA* 4.4 5.4 - - + +
206U VAL* 4.1 7.2 - - + -
208U VAL* 4.1 13.7 - - + -
234U VAL* 3.9 6.8 - - + +
235U ALA 5.4 0.2 - - - -
236U ALA* 3.7 23.1 - - + +
244U LEU 3.0 14.1 + - - +
245U GLN 3.6 8.1 - - - +
247U LEU* 1.3 75.2 - - - +
249U PRO* 1.3 66.1 - - + +
251U THR* 3.2 7.2 + - - -
252U ALA* 2.9 31.9 + - - +
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Residues in contact with PRO 249 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206U VAL* 4.0 5.6 - - + -
208U VAL* 4.0 15.3 - - + -
245U GLN 3.2 11.4 - - - +
246U TYR 3.9 4.7 - - - +
247U LEU 3.5 4.0 - - - -
248U ALA* 1.3 96.8 - - + +
250U PHE* 1.3 54.8 + - - +
252U ALA* 3.8 0.6 - - + -
253U ALA* 3.0 23.0 + - - +
270U TYR* 3.3 40.6 - - + -
273U LEU* 5.0 2.0 - - + -
276U GLN* 3.2 26.9 - - + +
307U LEU* 3.3 15.3 - - + +
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Residues in contact with PHE 250 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131U ALA* 3.6 16.1 - - + +
132U GLN* 3.3 35.4 - - - +
246U TYR* 3.0 41.5 - + - -
247U LEU* 2.7 15.5 + - - +
249U PRO* 1.3 69.3 - - - +
251U THR* 1.3 65.4 + - - +
252U ALA 3.1 1.3 - - - -
253U ALA* 3.1 15.9 + - - +
254U SER* 3.4 11.1 + - - -
276U GLN* 3.7 17.5 - - - -
303U LEU* 3.6 25.6 - - + -
306U ARG* 3.8 17.9 - - + -
307U LEU* 3.7 26.0 - - + -
310U ARG* 3.6 18.5 + - - +
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Residues in contact with THR 251 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U VAL* 5.3 1.8 - - + -
99U VAL* 3.5 34.0 - - + +
111U ASP 4.4 0.5 + - - -
112U ALA* 3.2 30.0 + - - +
131U ALA* 4.5 13.0 - - + +
234U VAL* 4.0 11.5 - - - +
247U LEU* 2.8 40.4 + - + +
248U ALA 3.2 9.2 + - - -
250U PHE* 1.3 72.8 - - - +
252U ALA* 1.3 63.2 + - - +
254U SER* 3.6 6.6 + - - -
255U ILE* 3.3 17.0 - - - +
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Residues in contact with ALA 252 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204U VAL* 3.8 2.7 - - + +
206U VAL* 3.6 26.0 - - + -
234U VAL* 3.5 26.9 - - + -
248U ALA 2.9 19.2 + - - +
249U PRO 3.9 2.5 - - - +
251U THR* 1.3 76.0 + - - +
253U ALA* 1.3 63.3 + - - +
254U SER 3.2 2.2 - - - -
255U ILE* 3.3 21.1 + - - +
256U GLY 3.4 7.6 + - - -
268U ILE* 3.5 10.5 - - + +
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Residues in contact with ALA 253 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249U PRO 3.0 18.9 + - - +
250U PHE 3.1 8.5 + - - +
252U ALA* 1.3 79.7 - - - +
254U SER* 1.3 55.9 + - - +
256U GLY* 3.4 1.4 + - - -
257U GLU* 2.9 34.3 + - + +
268U ILE* 3.9 4.0 - - - -
270U TYR* 3.4 19.5 - - - +
307U LEU* 3.7 12.6 - - + +
310U ARG* 3.7 19.5 - - + +
323U LEU* 4.3 5.3 - - + +
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Residues in contact with SER 254 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99U VAL* 4.4 3.3 - - - +
101U VAL* 3.7 23.0 - - - +
129U SER* 4.5 6.1 - - - -
130U ARG 3.2 21.4 + - - -
133U VAL* 4.1 2.2 - - - +
250U PHE 3.4 6.2 + - - -
251U THR* 3.7 10.6 + - - -
252U ALA 3.2 0.2 - - - -
253U ALA* 1.3 75.0 - - - +
255U ILE* 1.3 64.8 + - - +
256U GLY 3.1 2.0 - - - -
257U GLU* 3.2 11.8 + - - +
258U TRP* 3.0 23.4 + - - +
310U ARG* 3.1 16.5 + - - -
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Residues in contact with ILE 255 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U VAL* 4.4 6.3 - - + -
100U PRO 3.3 26.5 - - - +
101U VAL* 4.0 9.9 - - + -
102U GLY 4.7 6.9 - - - +
105U LEU* 3.5 26.0 - - + -
110U VAL* 5.9 3.8 - - + -
204U VAL* 4.5 5.8 - - + -
232U ILE* 4.1 30.5 - - + -
234U VAL* 4.6 9.9 - - + -
251U THR 3.3 19.5 - - - +
252U ALA* 3.3 13.4 + - - +
254U SER* 1.3 76.2 - - - +
256U GLY* 1.3 57.6 + - - +
258U TRP* 3.5 8.9 - - - +
259U PHE* 3.2 26.6 - - + -
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Residues in contact with GLY 256 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204U VAL* 4.0 18.6 - - - +
252U ALA 3.4 7.4 + - - -
253U ALA* 3.4 3.3 + - - -
254U SER 3.1 0.6 - - - -
255U ILE* 1.3 77.7 - - - +
257U GLU* 1.3 60.3 + - - +
258U TRP 3.0 5.4 + - - -
259U PHE* 3.3 11.8 + - - -
260U ARG* 3.5 7.1 + - - +
266U ALA* 3.7 12.3 - - - +
268U ILE* 5.4 2.0 - - - -
323U LEU* 4.0 21.0 - - - +
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Residues in contact with GLU 257 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133U VAL* 3.6 17.8 - - - +
134U LYS 4.7 1.0 - - - +
253U ALA 2.9 18.7 + - - +
254U SER* 3.2 7.9 + - - +
256U GLY* 1.3 75.6 - - - +
258U TRP* 1.3 56.4 + - - +
259U PHE 3.3 0.2 - - - -
260U ARG* 3.3 34.9 + - - +
261U ASP* 2.8 39.2 + - - +
310U ARG* 3.0 60.4 + - + +
323U LEU* 3.6 20.1 - - + +
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Residues in contact with TRP 258 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U VAL* 3.6 34.4 + - + -
102U GLY* 3.4 20.7 - - - +
103U PRO* 3.2 41.5 - - + -
126U ALA* 4.6 8.9 + - + +
254U SER 3.0 12.0 + - - +
255U ILE 3.5 12.8 - - - +
256U GLY 3.0 0.6 - - - -
257U GLU* 1.3 77.7 - - - +
259U PHE* 1.3 96.2 + + - +
261U ASP* 3.3 9.2 + - + +
262U ASN* 3.0 54.4 + - - +
264U LYS* 4.0 21.3 - - + -
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Residues in contact with PHE 259 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U GLY 4.6 7.2 - - - -
103U PRO* 5.3 0.4 - - + -
106U LEU* 4.0 19.3 - - + -
202U TYR* 3.3 47.3 - + + -
204U VAL* 4.8 0.4 - - + -
232U ILE* 4.2 13.9 - - + -
255U ILE* 3.2 24.7 - - + -
256U GLY* 3.3 1.5 + - - -
258U TRP* 1.3 95.8 - + - +
260U ARG* 1.3 62.9 + - - +
262U ASN* 3.0 7.0 + - - -
264U LYS* 2.8 61.4 + - + +
266U ALA* 3.6 34.1 - - + +
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Residues in contact with ARG 260 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133U VAL* 5.2 5.1 - - - +
134U LYS 5.4 1.8 + - - -
136U PRO* 3.4 21.2 - - - +
256U GLY 3.5 3.6 + - - +
257U GLU* 3.3 41.0 + - - +
259U PHE* 1.3 79.6 - - - +
261U ASP* 1.3 81.6 + - - +
262U ASN 3.5 0.2 + - - -
263U GLY 3.7 1.6 + - - -
264U LYS 3.6 9.6 + - - -
310U ARG 2.6 30.5 + - - -
312U ALA 3.6 15.9 - - - -
314U LEU* 3.5 33.4 - - + +
318U GLU 5.0 1.9 - - - +
321U GLY* 3.5 15.4 + - - -
322U SER* 3.5 31.0 + - - +
323U LEU* 4.1 9.0 - - + -
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Residues in contact with ASP 261 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257U GLU* 2.8 30.5 + - - +
258U TRP* 3.5 11.5 - - + +
259U PHE 3.1 0.2 - - - -
260U ARG* 1.3 103.7 + - - +
262U ASN* 1.3 64.7 + - - +
263U GLY 3.4 2.8 + - - -
314U LEU* 4.5 7.2 - - - +
318U GLU 3.8 15.1 - - - +
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Residues in contact with ASN 262 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U TRP* 3.0 57.9 + - - +
259U PHE* 3.0 4.8 + - - +
261U ASP* 1.3 84.5 - - - +
263U GLY* 1.3 61.2 + - - +
264U LYS* 3.2 24.7 + - - +
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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