Contacts of the helix formed by residues 241 - 262 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K LEU 4.8 0.7 - - - +
78K PHE* 3.9 25.6 - - - +
79K GLY* 4.3 14.1 - - - +
240K GLU* 1.3 79.7 + - - +
242K ALA* 1.3 68.1 + - - +
243K PRO* 3.3 11.2 - - + -
244K LEU* 3.2 15.0 + - + +
245K GLN* 3.4 10.1 + - - +
287N THR* 4.9 2.5 - - - -
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Residues in contact with ALA 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K GLU 3.9 0.6 + - - -
241K ALA* 1.3 70.0 - - - +
243K PRO* 1.3 72.0 - - + +
245K GLN* 3.0 16.6 + - - +
246K TYR* 2.9 22.2 + - - +
279K ALA* 3.8 23.3 - - + +
282K GLN* 3.8 36.1 - - + +
283K LEU* 4.6 8.5 - - + -
287N THR* 4.1 7.3 - - + +
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Residues in contact with PRO 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLY* 5.7 0.4 - - - +
76K VAL* 3.6 24.0 - - + -
77K LEU 3.3 21.3 - - - +
78K PHE* 3.8 25.4 - - + -
241K ALA* 3.4 12.3 - - + -
242K ALA* 1.3 95.4 - - + +
244K LEU* 1.3 52.1 + - - +
246K TYR* 3.0 18.9 + - + +
247K LEU* 2.7 37.2 + - - +
283K LEU* 3.9 9.6 - - + -
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Residues in contact with LEU 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K PHE* 3.2 49.1 - - + +
111K ASP* 5.0 9.4 - - + +
112K ALA* 3.0 24.8 - - + +
113K LEU* 3.7 29.4 - - + +
236K ALA* 3.4 5.4 - - + +
240K GLU* 3.3 35.2 - - + +
241K ALA* 3.2 13.0 + - + +
243K PRO* 1.3 78.5 - - - +
245K GLN* 1.3 58.3 + - - +
247K LEU* 4.6 0.4 - - - -
248K ALA* 3.0 23.6 + - - +
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Residues in contact with GLN 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K VAL* 3.7 19.8 - - + +
209K GLY* 3.5 23.8 - - - +
236K ALA* 3.7 13.5 - - - +
237K THR 3.7 21.1 - - - +
238K ALA* 4.1 6.2 - - - +
240K GLU* 3.5 20.6 - - + +
241K ALA 3.6 9.7 - - - +
242K ALA 3.0 5.3 + - - +
244K LEU* 1.3 75.4 - - - +
246K TYR* 1.3 66.0 + - - +
248K ALA* 3.1 13.0 + - - +
249K PRO* 3.1 12.5 - - - +
275K LYS* 4.2 5.7 + - - +
276K GLN* 4.3 0.6 - - - +
279K ALA* 4.1 18.7 - - + +
286N ALA* 5.7 7.1 - - - +
287N THR* 3.9 15.4 - - - +
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Residues in contact with TYR 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K MET* 4.9 19.1 - - + +
66K LEU* 6.1 0.7 - - - +
76K VAL* 6.3 1.1 - - + -
78K PHE* 5.9 1.8 - + - -
132K GLN* 4.2 10.2 + - - -
242K ALA 2.9 13.5 + - - +
243K PRO* 3.0 20.6 + - + +
245K GLN* 1.3 75.7 - - - +
247K LEU* 1.3 73.2 + - + +
250K PHE* 3.5 11.6 - + - -
276K GLN* 2.9 33.6 + - - -
279K ALA* 4.4 1.9 - - - +
280K TYR* 3.6 40.8 - + + +
283K LEU* 3.8 24.9 - - + -
303K LEU* 3.5 27.6 - - + -
306K ARG* 3.8 12.2 + - - -
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Residues in contact with LEU 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K MET* 5.5 5.4 - - - -
78K PHE* 3.9 24.9 - - + -
97K VAL* 3.9 24.5 - - + -
112K ALA* 4.2 10.5 - - + +
113K LEU* 4.5 8.1 - - + -
131K ALA* 4.2 16.8 - - + -
132K GLN* 4.4 16.4 - - - +
243K PRO 2.7 20.4 + - - +
244K LEU 4.1 2.7 - - - +
246K TYR* 1.3 88.1 - - + +
248K ALA* 1.3 67.4 + - - +
249K PRO 3.3 1.3 - - - -
250K PHE* 2.9 20.0 + - + +
251K THR* 3.2 25.9 + - + +
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Residues in contact with ALA 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K ALA* 3.7 13.4 - - + +
206K VAL* 3.9 8.6 - - + +
208K VAL* 3.7 11.0 - - + -
234K VAL* 4.3 4.7 - - + +
236K ALA* 3.5 22.0 - - + +
244K LEU 3.0 15.7 + - - +
245K GLN 3.3 8.5 - - - +
247K LEU* 1.3 75.1 - - - +
249K PRO* 1.3 70.3 - - + +
251K THR* 3.1 17.3 + - - -
252K ALA* 3.2 12.3 + - - +
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Residues in contact with PRO 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206K VAL* 3.8 11.2 - - + -
208K VAL* 3.5 19.3 - - + -
245K GLN 3.1 13.0 - - - +
246K TYR 3.6 6.7 - - - +
247K LEU 3.4 3.8 - - - -
248K ALA* 1.3 92.3 - - + +
250K PHE* 1.3 59.5 + - - +
252K ALA 3.8 1.0 + - - -
253K ALA 3.4 10.0 + - - -
270K TYR* 3.1 42.3 - - + -
273K LEU* 4.6 4.5 - - + -
276K GLN* 3.3 20.9 - - - +
307K LEU* 3.4 18.7 - - + +
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Residues in contact with PHE 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131K ALA 3.5 9.4 - - - +
132K GLN* 3.2 22.9 - - + +
246K TYR* 3.5 22.9 - + - -
247K LEU* 2.9 15.9 + - + +
249K PRO* 1.3 77.5 - - - +
251K THR* 1.3 63.5 + - - +
253K ALA 3.2 7.6 + - - -
254K SER* 3.3 5.7 + - - -
276K GLN* 3.7 11.9 - - - -
303K LEU* 3.1 41.7 - - + -
306K ARG* 3.4 37.7 - - + -
307K LEU* 3.5 30.3 - - + -
310K ARG* 3.2 29.9 + - - -
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Residues in contact with THR 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K VAL* 3.5 27.0 - - + +
111K ASP 4.6 0.2 + - - -
112K ALA* 2.9 34.7 + - - +
131K ALA* 4.0 11.4 - - + +
234K VAL* 4.2 5.0 - - - +
247K LEU* 3.2 28.7 + - + +
248K ALA 3.1 9.9 + - - -
250K PHE* 1.3 71.1 - - - +
252K ALA* 1.3 62.6 + - - +
253K ALA 3.1 5.9 + - - -
254K SER* 3.4 14.2 + - - -
255K ILE* 3.2 24.6 + - - +
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Residues in contact with ALA 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K VAL* 3.6 18.7 - - + +
206K VAL* 3.5 31.4 - - + -
234K VAL* 3.6 23.1 - - + -
248K ALA 3.2 11.5 + - - +
249K PRO 4.1 2.2 - - - +
250K PHE 3.3 0.4 - - - -
251K THR* 1.3 79.8 + - - +
253K ALA* 1.3 58.1 + - - +
254K SER 3.5 0.4 - - - -
255K ILE* 4.1 12.9 - - - +
256K GLY 3.7 9.7 + - - -
268K ILE* 3.7 8.3 - - - +
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Residues in contact with ALA 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249K PRO 3.4 7.7 + - - +
250K PHE 3.2 10.3 + - - +
251K THR 3.1 0.6 - - - -
252K ALA* 1.3 79.6 - - - +
254K SER* 1.3 58.4 + - - +
255K ILE 3.3 0.4 - - - -
256K GLY* 3.6 2.6 + - - +
257K GLU* 3.2 30.0 + - - +
268K ILE* 5.0 2.9 - - - -
270K TYR* 3.3 26.2 - - - +
307K LEU* 4.1 6.3 - - + +
310K ARG* 3.2 21.5 - - + +
323K LEU* 4.1 9.1 - - + +
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Residues in contact with SER 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K VAL* 4.3 4.3 - - - -
101K VAL* 3.9 17.2 - - - +
129K SER* 4.1 10.8 + - - -
130K ARG 2.8 25.9 + - - -
131K ALA* 3.5 4.5 + - - -
250K PHE 3.3 9.0 + - - -
251K THR* 3.4 8.7 + - - -
253K ALA* 1.3 77.7 - - - +
255K ILE* 1.3 64.4 + - - +
257K GLU* 3.2 21.2 + - - +
258K TRP* 3.4 5.4 + - - +
310K ARG* 2.8 20.7 + - - +
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Residues in contact with ILE 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K VAL* 5.0 3.8 - - + -
100K PRO 4.7 3.8 - - - +
101K VAL* 3.6 22.7 - - + -
102K GLY 4.6 1.8 - - - +
105K LEU* 3.6 23.3 - - + -
110K VAL* 5.1 6.5 - - + -
114K GLY* 6.5 0.7 - - - -
204K VAL* 5.0 4.7 - - + -
232K ILE* 3.6 36.3 - - + -
234K VAL* 4.1 25.6 - - + -
251K THR* 3.2 18.6 - - - +
252K ALA* 4.2 6.3 - - - +
253K ALA 3.3 0.2 - - - -
254K SER* 1.3 77.0 - - - +
256K GLY* 1.3 61.9 + - - +
258K TRP* 3.2 13.7 + - - +
259K PHE* 3.2 14.9 - - + -
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Residues in contact with GLY 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K VAL* 4.7 10.3 - - - +
252K ALA 3.7 10.0 + - - -
253K ALA 3.6 6.6 + - - -
254K SER 3.3 0.4 - - - -
255K ILE* 1.3 77.3 - - - +
257K GLU* 1.3 61.8 + - - +
259K PHE* 3.4 9.9 + - - -
260K ARG* 3.2 18.2 + - - +
266K ALA* 3.6 21.4 - - - +
323K LEU* 4.2 14.6 - - - +
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Residues in contact with GLU 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K SER* 4.7 3.2 + - - +
133K VAL* 3.6 24.4 - - - +
134K LYS 5.0 1.2 - - - +
136K PRO* 5.1 0.3 - - - +
253K ALA 3.2 16.5 + - - +
254K SER* 3.3 13.0 - - - +
255K ILE 3.1 0.4 - - - -
256K GLY* 1.3 75.6 - - - +
258K TRP* 1.3 56.6 + - - +
259K PHE 3.2 0.7 - - - -
260K ARG* 2.9 41.8 + - - +
261K ASP* 2.7 49.5 + - - +
310K ARG* 2.8 42.5 + - - +
323K LEU* 4.5 7.2 - - + -
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Residues in contact with TRP 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K VAL* 4.1 20.4 - - + -
102K GLY* 3.8 27.5 - - - +
103K PRO* 3.3 36.3 - - + +
126K ALA* 4.2 13.5 + - + +
254K SER 3.4 5.3 + - - +
255K ILE 3.2 15.5 + - - +
257K GLU* 1.3 79.6 - - - +
259K PHE* 1.3 80.8 + + + +
261K ASP* 4.9 2.9 - - - -
262K ASN* 2.9 58.2 + - + +
264K LYS* 4.2 32.5 - - + -
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Residues in contact with PHE 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K GLY 4.2 8.7 - - - -
103K PRO* 5.6 0.4 - - + -
106K LEU* 3.5 26.2 - - + -
202K TYR* 3.4 52.7 - + + -
204K VAL* 5.4 4.0 - - + -
232K ILE* 4.1 17.5 - - + -
255K ILE 3.2 20.9 - - - -
256K GLY* 3.7 11.7 - - - +
257K GLU 3.2 0.4 - - - -
258K TRP* 1.3 95.0 - + - +
260K ARG* 1.3 63.3 + - - +
262K ASN* 3.6 2.4 + - - -
264K LYS* 2.9 49.7 + - + +
265K HIS 4.0 6.1 - - - +
266K ALA* 3.8 16.8 - - + -
322K SER 4.9 0.2 - - - -
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Residues in contact with ARG 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K VAL* 5.3 2.8 - - - +
134K LYS 5.8 0.2 + - - -
136K PRO* 3.2 34.9 - - - +
256K GLY 3.2 14.1 + - - +
257K GLU* 2.9 41.0 + - - +
259K PHE* 1.3 78.6 - - - +
261K ASP* 1.3 87.5 + - - +
262K ASN 3.4 0.3 + - - -
263K GLY 3.7 0.5 + - - -
310K ARG 3.0 22.7 + - - -
312K ALA 4.0 13.7 - - - +
314K LEU* 3.3 23.7 - - + +
319K GLY 5.4 0.2 - - - -
321K GLY* 3.1 24.5 + - - -
322K SER* 3.9 33.1 + - - +
323K LEU* 4.1 11.7 - - + -
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Residues in contact with ASP 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257K GLU* 2.7 30.1 + - - +
258K TRP* 4.6 3.6 - - - +
260K ARG* 1.3 108.0 + - - +
262K ASN* 1.3 65.9 + - - +
263K GLY 3.4 2.3 + - - -
314K LEU* 3.8 12.1 - - - +
318K GLU 5.2 6.1 - - - +
319K GLY* 5.4 3.0 - - - -
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Residues in contact with ASN 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K TRP* 2.9 63.7 + - + +
259K PHE* 3.6 3.1 + - - +
260K ARG 3.2 1.2 - - - -
261K ASP* 1.3 86.5 - - - +
263K GLY* 1.3 55.1 + - - +
264K LYS* 3.1 20.0 + - + +
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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
------------------------------------------------------------
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