Contacts of the helix formed by residues 241 - 262 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J LEU 3.6 12.3 - - - +
78J PHE* 3.2 35.8 + - - +
79J GLY* 4.3 5.2 - - - +
240J GLU* 1.3 81.2 - - - +
242J ALA* 1.3 65.1 + - - +
243J PRO* 3.4 4.5 - - + -
244J LEU* 3.3 16.6 + - + +
245J GLN* 3.4 12.0 + - - +
287M THR* 5.3 1.3 - - - -
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Residues in contact with ALA 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240J GLU 3.8 0.4 + - - -
241J ALA* 1.3 67.6 - - - +
243J PRO* 1.3 76.0 - - + +
245J GLN* 3.1 8.7 + - - +
246J TYR* 2.9 21.2 + - - +
279J ALA* 3.7 21.1 - - + +
282J GLN* 3.6 37.4 - - - +
283J LEU* 3.9 12.3 - - + -
287M THR* 4.3 10.7 - - + +
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Residues in contact with PRO 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J GLY 5.7 0.4 - - - +
64J MET* 5.4 1.8 - - + -
76J VAL* 3.8 20.9 - - + -
77J LEU 3.5 17.9 - - - +
78J PHE* 3.5 24.7 - - + -
241J ALA* 3.5 10.5 - - + -
242J ALA* 1.3 95.6 - - + +
244J LEU* 1.3 55.7 + - - +
246J TYR* 3.0 6.6 + - + +
247J LEU* 2.9 33.5 + - + +
283J LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J PHE* 3.4 52.3 - - + +
111J ASP* 5.4 4.5 - - - +
112J ALA* 3.0 31.8 - - + +
113J LEU* 4.0 29.6 - - + -
236J ALA* 3.6 2.0 - - + +
240J GLU* 3.7 39.9 - - + +
241J ALA* 3.5 13.0 - - + +
242J ALA 3.2 0.6 - - - -
243J PRO* 1.3 77.3 - - - +
245J GLN* 1.3 60.1 + - - +
247J LEU* 3.5 2.6 + - + +
248J ALA* 3.1 9.7 + - - +
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Residues in contact with GLN 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J VAL* 4.0 15.4 - - + +
209J GLY* 4.4 7.1 + - - -
236J ALA* 3.4 28.9 - - + +
237J THR 3.1 21.4 + - - +
238J ALA* 3.3 19.4 + - - +
240J GLU 3.4 13.3 + - - -
241J ALA 3.4 9.2 + - - +
242J ALA* 3.1 8.6 + - - +
244J LEU* 1.3 75.0 - - + +
246J TYR* 1.3 64.7 + - - +
248J ALA* 3.6 0.9 + - - +
249J PRO* 3.1 20.4 - - - +
275J LYS* 3.9 15.4 - - - +
276J GLN* 3.9 7.2 - - - +
279J ALA* 4.0 13.5 - - + +
286M ALA* 6.1 0.9 - - - +
287M THR* 4.6 9.1 - - - +
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Residues in contact with TYR 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLU* 4.8 8.0 + - - -
64J MET* 4.9 13.7 - - + -
66J LEU* 5.1 10.2 - - + +
132J GLN* 3.8 19.4 + - - -
242J ALA 2.9 13.0 + - - +
243J PRO* 3.0 15.9 + - + +
245J GLN* 1.3 78.7 - - - +
247J LEU* 1.3 86.0 + - + +
250J PHE* 3.7 9.3 - + - -
276J GLN* 3.5 25.1 + - - -
279J ALA* 4.4 8.5 - - + +
280J TYR* 3.4 44.9 - + + +
283J LEU* 4.4 13.2 - - + -
303J LEU* 3.7 20.9 - - + -
306J ARG* 4.0 12.1 + - - -
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Residues in contact with LEU 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J MET* 4.3 11.2 - - + -
78J PHE* 3.7 33.4 - - + -
97J VAL* 3.8 32.1 - - + -
112J ALA* 4.7 3.6 - - + +
113J LEU* 4.6 11.0 - - + -
131J ALA* 4.9 8.1 - - + -
132J GLN* 5.1 5.8 - - - +
243J PRO 2.9 15.3 + - - +
244J LEU* 4.1 4.7 - - + +
246J TYR* 1.3 100.5 - - + +
248J ALA* 1.3 68.1 + - - +
249J PRO 3.3 1.1 - - - -
250J PHE* 2.7 10.5 + - + +
251J THR* 2.7 32.5 + - - +
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Residues in contact with ALA 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ALA* 4.0 11.0 - - + +
206J VAL* 4.2 4.0 - - + -
208J VAL* 4.1 9.4 - - + -
234J VAL* 3.9 14.0 - - + +
236J ALA* 3.6 22.0 - - + +
244J LEU 3.1 17.9 + - - +
245J GLN 3.7 2.7 - - - +
247J LEU* 1.3 75.1 - - - +
249J PRO* 1.3 65.1 - - + +
251J THR* 3.2 4.2 + - - -
252J ALA* 2.8 31.9 + - - +
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Residues in contact with PRO 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206J VAL* 4.0 11.9 - - + -
208J VAL* 4.3 12.3 - - + -
245J GLN 3.1 14.8 - - - +
246J TYR 3.7 4.3 - - - +
247J LEU 3.4 4.3 - - - -
248J ALA* 1.3 92.2 - - + +
250J PHE* 1.3 57.1 + - - +
252J ALA* 3.6 0.5 + - - +
253J ALA* 3.1 21.1 + - - +
270J TYR* 3.5 13.3 - - + -
273J LEU* 4.7 3.4 - - + -
276J GLN* 3.3 30.3 - - + +
307J LEU* 3.2 37.3 - - + +
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Residues in contact with PHE 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J ALA* 3.9 19.5 - - + +
132J GLN* 4.0 28.3 - - - +
246J TYR* 3.7 20.0 - + - -
247J LEU* 2.7 14.0 + - + +
249J PRO* 1.3 73.0 - - - +
251J THR* 1.3 63.7 + - - +
253J ALA* 3.1 15.6 + - - +
254J SER* 3.3 8.3 + - - -
276J GLN* 3.9 10.5 - - - -
303J LEU* 3.4 46.4 - - + -
306J ARG* 3.9 17.0 - - + -
307J LEU* 3.6 35.7 - - + -
310J ARG* 3.7 23.1 + - - -
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Residues in contact with THR 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J VAL* 4.9 4.9 - - - +
98J ASP 6.1 0.2 - - - -
99J VAL* 3.5 36.5 - - + +
111J ASP 5.0 1.3 - - - +
112J ALA* 3.0 31.0 + - - +
113J LEU 5.0 0.4 - - - -
114J GLY* 5.1 0.4 - - - +
131J ALA* 4.6 10.7 - - - +
234J VAL* 4.8 4.3 - - + -
247J LEU* 2.7 25.1 + - - +
248J ALA* 3.5 9.0 - - - -
250J PHE* 1.3 73.6 - - - +
252J ALA* 1.3 63.2 + - - +
254J SER* 3.2 12.2 + - - -
255J ILE* 3.2 21.0 + - + +
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Residues in contact with ALA 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204J VAL* 3.9 5.7 - - + +
206J VAL* 3.6 29.6 - - + -
234J VAL* 3.6 26.2 - - + +
248J ALA 2.8 17.0 + - - +
249J PRO 3.8 1.8 - - - +
251J THR* 1.3 77.1 - - - +
253J ALA* 1.3 63.2 + - - +
255J ILE* 3.0 16.2 + - - +
256J GLY 3.1 10.4 + - - -
268J ILE* 3.8 11.2 - - + +
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Residues in contact with ALA 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249J PRO 3.1 15.9 + - - +
250J PHE 3.1 11.4 + - - +
252J ALA* 1.3 76.5 - - - +
254J SER* 1.3 55.9 + - - +
256J GLY* 3.7 0.7 + - - -
257J GLU* 2.9 28.8 + - - +
268J ILE* 3.9 10.1 - - - +
270J TYR* 3.8 7.0 - - - +
307J LEU* 3.7 15.3 - - + +
310J ARG* 3.3 25.0 + - + +
323J LEU* 4.0 10.5 - - + +
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Residues in contact with SER 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J VAL* 3.8 13.5 - - - -
101J VAL* 3.4 12.8 - - - +
129J SER* 4.1 11.7 + - - -
130J ARG 2.9 27.1 + - - -
131J ALA 4.1 0.2 + - - -
133J VAL* 3.6 5.0 - - - +
250J PHE 3.3 4.3 + - - -
251J THR* 3.2 9.5 + - - -
252J ALA 3.1 0.8 - - - -
253J ALA* 1.3 74.1 - - - +
255J ILE* 1.3 65.3 + - - +
256J GLY 3.3 0.2 - - - -
257J GLU* 3.6 7.2 - - - +
258J TRP* 3.3 15.6 + - - +
310J ARG* 2.8 23.4 + - - +
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Residues in contact with ILE 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J VAL* 3.7 21.8 - - + -
100J PRO 5.1 0.7 - - - +
101J VAL* 3.9 9.8 - - + +
102J GLY 4.9 2.1 + - - +
105J LEU* 3.6 31.4 - - + -
110J VAL* 4.9 5.4 - - + -
114J GLY* 6.1 0.7 - - - -
204J VAL* 5.1 2.7 - - + -
232J ILE* 3.5 33.2 - - + -
234J VAL* 3.7 29.2 - - + -
251J THR* 3.2 19.7 - - + +
252J ALA* 3.0 7.7 + - - +
254J SER* 1.3 78.7 - - - +
256J GLY* 1.3 59.6 + - - +
258J TRP* 3.6 10.0 - - - +
259J PHE* 3.3 17.3 - - - -
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Residues in contact with GLY 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204J VAL* 4.3 16.1 - - - +
252J ALA 3.1 12.0 + - - -
253J ALA 4.1 0.9 - - - -
255J ILE* 1.3 73.2 - - - +
257J GLU* 1.3 66.0 + - - +
258J TRP 3.0 2.7 - - - -
259J PHE* 3.1 24.1 + - - +
260J ARG* 3.3 9.4 + - - +
266J ALA* 3.7 7.0 - - - +
268J ILE* 5.9 1.1 - - - -
323J LEU* 4.1 16.9 - - - +
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Residues in contact with GLU 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J VAL* 3.6 24.0 - - - +
134J LYS 4.4 4.3 - - - +
253J ALA 2.9 16.4 + - - +
254J SER* 3.7 9.8 + - - +
255J ILE 3.4 0.2 - - - -
256J GLY* 1.3 77.2 - - - +
258J TRP* 1.3 62.3 + - - +
260J ARG* 2.8 49.3 + - - +
261J ASP* 2.9 37.2 + - - +
310J ARG* 2.7 38.5 + - - +
323J LEU* 4.2 5.6 - - + +
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Residues in contact with TRP 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J VAL* 4.0 26.0 - - + -
102J GLY* 3.9 16.1 - - - +
103J PRO* 3.2 37.5 - - + -
126J ALA* 4.5 12.8 + - + +
127J GLY* 6.2 0.2 - - - -
129J SER* 5.9 0.2 - - - +
254J SER 3.3 9.7 + - - +
255J ILE 3.6 12.6 - - - +
256J GLY 3.0 0.2 - - - -
257J GLU* 1.3 78.1 - - - +
259J PHE* 1.3 103.9 + + - +
261J ASP* 3.1 6.8 + - - -
262J ASN* 2.9 70.3 + - + +
264J LYS* 4.7 17.5 - - + -
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Residues in contact with PHE 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102J GLY 4.3 8.1 - - - -
103J PRO* 4.8 1.1 - - + -
106J LEU* 4.1 15.5 - - + -
202J TYR* 3.3 52.5 - + + -
204J VAL* 5.4 2.2 - - + -
232J ILE* 4.0 24.7 - - + -
255J ILE 3.3 24.7 - - - -
256J GLY* 3.5 13.5 - - - +
258J TRP* 1.3 105.8 - + - +
260J ARG* 1.3 63.8 + - - +
262J ASN* 3.0 13.1 + - - +
264J LYS* 3.1 33.1 + - + -
265J HIS 4.6 1.6 - - - -
266J ALA* 3.7 16.2 - - + -
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Residues in contact with ARG 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J LYS 5.5 0.6 + - - -
136J PRO* 3.2 27.3 - - - +
256J GLY 3.3 2.4 + - - +
257J GLU* 2.8 45.7 + - - +
259J PHE* 1.3 78.5 - - - +
261J ASP* 1.3 86.1 + - - +
263J GLY 4.1 0.5 + - - -
310J ARG* 2.8 30.2 + - - +
312J ALA 4.1 9.4 - - - -
314J LEU* 3.2 34.7 - - + +
319J GLY 5.6 0.3 - - - -
321J GLY* 3.3 15.6 + - - -
322J SER* 3.4 40.9 + - - +
323J LEU* 3.9 19.7 - - + +
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Residues in contact with ASP 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J GLU* 2.9 29.3 + - - +
258J TRP* 3.6 6.3 + - + +
260J ARG* 1.3 110.4 + - - +
262J ASN* 1.3 66.2 + - - +
263J GLY 3.3 6.7 + - - -
314J LEU* 4.0 11.3 - - + +
318J GLU* 5.0 7.8 - - - +
319J GLY* 5.3 2.8 - - - -
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Residues in contact with ASN 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J TRP* 2.9 66.4 + - + +
259J PHE* 3.0 4.4 + - - +
261J ASP* 1.3 86.5 - - - +
263J GLY* 1.3 63.2 + - - +
264J LYS* 3.4 15.0 + - + +
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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