Contacts of the helix formed by residues 343 - 376 (chain A) in PDB entry 4M8J
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 THR 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA 3.0 14.8 + - - +
76A LYS* 3.1 14.8 - - - -
77A LYS 2.6 24.2 + - - -
78A ARG* 4.0 15.3 - - - +
79A LEU* 5.0 0.7 - - - -
342A ARG* 1.3 75.3 - - - +
344A VAL* 1.3 63.1 + - - +
345A ARG* 4.3 3.8 - - + +
346A GLU* 3.0 44.0 + - + +
347A LEU* 3.0 12.2 + - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.9 26.7 - - + +
74A TYR* 3.1 30.7 - - + +
75A ALA 3.7 1.6 - - - +
77A LYS 3.3 14.4 - - - +
79A LEU* 4.2 10.5 - - + +
155A VAL* 4.1 22.4 - - + -
342A ARG 4.2 0.2 + - - -
343A THR* 1.3 73.8 + - - +
345A ARG* 1.3 61.5 + - - +
347A LEU* 3.8 8.0 - - - +
348A CYS* 3.0 33.6 + - - -
502A TRP* 3.9 24.5 - - + -
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 2.7 52.9 + - + +
71A PHE* 4.1 18.2 - - - +
75A ALA* 3.1 37.9 + - + +
76A LYS* 5.4 0.7 - - - -
343A THR* 3.1 4.6 + - + -
344A VAL* 1.3 79.9 - - - +
346A GLU* 1.3 58.2 + - + +
348A CYS* 4.1 1.6 - - - +
349A LEU* 3.2 41.3 + - + +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 5.8 2.3 + - - -
88A THR* 4.7 8.5 - - - +
91A TRP* 3.5 15.9 - - - -
342A ARG* 3.4 37.5 + - + +
343A THR* 3.0 40.4 + - + +
345A ARG* 1.3 76.3 - - - +
347A LEU* 1.3 66.6 + - - +
349A LEU* 3.9 9.4 - - + -
350A GLY* 3.2 14.0 + - - -
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.4 11.4 - - + -
91A TRP* 3.9 14.3 - - + -
95A MET* 4.5 2.2 - - + -
154A SER* 4.1 24.7 - - - +
155A VAL* 3.7 26.2 - - + -
158A ALA* 4.7 0.4 - - + -
335A LEU* 4.8 3.6 - - + +
339A SER* 3.2 39.3 - - - +
342A ARG* 5.4 4.0 - - + -
343A THR 3.0 11.9 + - - +
344A VAL* 3.8 9.9 - - - +
345A ARG 3.3 0.2 - - - -
346A GLU* 1.3 79.3 - - - +
348A CYS* 1.3 57.6 + - - +
349A LEU 2.9 0.7 + - - -
351A MET* 2.8 50.6 + - + +
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Residues in contact with CYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.5 16.9 + - - +
69A LEU* 3.6 28.5 - - - -
70A VAL* 4.0 15.3 - - + -
151A SER* 2.4 33.2 - - - +
155A VAL* 4.1 4.3 - - - -
344A VAL 3.0 23.4 + - - +
345A ARG 4.1 0.4 - - - +
347A LEU* 1.3 77.9 - - - +
349A LEU* 1.3 61.7 + - - +
351A MET* 4.1 7.0 - - - -
352A VAL* 3.3 28.9 + - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.9 26.7 - - + -
70A VAL* 4.0 18.6 - - + -
345A ARG* 3.2 36.8 + - + +
346A GLU* 4.2 7.0 - - - +
347A LEU 2.9 1.8 + - - -
348A CYS* 1.3 76.5 - - - +
350A GLY* 1.3 65.4 + - - +
351A MET 3.2 1.1 - - - -
352A VAL* 4.1 1.4 - - - +
353A SER* 3.1 25.0 + - - -
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 4.4 5.6 - - - -
92A ILE* 3.3 26.7 - - - +
95A MET* 3.8 3.6 - - - +
346A GLU 3.2 13.3 + - - -
349A LEU* 1.3 78.2 - - - +
351A MET* 1.3 57.0 + - - +
353A SER* 2.9 7.6 + - - -
354A GLY* 2.9 24.8 + - - -
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Residues in contact with MET 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 3.6 22.9 - - + +
147A TRP* 3.2 27.4 - - + +
150A TYR* 3.5 14.6 - - + -
151A SER* 3.5 35.2 - - - +
154A SER* 3.9 9.9 - - - +
335A LEU* 3.6 22.4 - - + -
347A LEU* 2.8 22.2 + - + +
348A CYS* 4.1 6.3 - - - +
350A GLY* 1.3 74.5 - - - +
352A VAL* 1.3 62.9 + - - +
355A LEU* 2.8 52.1 + - + +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.3 27.6 - - + +
144A PRO* 3.6 31.9 - - + +
147A TRP* 4.2 11.0 - - - +
148A ALA* 4.0 22.2 - - + +
348A CYS 3.3 19.7 + - - +
349A LEU* 4.2 1.8 - - - +
351A MET* 1.3 82.9 - - + +
353A SER* 1.3 58.3 + - - +
356A THR* 2.5 37.2 + - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 4.6 3.1 - - - +
349A LEU 3.1 15.8 + - - -
350A GLY* 2.9 16.5 + - - -
352A VAL* 1.3 79.4 - - - +
354A GLY* 1.3 70.8 + - - +
356A THR* 3.9 2.2 - - - -
357A ALA* 3.0 26.6 + - - +
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Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 4.2 23.3 - - - -
95A MET* 4.6 5.6 - - - -
96A PHE* 3.9 16.4 - - - -
350A GLY 2.9 14.2 + - - -
351A MET 3.9 0.2 - - - -
353A SER* 1.3 81.9 + - - +
355A LEU* 1.3 64.7 + - - +
357A ALA* 3.8 6.7 + - - +
358A GLY 3.5 11.6 + - - -
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 3.5 40.4 - - + +
98A SER* 4.1 6.7 - - - +
99A CYS* 3.7 10.8 - - - -
147A TRP* 3.5 52.9 - - + -
331A MET* 4.7 3.8 - - + -
335A LEU* 4.2 15.7 - - + -
351A MET* 2.8 42.0 + - + +
352A VAL 4.1 0.2 - - - +
354A GLY* 1.3 74.3 - - - +
356A THR* 1.3 56.6 - - - +
358A GLY* 2.8 23.7 + - - -
359A THR* 3.0 11.3 + - - -
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Residues in contact with THR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY* 4.0 1.1 - - - -
144A PRO* 3.3 44.4 - - + +
147A TRP* 3.6 5.5 - - - -
352A VAL 2.5 23.0 + - - -
353A SER* 3.9 3.4 - - - -
355A LEU* 1.3 76.6 - - - +
357A ALA* 1.3 55.2 + - - +
359A THR* 3.4 8.3 - - - -
360A TRP* 2.6 72.2 + - + +
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Residues in contact with ALA 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.7 13.9 - - + -
353A SER 3.0 19.2 + - - +
354A GLY* 3.8 8.7 - - - +
356A THR* 1.3 76.6 - - - +
358A GLY* 1.3 57.2 + - - +
360A TRP* 4.5 4.7 - - - +
361A LEU* 3.1 32.8 + - + +
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Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.4 24.0 - - - -
99A CYS* 4.0 15.3 - - - -
354A GLY 3.5 3.6 + - - -
355A LEU 2.8 9.8 + - - -
357A ALA* 1.3 80.9 - - - +
359A THR* 1.3 58.9 + - - -
361A LEU* 3.7 2.8 - - - +
362A ILE* 3.2 30.1 + - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A CYS* 4.1 15.3 - - + +
142A TRP* 2.9 32.8 + - + +
147A TRP* 3.2 40.9 + - + +
355A LEU 3.0 3.8 + - - -
356A THR* 3.2 9.9 + - - -
358A GLY* 1.3 73.1 - - - +
360A TRP* 1.3 62.8 + - - +
361A LEU 3.2 0.2 - - - -
362A ILE* 3.3 2.9 + - - -
363A TRP* 3.1 50.6 + - + +
601A NM2 5.5 6.3 - - + -
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Residues in contact with TRP 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER 5.1 0.2 - - - -
139A LEU* 2.9 45.9 + - + +
142A TRP* 3.6 15.3 - - + -
143A GLY* 3.5 4.6 - - - -
144A PRO* 3.8 18.8 - - + -
286A PHE* 3.7 32.8 - + + -
290A VAL* 4.7 16.2 - - + -
293A LEU* 3.8 28.7 - - + -
294A LEU* 6.3 1.1 - - + -
356A THR* 2.6 37.6 + - + +
357A ALA* 4.5 4.0 - - - +
359A THR* 1.3 74.0 + - - +
361A LEU* 1.3 60.9 + - - +
363A TRP* 4.3 2.9 - - + -
364A THR* 3.1 32.4 + - - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.3 22.4 - - + -
267A PHE* 5.4 6.7 - - + -
270A LEU* 3.7 26.7 - - + -
357A ALA* 3.1 20.2 + - + +
358A GLY 3.7 5.8 - - - +
359A THR 3.2 0.2 - - - -
360A TRP* 1.3 79.3 - - - +
362A ILE* 1.3 62.4 + - - +
364A THR* 3.2 3.3 + - - -
365A ILE* 3.1 44.1 + - + +
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Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A CYS* 3.5 29.2 - - + +
100A THR* 5.2 3.1 - - + -
104A VAL* 3.6 32.8 - - + +
105A LEU* 5.4 1.6 - - + -
108A GLY* 4.7 0.9 - - - -
266A SER* 5.5 4.3 - - - +
270A LEU* 3.9 25.8 - - + -
358A GLY 3.2 20.9 - - - +
359A THR* 3.3 8.4 + - - +
360A TRP 3.2 0.6 - - - -
361A LEU* 1.3 76.7 - - - +
363A TRP* 1.3 62.7 + - + +
364A THR 3.2 0.3 + - - -
365A ILE* 3.3 1.2 + - - +
366A LEU* 2.8 55.1 + - + +
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Residues in contact with TRP 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 3.4 32.8 - - + -
107A TRP* 3.7 22.5 + + + -
108A GLY* 4.0 20.8 - - - +
111A GLU* 3.2 26.6 + - + -
135A LEU* 3.6 8.6 - - + +
138A SER* 3.3 23.1 - - - +
139A LEU* 5.1 3.1 - - + -
142A TRP* 3.2 60.2 - + + +
323A TRP* 6.2 0.4 - + - -
359A THR* 3.1 49.4 + - + +
360A TRP* 4.4 2.9 - - + +
362A ILE* 1.3 85.4 - - + +
364A THR* 1.3 59.8 + - + +
367A GLY* 2.9 26.6 + - - -
601A NM2 6.1 2.7 - - + -
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.7 17.2 - - + +
139A LEU* 3.7 23.1 - - + -
282A ILE* 4.1 17.0 - - - +
286A PHE* 3.5 34.1 - - + -
360A TRP 3.1 19.7 + - - +
361A LEU* 3.2 6.9 + - - -
363A TRP* 1.3 76.8 - - - +
365A ILE* 1.3 72.8 + - - +
368A GLY* 2.9 27.2 + - - -
369A ASN 4.1 0.2 + - - -
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 3.8 39.0 - - + +
273A VAL* 3.8 20.6 - - + +
274A PHE* 3.6 37.9 - - + +
282A ILE* 4.1 12.3 - - + +
361A LEU* 3.1 42.6 + - + +
362A ILE 3.9 1.1 - - - +
364A THR* 1.3 90.4 + - - +
366A LEU* 1.3 61.5 + - + +
369A ASN* 3.1 27.5 + - - +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.0 28.7 - - + +
108A GLY 3.2 20.4 - - - +
109A SER* 4.0 17.3 - - - +
270A LEU* 4.2 13.0 - - + -
273A VAL* 4.5 16.4 - - + -
362A ILE* 2.8 39.6 + - + +
365A ILE* 1.3 84.2 - - + +
367A GLY* 1.3 58.5 + - - +
369A ASN* 3.5 8.7 + - - +
370A THR* 3.1 30.1 + - - -
398A TRP* 4.8 9.2 - - + +
411A PHE* 4.7 12.3 - - + -
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Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY 3.0 11.9 + - - -
112A ILE* 3.4 34.1 - - - +
135A LEU* 5.2 0.7 - - - -
363A TRP* 2.9 19.3 + - - -
366A LEU* 1.3 74.1 - - - +
368A GLY* 1.3 59.3 + - - +
369A ASN 3.1 1.3 - - - -
370A THR* 3.2 2.1 + - - -
371A LEU 3.0 24.6 + - - -
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Residues in contact with GLY 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 4.4 0.6 - - - +
135A LEU* 4.7 1.2 - - - +
281A PHE* 3.6 9.8 - - - -
282A ILE* 4.8 6.7 - - - -
285A TYR* 4.4 23.3 - - - -
363A TRP 3.8 1.0 + - - -
364A THR* 2.9 21.0 + - - +
367A GLY* 1.3 76.9 - - - +
369A ASN* 1.3 60.6 + - - +
371A LEU* 3.8 3.3 + - - +
372A GLN* 3.3 27.6 + - - +
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Residues in contact with ASN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A VAL* 3.8 21.7 - - + +
277A GLY* 4.9 7.2 - - - +
282A ILE* 4.9 2.1 - - + +
365A ILE 3.1 21.4 + - - +
366A LEU* 3.5 10.0 + - - +
367A GLY 3.1 0.4 - - - -
368A GLY* 1.3 76.3 - - - +
370A THR* 1.3 80.0 + - - +
372A GLN* 3.2 28.3 + - - +
373A LEU* 3.3 25.4 + - - +
397A THR* 4.2 21.8 + - - -
398A TRP* 5.2 3.8 - - - -
401A LEU* 4.2 15.2 - - - +
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A SER* 2.7 32.6 + - - +
110A ILE* 5.1 1.8 - - + -
112A ILE* 3.8 11.7 - - + -
113A TYR* 4.9 5.8 - - + -
366A LEU 3.1 13.1 + - - -
367A GLY 3.2 7.4 + - - -
369A ASN* 1.3 80.1 + - - +
371A LEU* 1.3 63.9 + - - +
373A LEU* 3.2 20.0 + - - +
374A ILE* 3.2 25.5 + - + +
381A ILE* 5.0 6.3 - - + -
397A THR* 3.9 21.7 + - + +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.6 18.8 - - + +
116A ILE* 5.3 6.7 - - + -
131A LYS* 4.5 22.2 - - + +
134A GLY* 6.0 0.4 - - - -
281A PHE* 3.5 28.7 - - + -
285A TYR* 3.3 31.2 - - + +
367A GLY 3.0 15.4 + - - +
368A GLY* 3.9 5.2 - - - +
369A ASN 3.2 0.2 - - - -
370A THR* 1.3 76.7 - - - +
372A GLN* 1.3 53.1 + - + +
374A ILE* 3.0 15.4 + - + +
375A ASP* 2.6 59.4 + - - +
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLY* 2.7 34.2 + - - +
278A GLY* 4.0 5.0 - - - +
281A PHE* 3.4 39.8 - - + +
282A ILE* 5.0 0.6 - - - +
368A GLY 3.3 10.9 + - - +
369A ASN* 3.2 24.9 + - - +
371A LEU* 1.3 78.1 - - + +
373A LEU* 1.3 59.3 + - + +
375A ASP* 3.9 8.1 - - - +
376A GLN* 2.7 59.0 + - - +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASN* 3.3 27.6 - - - +
370A THR* 3.2 8.2 + - - +
372A GLN* 1.3 81.1 - - + +
374A ILE* 1.3 60.9 + - + +
376A GLN* 5.0 0.7 - - - +
377A ASN 3.4 0.5 + - - -
378A ILE* 3.1 50.3 + - + -
379A LEU* 3.2 26.5 + - + -
381A ILE* 6.0 1.8 - - + -
397A THR* 3.5 47.8 - - + +
400A ALA* 4.1 22.2 - - + +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 5.3 0.9 - - + -
113A TYR* 4.1 26.7 - - + +
116A ILE* 4.3 12.6 - - + -
126A TYR* 3.9 29.8 - - + +
131A LYS* 6.2 2.0 - - - -
370A THR* 3.2 28.9 + - + +
371A LEU* 3.0 12.0 + - + +
373A LEU* 1.3 76.1 - - - +
375A ASP* 1.3 67.1 + - - +
377A ASN* 3.2 17.8 + - - +
379A LEU 4.4 8.6 - - - +
381A ILE* 3.9 24.0 - - + -
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 3.5 30.8 + - - +
281A PHE* 5.2 4.9 - - - -
371A LEU* 2.6 37.6 + - - +
372A GLN* 3.5 9.6 - - - +
374A ILE* 1.3 76.0 - - - +
376A GLN* 1.3 61.4 + - + +
377A ASN* 3.2 9.7 + - - +
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Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A GLN* 2.7 39.1 + - - +
373A LEU* 5.0 0.7 - - - +
375A ASP* 1.3 76.0 - - + +
377A ASN* 1.3 62.6 + - - +
378A ILE* 2.9 40.8 + - + +
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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
------------------------------------------------------------
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