Contacts of the helix formed by residues 348 - 370 (chain A) in PDB entry 1MF8
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 ASP 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.3 0.4 - - - -
346A PHE 3.8 0.4 + - - +
347A MET* 1.3 76.3 - - - +
349A VAL* 1.3 58.0 + - - +
350A PHE* 2.7 40.9 + - - +
351A THR* 2.7 27.0 + - - -
352A TRP* 3.0 20.0 + - - +
135B THR* 3.6 21.8 - - + +
155B VAL* 3.2 22.3 - - + +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.1 4.3 - - + -
347A MET 4.2 0.2 + - - -
348A ASP* 1.3 69.8 - - - +
350A PHE* 1.3 52.1 + - + +
352A TRP* 3.7 12.0 - - + +
353A SER* 2.6 37.1 + - - -
111B LEU* 3.4 25.8 - - + -
115B LEU* 3.7 23.0 - - + +
131B ILE* 3.5 42.0 - - + +
135B THR* 3.0 34.3 + - + +
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP* 2.7 19.4 + - - +
349A VAL* 1.3 72.3 - - + +
351A THR* 1.3 60.3 + - - +
352A TRP 3.0 1.1 - - - -
353A SER* 4.1 1.8 - - - -
354A LEU* 2.8 37.0 + - + +
98B TYR* 4.0 15.7 - + - -
106B ILE* 3.7 25.8 - - + -
111B LEU* 3.1 36.1 - - + -
135B THR* 4.0 18.2 - - + -
139B ALA* 5.1 4.0 - - + -
147B ILE* 4.2 24.5 - - + -
152B PHE* 3.5 26.5 - + + -
155B VAL* 4.5 14.4 - - + -
156B VAL* 3.3 21.3 - - + -
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 3.7 23.7 - - + +
348A ASP* 2.7 31.2 + - - -
350A PHE* 1.3 75.5 - - - +
352A TRP* 1.3 64.0 + - - +
355A PRO* 3.1 21.7 - - - +
155B VAL* 4.0 8.3 + - - +
156B VAL* 4.3 0.4 - - - +
159B LEU* 3.8 36.3 - - + +
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Residues in contact with TRP 352 (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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343A LEU* 3.1 34.8 - - + +
347A MET* 3.6 21.1 - - + -
348A ASP 3.0 16.2 + - - +
349A VAL* 3.7 18.2 - - + +
351A THR* 1.3 80.6 - - - +
353A SER* 1.3 66.2 + - - +
355A PRO* 3.5 7.8 - - - +
115B LEU* 4.7 11.0 - - + -
119B VAL* 4.3 4.9 - - + -
123B LEU* 3.4 27.1 - - + -
128B LEU* 5.2 4.0 - - + -
131B ILE* 4.2 11.4 - - + -
7D SAR 4.4 4.2 - - - +
8D MLE 3.6 39.1 - - + +
9D VAL* 2.6 31.5 + - + +
10D MLE 3.0 27.1 - - + -
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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
----------------------------------------------------------
349A VAL 2.6 21.4 + - - -
352A TRP* 1.3 77.9 - - - +
354A LEU* 1.3 55.1 + - - +
355A PRO* 3.2 3.8 - - - -
356A PHE* 2.9 6.5 + - - +
357A VAL* 2.7 33.9 + - - +
98B TYR* 2.7 24.0 + - - -
115B LEU* 3.6 14.5 - - - +
118B MET* 3.8 20.0 - - - -
8D MLE 4.0 15.5 - - - -
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Residues in contact with LEU 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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350A PHE 2.8 22.0 + - - +
351A THR* 4.4 1.8 - - - +
353A SER* 1.3 74.8 + - - +
355A PRO* 1.3 62.2 - - + +
357A VAL* 3.7 5.6 - - + +
358A GLY 2.8 24.3 + - - -
91B LEU* 6.2 0.2 - - + -
94B ALA* 4.4 14.6 - - + -
98B TYR* 3.6 31.8 + - + +
152B PHE* 3.8 17.0 - - + -
156B VAL* 3.6 34.1 - - + +
159B LEU* 4.3 5.8 - - + -
161B ILE* 3.4 38.9 - - + +
165B MET* 6.1 0.4 - - + -
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Residues in contact with PRO 355 (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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351A THR 3.1 21.8 - - - +
352A TRP 3.5 7.2 - - - +
353A SER 3.3 4.5 - - - -
354A LEU* 1.3 91.3 - - + +
356A PHE* 1.3 63.4 + - - +
358A GLY 3.8 1.2 - - - -
359A GLU* 3.3 24.3 + - - +
159B LEU* 4.4 6.7 - - + -
161B ILE* 4.1 23.3 - - + -
164B LYS* 4.6 5.9 + - + +
71C ASN* 6.0 3.4 - - - +
73C THR* 4.0 18.6 - - + +
7D SAR 5.6 2.0 - - - +
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Residues in contact with PHE 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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353A SER 2.9 7.8 + - - +
355A PRO* 1.3 77.5 - - - +
357A VAL* 1.3 66.0 + - - +
359A GLU* 3.2 6.6 + - + +
360A LYS* 3.1 59.6 + - + +
52B PRO* 4.5 10.3 - - + -
53B LEU* 4.9 0.7 - - + -
118B MET* 3.1 65.3 - - + -
73C THR* 4.6 6.6 - - + +
103C ALA* 5.6 5.2 - - + -
5D BMT 6.3 0.7 - - + -
6D ABA 4.9 4.0 - - - -
7D SAR 3.9 27.3 + - - +
8D MLE 3.5 27.6 - - + -
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Residues in contact with VAL 357 (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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353A SER 2.7 22.8 + - - +
354A LEU* 3.7 7.2 - - + +
356A PHE* 1.3 73.6 - - - +
358A GLY* 1.3 55.9 + - - +
359A GLU 2.6 13.3 + - - -
360A LYS* 3.1 8.1 + - - -
361A VAL* 3.1 24.8 + - + +
53B LEU* 3.7 8.9 - - + +
94B ALA* 5.4 3.6 - - + -
97B ILE* 3.7 38.1 - - + -
98B TYR* 3.4 21.8 - - + +
118B MET* 3.6 25.4 - - + -
165B MET* 4.1 9.6 - - + -
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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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354A LEU 2.8 21.6 + - - -
355A PRO 3.6 3.3 + - - -
357A VAL* 1.3 72.3 - - - +
359A GLU* 1.3 56.8 + - - +
361A VAL* 4.2 2.7 - - - -
362A THR* 3.1 21.3 + - - -
161B ILE* 4.1 7.4 - - - -
164B LYS* 3.7 16.1 - - - +
165B MET* 3.8 28.7 - - - +
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Residues in contact with GLU 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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355A PRO 3.3 15.4 + - - +
356A PHE* 3.2 6.5 + - + +
357A VAL 2.6 6.3 + - - -
358A GLY* 1.3 75.8 - - - +
360A LYS* 1.3 72.9 + - + +
361A VAL 3.3 0.9 - - - -
362A THR* 3.2 3.9 + - - +
363A GLU* 2.7 45.3 + - - +
164B LYS* 3.7 19.1 - - - +
69C ARG* 4.2 17.4 + - - +
73C THR* 3.0 37.0 - - - +
74C GLY* 3.9 7.3 - - - -
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Residues in contact with LYS 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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356A PHE* 3.1 38.1 + - + +
357A VAL 3.1 1.2 + - - -
359A GLU* 1.3 93.4 + - + +
361A VAL* 1.3 60.7 + - - +
363A GLU* 3.1 25.5 + - - +
364A MET* 2.8 25.5 + - - +
50B GLN 4.2 10.9 + - - -
51B ASN* 3.1 26.3 + - - +
52B PRO* 3.9 21.1 - - + -
53B LEU* 3.2 24.9 - - + -
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Residues in contact with VAL 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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357A VAL* 3.1 32.4 + - + +
358A GLY* 4.2 1.1 - - - -
360A LYS* 1.3 75.9 - - - +
362A THR* 1.3 68.1 + - - +
364A MET* 3.3 6.6 + - - +
365A LEU* 3.1 28.5 + - - +
53B LEU* 4.1 10.5 - - + -
57B VAL* 4.1 23.3 - - + +
81B PHE* 3.9 22.9 - - + -
93B PHE* 4.2 8.5 - - + -
97B ILE* 4.2 12.3 - - + -
165B MET* 4.0 23.6 - - + -
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Residues in contact with THR 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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358A GLY 3.1 14.5 + - - -
359A GLU* 3.2 11.3 + - - +
360A LYS 3.1 0.2 - - - -
361A VAL* 1.3 84.5 - - - +
363A GLU* 1.3 66.1 + - - +
365A LEU* 3.4 4.0 + - - +
366A VAL* 3.0 37.0 + - + +
81B PHE* 5.6 0.7 - - - -
164B LYS* 3.0 27.1 + - + +
165B MET* 3.7 8.8 - - - -
166B VAL 4.2 11.4 + - - +
167B VAL* 5.1 5.6 - - + +
69C ARG* 4.8 18.6 - - - +
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Residues in contact with GLU 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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359A GLU* 2.7 38.4 + - - +
360A LYS* 3.1 29.5 + - - +
362A THR* 1.3 81.3 - - - +
364A MET* 1.3 59.4 + - - +
366A VAL* 3.4 5.0 + - - +
367A ASN* 2.8 42.7 + - - +
47B GLU 4.2 3.8 - - - +
50B GLN 4.2 4.2 - - - +
51B ASN* 4.0 11.4 + - - +
81C GLU* 4.0 19.8 - - - +
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Residues in contact with MET 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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360A LYS 2.8 18.5 + - - +
361A VAL* 3.7 5.8 - - - +
362A THR 3.3 0.2 - - - -
363A GLU* 1.3 71.1 - - - +
365A LEU* 1.3 72.4 + - + +
367A ASN* 3.2 4.8 + - - +
368A VAL* 3.0 30.5 + - + +
42B PHE* 3.9 32.3 - - + -
48B LEU* 3.9 23.5 - - + +
51B ASN* 4.0 12.8 - - - +
53B LEU 6.2 0.2 - - - -
54B VAL* 3.9 20.6 - - + -
57B VAL* 3.6 37.9 - - + -
58B ILE* 4.0 20.2 - - + -
61B PHE* 6.0 1.6 - - + -
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Residues in contact with LEU 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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361A VAL 3.1 13.5 + - - +
362A THR 4.0 2.5 - - - +
364A MET* 1.3 84.1 - - + +
366A VAL* 1.3 59.0 + - - +
368A VAL* 3.0 11.7 + - + +
369A LEU* 2.8 42.2 + - + +
42B PHE* 6.4 0.2 - - + -
57B VAL* 4.5 12.1 - - + -
61B PHE* 3.7 28.5 - - + -
78B VAL* 4.9 9.4 - - + -
81B PHE* 3.6 52.5 - - + -
167B VAL* 4.0 16.8 - - + -
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Residues in contact with VAL 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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362A THR* 3.0 34.3 + - + +
363A GLU* 3.5 7.4 - - - +
364A MET 3.2 0.2 - - - -
365A LEU* 1.3 78.1 - - - +
367A ASN* 1.3 67.6 + - - +
369A LEU* 4.9 3.6 - - - -
370A ASN* 2.5 47.0 + - - +
166B VAL 5.6 0.2 - - - +
167B VAL* 4.9 14.6 - - + -
69C ARG* 6.0 2.0 - - - +
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Residues in contact with ASN 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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363A GLU* 2.8 31.9 + - - +
364A MET* 3.2 1.2 + - - +
365A LEU 3.2 0.6 - - - -
366A VAL* 1.3 87.9 - - - +
368A VAL* 1.3 64.5 - - - +
369A LEU 3.3 0.2 - - - -
370A ASN* 3.6 11.7 + - - +
371A ILE* 3.7 5.5 + - - -
45B LEU* 3.1 21.2 - - + +
47B GLU* 2.4 54.5 + - + +
48B LEU* 3.7 18.4 - - + +
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Residues in contact with VAL 368 (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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364A MET* 3.0 31.0 + - + +
365A LEU* 3.4 14.6 - - + +
367A ASN* 1.3 80.1 - - - +
369A LEU* 1.3 62.1 + - + +
371A ILE* 3.2 25.7 - - - +
25B ARG* 4.6 0.3 - - - +
29B LEU* 4.1 12.4 - - + +
42B PHE* 4.4 17.0 - - + -
45B LEU* 4.4 10.8 - - + -
48B LEU* 4.0 24.9 - - + -
74B PHE* 3.8 31.9 - - + -
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Residues in contact with LEU 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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365A LEU* 2.8 22.9 + - + +
366A VAL* 4.5 3.8 - - - +
368A VAL* 1.3 77.4 - - + +
370A ASN* 1.3 64.0 + - - +
371A ILE 3.0 8.0 + - - -
22B LEU* 4.0 24.9 - - + -
25B ARG* 2.8 48.1 + - - +
74B PHE* 4.1 22.7 - - + -
78B VAL* 4.2 14.8 - - + -
167B VAL* 3.4 35.2 - - + -
168B ASP 3.7 13.0 - - - +
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Residues in contact with ASN 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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366A VAL* 2.5 38.6 + - - +
367A ASN* 3.6 9.4 + - - +
368A VAL 3.4 0.6 - - - -
369A LEU* 1.3 80.4 - - - +
371A ILE* 1.3 60.8 + - - +
25B ARG* 5.9 1.2 - - - +
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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
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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