Contacts of the helix formed by residues 338 - 368 (chain A) in PDB entry 6TPG
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 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A THR* 3.3 2.7 + - - -
337A GLU* 1.4 88.1 - - + +
339A ARG* 1.3 60.2 + - - +
340A GLU* 3.4 13.3 + - - +
341A THR* 2.7 47.9 + - - -
342A VAL* 3.3 22.3 + - - +
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Residues in contact with ARG 339 (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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49A HIS* 2.9 37.0 + - - -
51A LYS* 5.4 1.6 - - - +
118A GLU* 3.4 27.9 + - - -
336A THR* 2.9 31.7 + - + +
337A GLU 4.0 0.8 - - - -
338A ASP* 1.3 70.9 - - - +
340A GLU* 1.3 88.5 + - - +
342A VAL* 3.2 5.4 + - - +
343A TYR* 2.9 77.4 + - + +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS* 5.5 2.8 + - - +
53A TYR* 5.4 0.5 + - - -
338A ASP* 3.2 9.6 + - - +
339A ARG* 1.3 109.2 + - - +
341A THR* 1.3 57.2 + - - +
343A TYR* 3.4 3.9 + - - +
344A ALA* 2.9 29.7 + - - +
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASP* 2.7 40.2 + - - -
340A GLU* 1.3 71.7 - - - +
342A VAL* 1.3 61.5 + - + +
344A ALA* 3.3 6.2 + - - +
345A TRP* 3.0 47.9 + - + +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 5.9 0.9 - - + -
333A PHE* 3.9 39.3 - - + -
336A THR* 4.7 5.2 - - - +
338A ASP 3.3 15.9 + - - +
339A ARG* 3.2 9.9 + - - +
341A THR* 1.3 81.7 - - + +
343A TYR* 1.3 64.5 + - + +
345A TRP* 3.2 6.8 + - - +
346A PHE* 3.1 51.2 + - + -
1202A PG4 4.1 10.5 - - - +
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Residues in contact with TYR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 6.0 1.6 - - - +
53A TYR* 4.6 5.3 + - - +
118A GLU* 4.2 24.5 - - + +
339A ARG* 2.9 65.2 + - + +
340A GLU* 4.0 4.7 - - - +
342A VAL* 1.3 77.7 - - + +
344A ALA* 1.3 61.8 + - - +
346A PHE* 3.6 7.5 + - + +
347A ALA* 3.2 22.3 + - - +
1202A PG4 3.9 55.0 + - - -
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.2 24.1 + - + +
340A GLU 2.9 19.4 + - - +
341A THR* 3.6 8.3 - - - +
343A TYR* 1.3 74.6 - - - +
345A TRP* 1.3 64.8 + - + +
347A ALA* 3.3 4.8 + - - +
348A PHE* 3.1 21.7 + - - +
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Residues in contact with TRP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PRO* 5.1 11.7 - - + -
323A LEU* 3.9 25.6 - - + +
341A THR* 3.0 38.7 + - + +
342A VAL* 3.2 11.2 + - + +
344A ALA* 1.3 76.9 - - + +
346A PHE* 1.3 57.6 + - - +
348A PHE* 3.2 29.9 + + + +
349A SER* 3.0 28.6 + - - -
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 6.1 2.7 - - + -
323A LEU* 3.9 43.7 - - + -
324A ASN* 5.2 2.5 - - - -
327A LYS* 4.1 15.5 - - + -
333A PHE* 4.1 13.7 - + - -
342A VAL* 3.1 39.0 + - + +
343A TYR* 3.8 8.7 - - + +
344A ALA 3.3 0.4 - - - -
345A TRP* 1.3 75.1 - - - +
347A ALA* 1.3 64.0 + - - +
349A SER* 2.8 20.7 + - - -
350A HIS* 2.9 40.9 - + + -
1201A 7MA 5.5 5.2 - - - -
1202A PG4 3.7 45.8 - - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.7 11.2 - - + +
57A LEU* 4.1 28.2 - - + +
61A TYR* 4.4 0.3 + - - -
115A ASP* 3.7 27.2 - - + +
343A TYR 3.2 17.0 + - - +
344A ALA* 3.3 7.8 + - - +
346A PHE* 1.3 76.9 - - - +
348A PHE* 1.3 61.2 + - - +
350A HIS* 3.4 2.5 + - - +
351A TRP* 3.1 23.4 + - - +
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 5.5 1.8 - - - -
319A PRO* 5.1 5.4 - - + -
344A ALA 3.1 12.8 + - - +
345A TRP* 3.6 34.3 - + + +
346A PHE 3.2 0.2 - - - -
347A ALA* 1.3 75.6 - - - +
349A SER* 1.3 62.9 + - - +
350A HIS 3.2 0.2 + - - -
351A TRP* 3.3 26.1 + + - +
352A LEU* 2.9 54.9 + - + +
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A CYS 4.6 0.9 - - - +
319A PRO* 3.8 14.4 - - - -
320A ILE* 3.7 31.7 - - - +
323A LEU* 3.8 7.3 - - - +
345A TRP* 3.0 13.6 + - - -
346A PHE* 2.8 25.5 + - - -
348A PHE* 1.3 79.4 - - - +
350A HIS* 1.3 68.1 + - - +
352A LEU* 3.5 7.9 + - - +
353A VAL* 3.1 27.6 + - - +
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.6 8.7 - - - +
111A THR* 4.1 1.3 - - + +
115A ASP* 2.8 39.1 + - - +
320A ILE* 3.8 9.8 - - + +
346A PHE* 2.9 49.0 + + + +
347A ALA 3.6 1.3 - - - +
348A PHE 3.1 0.2 - - - -
349A SER* 1.3 80.5 - - - +
351A TRP* 1.3 67.4 + - - +
353A VAL* 3.0 14.1 + - - +
354A TYR* 3.3 15.2 + - - -
1201A 7MA 3.3 54.1 + + - +
1202A PG4 5.6 6.1 - - - -
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Residues in contact with TRP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.4 8.7 - - + -
60A GLY* 2.9 35.7 + - - -
61A TYR* 3.3 46.1 + + + -
63A ILE* 6.4 0.7 - - + -
64A VAL* 3.5 23.8 - - + +
347A ALA 3.1 12.6 + - - +
348A PHE* 3.8 25.4 - + + +
350A HIS* 1.3 77.0 - - - +
352A LEU* 1.3 79.9 + - + +
354A TYR* 3.1 6.5 + - + +
355A ALA* 2.7 46.4 + - + +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 4.1 8.3 - - + +
316A CYS* 3.6 45.0 - - - +
319A PRO* 4.0 14.1 - - + -
348A PHE* 2.9 43.1 + - + +
349A SER* 3.6 7.2 - - - +
350A HIS 3.1 0.4 - - - -
351A TRP* 1.3 97.9 - - + +
353A VAL* 1.3 62.0 + - - +
355A ALA* 3.9 5.8 - - + -
356A ASN 3.2 16.6 + - - -
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 4.1 14.1 - - - +
138A VAL* 5.3 0.2 - - + -
316A CYS* 4.5 6.7 - - - +
317A TYR* 3.8 35.0 + - + +
320A ILE* 3.8 35.7 - - + -
349A SER 3.1 15.3 + - - +
350A HIS 3.0 8.7 + - - +
352A LEU* 1.3 77.0 - - - +
354A TYR* 1.3 66.8 + - + +
356A ASN* 3.3 20.1 + - - +
357A SER* 3.8 6.6 + - - -
1201A 7MA 3.8 17.9 - - - +
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Residues in contact with TYR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.6 21.5 - + + -
64A VAL* 3.3 20.6 - - + +
68A ALA* 4.6 0.7 - - - +
103A VAL* 4.3 17.9 - - + -
104A THR* 5.2 4.3 - - - +
107A CYS* 3.4 7.1 + - - +
108A LEU* 3.7 33.4 - - + -
111A THR* 2.7 40.7 + - + -
134A GLN* 3.1 30.9 + - - +
350A HIS 3.3 15.0 + - - -
351A TRP* 3.1 6.1 + - + +
353A VAL* 1.3 77.1 - - + +
355A ALA* 1.3 65.9 + - - +
357A SER* 3.1 19.5 + - - -
358A ALA 3.3 7.6 + - - -
1201A 7MA 3.4 22.8 - - - -
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.8 18.8 - - + +
316A CYS* 5.0 0.9 - - - -
351A TRP* 2.7 47.0 + - + +
352A LEU* 3.6 14.1 - - + +
354A TYR* 1.3 72.7 - - - +
356A ASN* 1.3 57.2 + - - +
358A ALA* 3.0 5.4 + - - +
359A ALA* 2.8 28.2 + - - +
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Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER* 6.4 0.2 - - - -
312A VAL* 3.8 8.5 - - - +
313A PHE* 3.7 28.2 + - - +
316A CYS* 3.4 27.0 - - + -
317A TYR* 3.7 27.6 + - + -
352A LEU 3.2 5.3 + - - -
353A VAL 3.3 11.0 - - - +
354A TYR 3.1 0.6 - - - -
355A ALA* 1.3 77.0 - - - +
357A SER* 1.3 68.0 + - - +
359A ALA* 3.0 14.4 + - - +
360A ASN* 3.1 35.2 + - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 4.1 7.6 - - - -
72A ASN* 3.1 23.6 + - - +
100A ALA* 3.7 32.3 + - - +
103A VAL* 5.0 6.0 - - - +
104A THR* 4.7 4.9 - - - -
317A TYR* 5.0 3.5 + - - -
353A VAL 3.8 6.6 + - - -
354A TYR* 3.1 13.7 + - - -
356A ASN* 1.3 84.9 + - - +
358A ALA* 1.3 57.3 + - - +
360A ASN* 4.5 4.2 - - - +
361A PRO* 3.1 16.3 - - - +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.0 19.1 - - + +
67A VAL* 3.8 15.8 - - + +
68A ALA* 3.7 32.1 - - + +
354A TYR 3.3 3.2 + - - -
355A ALA* 3.0 10.4 + - - +
357A SER* 1.3 77.1 - - - +
359A ALA* 1.3 63.9 + - - +
360A ASN 3.6 0.2 + - - -
361A PRO* 3.7 9.5 - - - +
362A ILE* 3.5 20.0 - - + +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 4.4 20.0 - - + -
316A CYS* 5.6 0.7 - - - -
355A ALA 2.8 12.5 + - - +
356A ASN* 3.0 13.4 + - - +
358A ALA* 1.3 77.4 - - - +
360A ASN* 1.3 67.9 + - - +
362A ILE* 3.0 21.2 + - - +
363A ILE* 3.0 18.0 + - + +
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Residues in contact with ASN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 5.4 1.8 - - - +
96A LEU* 5.3 10.5 - - - +
309A VAL* 3.6 24.7 - - - +
312A VAL* 5.2 0.7 - - - +
356A ASN* 3.1 36.2 + - - +
357A SER* 4.5 3.9 - - - +
359A ALA* 1.3 76.2 - - - +
361A PRO* 1.3 72.1 - - + +
363A ILE* 2.8 33.4 + - - +
364A TYR* 3.0 35.5 + - + +
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Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.1 1.3 - - + +
71A GLY* 3.5 43.7 - - - +
72A ASN* 3.6 18.6 - - - +
75A VAL* 4.2 6.7 - - + -
357A SER 3.1 21.3 - - - +
358A ALA 3.7 7.9 - - - +
360A ASN* 1.3 88.9 - - + +
362A ILE* 1.3 58.3 + - + +
364A TYR* 3.3 14.9 + - + +
365A ASN* 3.0 22.7 + - - +
375A PHE* 3.6 12.0 - - + -
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Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.9 20.6 - - + -
358A ALA* 3.5 20.6 - - + +
359A ALA* 3.0 10.8 + - - +
361A PRO* 1.3 74.6 - - + +
363A ILE* 1.3 67.0 + - + +
365A ASN* 3.3 6.3 + - - +
366A PHE* 3.2 50.0 + - + -
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Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 4.1 12.8 - - + +
308A VAL* 4.1 19.7 - - + -
309A VAL* 3.8 27.8 - - + -
312A VAL* 3.9 31.6 - - + -
359A ALA* 3.0 15.9 + - + +
360A ASN* 2.8 30.2 + - - +
362A ILE* 1.3 79.0 - - + +
364A TYR* 1.3 57.0 + - + +
366A PHE* 3.4 2.4 + - - -
367A LEU* 3.0 36.3 + - + +
----------------------------------------------------------
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.8 22.2 - - + -
93A ILE* 3.1 46.9 + - + +
96A LEU* 4.1 16.1 - - - +
97A SER* 4.6 4.8 + - - -
305A MET* 3.9 23.6 - - + -
306A LEU* 6.1 0.2 - - + -
309A VAL* 4.0 23.0 - - + +
360A ASN* 3.0 36.6 + - + +
361A PRO* 3.3 13.2 + - + +
363A ILE* 1.3 78.2 - - + +
365A ASN* 1.3 63.0 + - - +
368A SER* 3.2 23.9 + - - +
371A PHE* 3.3 30.8 - + + +
375A PHE* 4.3 2.2 - - + -
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Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO 3.0 13.0 + - - +
362A ILE* 3.7 12.6 - - - +
363A ILE 3.2 0.8 - - - -
364A TYR* 1.3 78.5 - - - +
366A PHE* 1.3 80.8 + - + +
372A ARG* 3.0 54.2 + - - +
375A PHE* 3.3 31.4 - - + +
376A LYS* 5.8 1.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 5.5 0.5 + - - -
362A ILE* 3.2 41.4 + - + +
363A ILE* 4.3 2.5 - - - +
365A ASN* 1.3 97.7 - - + +
367A LEU* 1.3 71.6 + - + +
368A SER 3.6 0.7 - - - -
372A ARG* 3.5 15.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LYS* 4.1 20.5 - - - +
302A THR* 5.8 0.2 - - - -
304A ARG* 3.9 35.3 + - + +
305A MET* 3.6 28.2 - - + +
308A VAL* 3.4 39.0 - - + -
363A ILE* 3.0 23.3 + - + +
366A PHE* 1.3 91.1 - - + +
368A SER* 1.3 60.6 + - - +
369A GLY 4.3 0.2 - - - -
372A ARG* 5.0 0.7 - - - -
----------------------------------------------------------
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 3.5 20.2 - - - -
364A TYR 3.2 15.8 + - - +
365A ASN 3.9 0.3 - - - +
366A PHE 3.6 0.8 - - - -
367A LEU* 1.3 79.2 - - - +
369A GLY* 1.3 60.2 + - - +
370A LYS* 3.6 7.3 + - - +
371A PHE* 3.4 26.6 + - - -
372A ARG* 2.9 29.6 + - - +
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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