Contacts of the helix formed by residues 345 - 369 (chain A) in PDB entry 3DRB
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 SER 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.2 29.6 + - - +
109A ASP* 3.6 23.9 + - - +
289A THR* 3.9 0.9 - - - -
344A PHE* 1.3 75.8 - - - +
346A GLU* 1.3 68.2 + - - +
347A VAL* 3.5 3.8 + - - +
348A GLU* 2.8 39.8 + - - +
349A LEU* 3.0 21.0 + - - +
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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
----------------------------------------------------------
108A THR* 3.6 11.1 + - - +
109A ASP 2.9 30.6 + - - +
110A LEU* 3.7 23.6 - - + +
135A ARG* 4.3 3.1 + - - +
250A PHE* 4.2 7.2 - - + -
253A PHE* 4.9 2.0 - - + -
279A TYR* 3.8 22.2 - - - -
289A THR* 3.6 32.7 - - + +
291A LEU* 3.6 27.6 - - + -
345A SER* 1.3 71.3 - - - +
347A VAL* 1.3 62.8 + - - +
349A LEU* 3.3 4.0 + - - +
350A VAL* 3.0 28.9 + - - +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 3.4 39.8 + - - +
111A ASN 3.4 21.5 - - - +
114A ASN* 3.7 31.4 - - + +
115A LEU* 4.2 6.8 - - + +
250A PHE* 4.0 16.4 - - + -
345A SER* 3.5 4.0 + - - +
346A GLU* 1.3 78.1 - - - +
348A GLU* 1.3 62.5 + - + +
350A VAL* 3.4 2.8 + - - +
351A GLN* 2.9 30.9 + - + +
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 6.0 0.5 - - - +
343A GLY 4.4 2.1 - - - +
344A PHE* 3.3 24.0 - - + +
345A SER* 2.8 47.1 + - - +
347A VAL* 1.3 78.9 - - + +
349A LEU* 1.3 60.3 + - - +
351A GLN* 3.4 7.4 + - - +
352A MET* 3.0 35.3 + - + +
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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
----------------------------------------------------------
289A THR* 3.2 39.5 - - + +
291A LEU* 4.2 11.4 - - + -
293A ALA* 5.3 0.2 - - - -
338A ASN* 3.3 29.5 - - + +
340A ASP* 3.6 30.5 - - + +
341A ARG 4.3 2.9 - - - +
344A PHE* 3.3 35.2 - - + +
345A SER 3.0 7.5 + - - +
346A GLU* 3.5 7.4 - - - +
348A GLU* 1.3 75.3 - - - +
350A VAL* 1.3 65.3 + - - +
352A MET* 3.2 18.0 + - - +
353A VAL* 3.3 17.1 + - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.8 21.5 - - + -
131A VAL* 4.8 1.8 - - + -
246A MET* 3.6 33.7 - - + -
250A PHE* 3.7 31.4 - - + -
291A LEU* 4.4 7.4 - - + -
293A ALA* 4.1 22.2 - - + -
346A GLU 3.0 17.2 + - - +
347A VAL* 4.0 3.4 - - - +
349A LEU* 1.3 75.5 - - - +
351A GLN* 1.3 62.6 + - - +
353A VAL* 3.2 3.4 + - - +
354A VAL* 3.0 21.4 + - + +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 4.2 2.4 - - - +
115A LEU* 3.5 12.1 - - + +
116A GLN* 2.8 57.0 + - - +
347A VAL* 2.9 20.1 + - + +
348A GLU* 3.5 9.6 - - - +
349A LEU 3.2 0.2 - - - -
350A VAL* 1.3 78.1 - - - +
352A MET* 1.3 57.8 + - + +
354A VAL* 3.3 7.7 + - - +
355A ASP* 2.8 66.5 + - - +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU 3.2 26.8 - - - +
316A ARG* 3.4 33.0 - - + +
317A LEU* 3.9 12.9 - - + +
338A ASN* 5.5 2.9 - - + -
340A ASP* 4.4 7.4 - - - +
344A PHE* 4.5 16.8 - - - -
348A GLU* 3.0 21.2 + - + +
349A LEU* 3.2 13.6 + - - +
351A GLN* 1.3 77.1 - - + +
353A VAL* 1.3 57.2 + - - +
355A ASP* 4.1 5.3 - - - +
356A GLY* 2.9 26.3 + - - -
381A LYS* 3.6 29.7 + - - +
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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
----------------------------------------------------------
121A LEU* 5.7 0.2 - - + -
246A MET* 4.3 20.9 - - + -
293A ALA* 3.3 33.0 - - + +
294A GLY* 4.5 5.8 - - - -
295A VAL* 4.7 1.8 - - + -
317A LEU* 4.2 9.2 - - + -
336A VAL* 4.7 5.2 - - + +
337A SER* 4.2 2.0 - - - -
338A ASN* 3.5 23.8 - - + +
349A LEU 3.6 12.6 - - - +
350A VAL* 3.2 8.6 + - - +
351A GLN 3.2 0.6 - - - -
352A MET* 1.3 73.1 - - - +
354A VAL* 1.3 59.4 + - - +
357A VAL* 2.8 54.2 + - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.5 7.0 - - + -
116A GLN 4.4 1.6 - - - +
118A GLY* 3.6 37.9 - - - +
121A LEU* 4.2 11.2 - - + +
246A MET* 3.9 24.0 - - + -
350A VAL* 3.0 22.2 + - + +
351A GLN* 3.6 15.5 - - - +
353A VAL* 1.3 77.1 - - + +
355A ASP* 1.3 69.2 + - - +
357A VAL* 3.9 2.1 - - - +
358A LYS* 3.1 46.5 + - + +
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Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 5.6 0.4 - - - -
351A GLN* 2.8 53.2 + - - +
352A MET* 4.1 2.5 - - - +
354A VAL* 1.3 74.0 - - - +
356A GLY* 1.3 67.9 + - - +
358A LYS* 3.5 12.0 + - - +
359A LEU* 3.4 18.4 + - - +
381A LYS* 4.4 17.8 + - - +
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Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.8 27.3 - - - +
317A LEU* 4.1 7.4 - - - -
352A MET 2.9 18.4 + - - -
353A VAL 3.8 0.2 - - - -
355A ASP* 1.3 75.6 - - - +
357A VAL* 1.3 64.4 + - - +
359A LEU* 3.0 5.1 + - - +
360A LEU* 3.0 29.7 + - - +
381A LYS* 5.4 0.2 - - - +
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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
----------------------------------------------------------
121A LEU* 3.9 20.9 - - + -
126A VAL* 4.0 11.7 - - + -
295A VAL* 3.8 24.9 - - + -
297A ILE* 4.1 9.2 - - + -
317A LEU* 4.6 1.7 - - + +
336A VAL* 5.2 5.2 - - + -
353A VAL* 2.8 41.7 + - + +
354A VAL 3.9 3.1 - - - +
356A GLY* 1.3 71.3 - - - +
358A LYS* 1.3 59.8 + - - +
360A LEU* 3.0 17.0 + - + +
361A ILE* 2.9 46.1 + - + +
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Residues in contact with LYS 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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116A GLN 5.7 1.4 + - - -
117A GLY* 5.8 2.8 - - - -
118A GLY 5.3 4.2 - - - +
120A ASP* 5.0 11.6 + - - +
121A LEU* 4.0 17.7 - - + -
354A VAL* 3.1 37.2 + - + +
355A ASP* 3.8 11.5 + - - +
356A GLY 3.3 0.2 - - - -
357A VAL* 1.3 76.8 - - - +
359A LEU* 1.3 60.8 + - - +
361A ILE* 3.6 10.2 + - + +
362A GLU* 3.2 27.8 + - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.1 16.4 - - + -
355A ASP 3.4 8.3 + - - +
356A GLY* 3.0 10.5 + - - +
358A LYS* 1.3 76.9 - - - +
360A LEU* 1.3 67.6 + - - +
362A GLU* 3.1 24.2 + - + +
363A MET* 3.0 35.3 + - + +
376A LEU* 3.7 29.2 - - + +
378A PRO* 3.8 41.3 - - + -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 4.9 4.3 - - + -
299A LEU* 4.0 22.8 - - + +
302A LEU* 3.8 23.0 - - + +
308A PHE* 4.7 0.7 - - + -
311A VAL* 4.0 15.9 - - + -
312A LEU* 3.9 25.4 - - + -
315A LEU* 3.4 24.0 - - + -
317A LEU* 4.7 1.3 - - + -
336A VAL* 4.3 16.4 - - + -
356A GLY 3.0 21.9 + - - +
357A VAL* 3.0 16.6 + - + +
359A LEU* 1.3 77.3 - - - +
361A ILE* 1.3 56.5 + - - +
363A MET* 3.3 4.6 + - - +
364A GLU* 2.9 27.9 + - - +
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Residues in contact with ILE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.2 1.3 - - + -
122A ASP* 3.9 34.1 - - + +
125A TYR* 3.6 39.5 - - + -
126A VAL* 4.2 4.5 - - + -
297A ILE* 4.0 15.5 - - + -
299A LEU* 4.8 1.1 - - - -
357A VAL* 2.9 36.3 + - + +
358A LYS* 3.8 10.8 - - + +
360A LEU* 1.3 74.7 - - - +
362A GLU* 1.3 64.9 + - + +
364A GLU* 3.3 6.9 + - - +
365A GLN* 3.0 34.1 + - - +
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 3.2 15.6 + - - +
359A LEU* 3.1 29.4 + - - +
361A ILE* 1.3 78.9 - - + +
363A MET* 1.3 61.6 + - - +
365A GLN* 3.3 14.5 + - - +
366A ARG* 3.1 25.5 + - - +
376A LEU* 4.1 21.2 - - + +
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Residues in contact with MET 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 4.1 18.6 - - + -
311A VAL* 3.9 23.1 - - + -
359A LEU* 3.0 24.6 + - + +
360A LEU* 3.6 7.2 - - - +
362A GLU* 1.3 72.4 - - - +
364A GLU* 1.3 67.4 + - - +
366A ARG* 3.1 3.6 + - - +
367A LEU* 3.0 28.6 + - - +
373A ILE* 3.5 27.3 - - + +
376A LEU* 3.6 46.9 - - + +
377A MET* 3.8 25.4 - - - +
378A PRO* 3.9 9.4 - - + -
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.6 26.2 - - + -
298A LYS 4.3 0.4 - - - +
299A LEU* 3.4 25.8 - - + -
300A PRO* 3.5 8.9 - - + +
301A ASN* 2.7 40.4 + - - -
302A LEU* 2.8 32.1 + - - +
360A LEU 2.9 14.7 + - - +
361A ILE* 3.4 10.8 - - - +
363A MET* 1.3 76.1 - - - +
365A GLN* 1.3 59.3 + - - +
367A LEU* 3.2 6.3 + - - +
368A GLU* 2.9 31.0 + - - +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 4.3 8.5 + - - -
125A TYR* 3.4 32.5 + - + +
361A ILE* 3.0 33.0 + - - +
362A GLU* 3.7 13.5 - - - +
364A GLU* 1.3 75.7 - - - +
366A ARG* 1.3 62.3 + - + +
368A GLU* 3.4 16.0 + - - +
369A GLN* 3.3 26.4 + - - +
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Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU 3.1 18.4 + - - +
363A MET 3.1 8.5 + - - +
365A GLN* 1.3 77.4 - - - +
367A LEU* 1.3 57.8 + - - +
369A GLN* 3.0 21.5 + - - +
371A GLN* 3.0 44.5 + - + +
372A ALA 2.9 22.8 + - - +
373A ILE* 3.8 11.6 - - + +
375A ASP* 2.6 44.4 + - - -
376A LEU* 3.5 28.7 - - + +
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 3.5 27.4 - - + +
302A LEU* 3.4 50.0 - - + +
305A HIS* 3.7 27.8 - - + +
363A MET 3.0 15.9 + - - +
364A GLU 3.2 3.3 + - - +
366A ARG* 1.3 74.0 - - - +
368A GLU* 1.3 64.2 + - - +
370A GLY* 3.0 13.2 + - - -
371A GLN 3.5 19.5 - - - +
372A ALA* 5.2 0.4 - - - -
373A ILE* 3.9 11.2 - - + +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 2.9 38.0 + - - -
300A PRO* 6.0 0.5 - - - +
301A ASN* 3.5 18.9 + - - +
364A GLU* 2.9 27.1 + - - +
365A GLN* 3.4 16.7 - - - +
366A ARG 3.1 0.4 - - - -
367A LEU* 1.3 78.0 - - - +
369A GLN* 1.3 67.7 + - - +
370A GLY 3.1 4.0 + - - -
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN 3.3 15.9 - - - +
366A ARG* 3.0 7.9 + - - +
368A GLU* 1.3 82.7 - - - +
370A GLY* 1.3 59.3 + - - +
371A GLN* 3.1 36.5 + - - +
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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