Contacts of the helix formed by residues 327 - 350 (chain A) in PDB entry 2QJK
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 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A VAL* 4.7 2.7 - - - -
319A ASN* 4.0 19.5 - - - +
324A GLY 3.3 8.4 + - - +
325A ILE 3.4 4.4 + - - -
326A ILE* 1.3 76.5 - - - +
328A ALA* 1.3 65.1 + - - +
329A LYS* 3.0 20.5 + - - +
330A PHE* 3.2 13.1 + - - +
331A PHE* 3.0 21.9 + - - +
168F PRO* 3.7 24.6 - - + +
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Residues in contact with ALA 328 (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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308A PHE 4.2 10.6 - - - +
309A THR 3.8 5.8 - - - +
310A ALA* 3.6 39.5 - - + +
315A VAL* 4.1 13.6 - - + +
327A ASP* 1.3 77.4 - - - +
329A LYS* 1.3 64.8 + - - +
331A PHE* 2.9 5.4 + - - +
332A GLY* 2.8 22.7 + - - -
166F PRO* 4.0 14.4 - - + +
168F PRO* 6.1 0.7 - - + -
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Residues in contact with LYS 329 (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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164A GLY 5.1 1.3 - - - -
167A GLY* 4.6 7.8 + - - -
168A ALA* 4.2 29.6 - - + +
305A LEU* 5.3 0.3 - - - +
327A ASP* 3.0 13.5 + - - +
328A ALA* 1.3 80.3 - - - +
330A PHE* 1.3 58.4 + - + +
332A GLY* 3.2 2.6 + - - -
333A VAL* 3.1 26.0 + - - +
130F THR 3.2 21.7 + - - +
131F HIS* 2.8 44.7 + - + +
132F LEU* 4.6 5.6 - - + -
166F PRO* 3.7 16.1 + - - +
168F PRO* 4.1 14.5 - - + +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 3.5 29.8 - - + +
169A ILE* 4.0 14.6 - - + -
170A PRO* 3.5 35.7 - - + -
325A ILE* 4.3 3.6 - - + +
326A ILE* 4.3 24.5 - - + -
327A ASP* 3.2 14.2 + - - +
329A LYS* 1.3 76.6 - - + +
331A PHE* 1.3 60.5 + - - +
333A VAL* 3.4 14.0 + - + -
334A LEU* 2.8 68.9 + - + +
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.3 56.3 - + + -
314A VAL* 4.5 24.5 - - + -
315A VAL* 4.0 12.6 - - + -
318A ALA* 4.3 19.5 - - + -
326A ILE* 4.1 17.9 - - + +
327A ASP 3.0 19.5 + - - +
328A ALA* 2.9 7.8 + - - +
330A PHE* 1.3 75.9 - - - +
332A GLY* 1.3 52.8 + - - +
334A LEU* 2.9 14.1 + - + +
335A ALA* 2.6 39.1 + - + +
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Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.5 37.0 - - - +
308A PHE* 4.5 5.8 - - - +
328A ALA 2.8 13.8 + - - -
329A LYS 3.6 4.5 - - - -
331A PHE* 1.3 79.0 - - - +
333A VAL* 1.3 61.1 + - - +
335A ALA* 3.3 8.8 + - - +
336A MET* 3.0 18.4 + - - +
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Residues in contact with VAL 333 (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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165A LEU* 4.1 32.1 - - + +
168A ALA* 3.5 24.5 - - + -
169A ILE* 6.0 2.7 - - + +
305A LEU* 3.7 9.4 - - + +
329A LYS* 3.1 15.7 + - + +
330A PHE* 3.5 18.4 - - + +
332A GLY* 1.3 76.6 - - - +
334A LEU* 1.3 63.9 + - + +
336A MET* 3.0 13.1 + - - +
337A PHE* 3.1 41.7 + - + -
131F HIS* 6.0 0.4 - - - +
132F LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 334 (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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326A ILE* 4.4 15.3 - - + -
330A PHE* 2.8 65.8 + - + +
331A PHE* 3.3 11.7 - - + +
333A VAL* 1.3 76.9 - - + +
335A ALA* 1.3 58.3 + - - +
337A PHE* 4.8 3.4 - - - +
338A GLY* 2.8 31.1 + - - +
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Residues in contact with ALA 335 (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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304A ILE* 4.0 6.9 - - + +
308A PHE* 3.4 37.0 - - + -
331A PHE* 2.6 21.6 + - + +
332A GLY 3.4 10.3 - - - +
334A LEU* 1.3 72.7 - - - +
336A MET* 1.3 57.6 + - - +
339A ALA* 2.8 25.3 + - - +
401A PHE* 3.2 18.4 - - + -
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Residues in contact with MET 336 (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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1A SMA 3.3 59.2 - - - +
165A LEU* 3.7 24.5 - - + -
301A PHE* 3.4 39.0 - - + +
304A ILE* 4.2 7.6 - - - -
305A LEU* 4.1 13.0 - - + -
332A GLY 3.0 12.6 + - - +
333A VAL* 3.0 6.7 + - - +
335A ALA* 1.3 72.0 - - - +
337A PHE* 1.3 84.9 + - + +
338A GLY 2.9 0.9 - - - -
339A ALA* 2.9 20.6 + - - +
340A ILE* 3.3 8.5 + - - +
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Residues in contact with PHE 337 (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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1A SMA 3.7 43.1 - - - -
137A LEU* 5.6 4.7 - - + -
165A LEU* 4.5 14.8 - - + -
166A PHE* 4.7 18.6 - + - -
333A VAL* 3.1 39.4 + - + +
334A LEU* 4.4 2.9 - - - +
336A MET* 1.3 95.2 - - + +
338A GLY* 1.3 57.0 + - - +
340A ILE* 3.2 13.0 + - + +
341A LEU* 2.8 28.7 + - - +
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Residues in contact with GLY 338 (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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334A LEU 2.8 21.0 + - - -
335A ALA 3.7 0.9 - - - -
337A PHE* 1.3 72.9 - - - +
339A ALA* 1.3 65.0 + - - +
340A ILE 2.9 2.5 + - - -
341A LEU* 2.9 11.6 + - - +
342A VAL* 2.8 30.2 + - - +
401A PHE* 4.0 9.6 - - - -
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Residues in contact with ALA 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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301A PHE* 4.5 9.9 - - + -
304A ILE* 3.7 21.1 - - + -
335A ALA 2.8 15.1 + - - +
336A MET* 2.9 11.0 + - - +
338A GLY* 1.3 74.3 - - - +
340A ILE* 1.3 58.6 + - - +
342A VAL* 3.1 12.0 - - - +
343A MET* 3.9 1.9 + - - +
400A TRP* 2.9 36.4 + - - +
401A PHE* 3.6 20.1 - - + -
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Residues in contact with ILE 340 (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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1A SMA 3.8 29.2 - - - -
133A MET* 3.8 22.3 - - + +
136A TYR* 4.5 8.7 - - + -
137A LEU* 5.0 12.1 - - + -
140A MET* 3.9 15.0 - - + -
301A PHE* 3.2 35.2 - - + -
336A MET 3.8 8.3 - - - +
337A PHE* 3.2 13.4 + - + +
338A GLY 2.9 0.6 - - - -
339A ALA* 1.3 76.5 - - - +
341A LEU* 1.3 68.4 + - - +
343A MET* 2.8 30.1 + - + +
344A ALA 3.2 4.0 + - - -
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Residues in contact with LEU 341 (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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337A PHE 2.8 17.4 + - - +
338A GLY* 2.9 10.5 + - - +
340A ILE* 1.3 78.2 - - - +
342A VAL* 1.3 66.7 + - + +
344A ALA* 2.9 19.7 + - + +
345A LEU* 3.2 37.2 + - + +
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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
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338A GLY* 2.8 21.5 + - - +
339A ALA* 3.1 20.0 - - - +
341A LEU* 1.3 74.1 - - + +
343A MET* 1.3 67.7 + - - +
345A LEU* 2.8 32.2 + - + +
346A VAL* 3.1 10.2 + - - -
349A LEU* 4.7 3.5 - - + +
400A TRP* 4.0 11.0 - - + +
401A PHE* 4.1 20.9 - - + -
404A PHE* 4.0 30.8 - - + -
405A LEU* 4.3 21.5 - - + -
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Residues in contact with MET 343 (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 TYR* 6.5 0.2 - - + -
112A ILE* 4.3 25.1 - - + -
116A LEU* 4.9 6.1 - - + -
129A TRP* 3.2 20.2 + - + -
133A MET* 3.9 21.1 - - + -
136A TYR* 4.4 20.4 - - + -
301A PHE* 4.8 9.6 - - + -
339A ALA 4.1 6.1 - - - +
340A ILE* 2.8 23.4 + - + +
342A VAL* 1.3 81.1 - - - +
344A ALA* 1.3 55.4 + - - +
346A VAL* 3.0 27.8 - - - +
400A TRP* 4.2 21.3 - - + -
404A PHE* 3.9 26.0 - - + -
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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
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129A TRP* 3.6 14.9 + - - +
130A ILE* 5.2 3.6 - - + +
133A MET* 3.9 28.9 - - + +
340A ILE 3.2 3.0 + - - -
341A LEU* 2.9 21.8 + - + +
343A MET* 1.3 78.8 - - - +
345A LEU* 1.3 61.0 + - + +
346A VAL 3.1 0.4 - - - -
347A PRO* 3.0 17.0 - - - +
348A TRP* 3.6 7.6 - - - -
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Residues in contact with LEU 345 (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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341A LEU* 3.3 43.1 - - + +
342A VAL* 2.8 13.5 + - + +
344A ALA* 1.3 78.0 - - + +
346A VAL* 1.3 50.3 + - - +
347A PRO* 3.0 7.2 - - - -
348A TRP* 2.6 48.0 + - + +
349A LEU* 3.2 23.4 + - + +
405A LEU* 6.6 0.2 - - + -
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Residues in contact with VAL 346 (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 LEU* 4.1 6.7 - - + -
121A TYR* 3.7 30.1 - - + -
129A TRP* 3.4 22.2 - - + +
342A VAL 3.1 5.8 + - - -
343A MET 3.0 23.3 - - - +
345A LEU* 1.3 76.6 - - - +
347A PRO* 1.3 72.4 - - + +
348A TRP 3.0 0.9 + - - -
349A LEU* 3.7 8.5 - - - +
350A ASP* 3.2 19.9 + - - +
404A PHE* 4.0 19.3 - - + -
408A LEU* 4.0 22.4 - - + -
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Residues in contact with PRO 347 (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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121A TYR* 3.7 33.2 - - + +
122A LYS* 5.2 5.3 - - - +
123A ALA 5.9 0.2 + - - -
126A GLU* 4.1 14.5 - - + +
129A TRP* 3.7 22.0 - - + -
344A ALA 3.0 12.3 - - - +
345A LEU 3.0 7.4 - - - -
346A VAL* 1.3 98.1 - - + +
348A TRP* 1.3 80.4 + - + +
350A ASP* 3.9 12.1 - - - +
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Residues in contact with TRP 348 (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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126A GLU* 4.4 22.4 + - + +
130A ILE* 3.8 29.2 - - + -
344A ALA 3.6 9.6 - - - -
345A LEU* 2.6 39.3 + - + +
347A PRO* 1.3 106.0 - - + +
349A LEU* 1.3 71.5 + - + +
350A ASP 3.3 3.6 - - - +
351A THR* 4.7 7.8 - - - +
18D TRP* 4.7 12.7 - + - -
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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
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342A VAL* 4.7 9.0 - - + +
345A LEU* 3.2 25.7 + - + +
346A VAL* 3.4 6.7 + - - +
348A TRP* 1.3 85.0 - - + +
350A ASP* 1.3 60.9 + - - +
351A THR* 3.2 8.5 + - - +
404A PHE* 2.9 44.2 - - + +
405A LEU* 3.5 23.6 - - + -
408A LEU* 4.3 4.7 - - + -
409A PRO* 3.3 31.9 - - + +
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Residues in contact with ASP 350 (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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121A TYR* 2.9 23.5 + - + +
122A LYS* 2.5 38.4 + - + +
346A VAL 3.2 17.3 + - - +
347A PRO 3.9 11.9 - - - +
348A TRP 4.6 1.8 - - - +
349A LEU* 1.3 75.3 - - - +
351A THR* 1.3 60.0 + - - +
352A SER* 2.9 21.0 + - - +
360A ARG* 3.1 14.8 + - - -
363A PHE* 4.1 4.5 - - - -
408A LEU* 4.2 19.6 - - + +
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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) + - + + + + + -
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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