Contacts of the helix formed by residues 327 - 350 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G VAL* 5.3 2.9 - - - -
319G ASN* 3.8 19.7 - - - +
324G GLY 3.4 9.2 + - - +
325G ILE 3.5 3.1 + - - -
326G ILE* 1.3 76.6 - - - +
328G ALA* 1.3 66.9 + - - +
329G LYS* 3.1 16.4 + - - +
330G PHE* 3.2 13.8 + - - +
331G PHE* 3.0 20.4 + - - +
168L PRO* 3.6 28.4 - - + +
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE 4.1 10.6 - - - +
309G THR 3.8 6.5 - - - +
310G ALA* 3.6 39.0 - - + +
315G VAL* 4.5 11.4 - - + +
319G ASN* 5.7 0.2 - - - +
327G ASP* 1.3 75.4 - - - +
329G LYS* 1.3 65.5 + - - +
331G PHE* 2.9 8.9 + - - +
332G GLY* 2.8 22.3 + - - -
166L PRO* 4.1 13.7 - - + +
168L PRO* 6.3 0.2 - - + -
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Residues in contact with LYS 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G GLY 5.1 0.7 - - - -
167G GLY 4.7 6.3 + - - -
168G ALA* 4.1 31.4 - - + +
305G LEU* 5.3 0.5 - - - +
327G ASP* 3.1 11.5 + - - +
328G ALA* 1.3 80.7 - - - +
330G PHE* 1.3 62.1 + - - +
332G GLY* 3.1 9.4 + - - -
333G VAL* 3.1 16.0 + - + +
130L THR 2.9 24.1 + - - +
131L HIS* 2.8 47.7 + - + +
132L LEU* 4.7 4.5 - - + -
166L PRO* 3.7 16.6 + - - +
168L PRO* 4.0 12.5 - - + +
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Residues in contact with PHE 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ALA* 3.5 30.1 - - + +
169G ILE* 4.0 15.0 - - + -
170G PRO* 3.5 35.0 - - + -
325G ILE* 4.2 11.7 - - + +
326G ILE* 4.3 14.8 - - + -
327G ASP* 3.2 15.8 + - - +
329G LYS* 1.3 77.1 - - + +
331G PHE* 1.3 60.5 + - - +
333G VAL* 3.4 12.7 + - + -
334G LEU* 2.9 68.7 + - + +
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Residues in contact with PHE 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 3.3 52.3 - + + -
314G VAL* 3.4 31.0 - - + -
315G VAL* 3.7 11.0 - - + -
318G ALA* 4.2 16.4 - - + -
326G ILE* 4.1 17.7 - - + +
327G ASP 3.0 20.5 + - - +
328G ALA* 2.9 8.4 + - - +
330G PHE* 1.3 76.3 - - - +
332G GLY* 1.3 51.8 + - - +
334G LEU* 2.9 13.5 + - + +
335G ALA* 2.6 40.5 + - + +
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Residues in contact with GLY 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G LEU* 3.5 36.8 - - - +
308G PHE* 4.5 5.6 - - - -
328G ALA 2.8 12.5 + - - -
329G LYS 3.1 4.5 + - - -
331G PHE* 1.3 80.1 - - - +
333G VAL* 1.3 61.5 + - - +
335G ALA* 3.3 9.4 + - - +
336G MET* 3.0 18.4 + - - +
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Residues in contact with VAL 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G LEU* 4.0 31.6 - - + +
168G ALA* 3.5 23.8 - - + -
169G ILE* 6.2 2.2 - - + -
305G LEU* 3.8 9.8 - - + +
329G LYS* 3.1 15.7 + - + +
330G PHE* 3.5 18.8 - - + +
332G GLY* 1.3 76.4 - - - +
334G LEU* 1.3 64.8 + - + +
336G MET* 3.0 13.8 + - - +
337G PHE* 3.1 40.7 + - + -
131L HIS* 6.0 0.4 - - - +
132L LEU* 5.2 2.5 - - + -
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Residues in contact with LEU 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326G ILE* 4.4 14.6 - - + -
330G PHE* 2.9 68.7 + - + +
331G PHE* 3.3 12.6 - - + +
333G VAL* 1.3 76.4 - - + +
335G ALA* 1.3 54.3 + - - +
337G PHE* 4.4 4.0 - - + +
338G GLY* 2.7 35.0 + - - -
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Residues in contact with ALA 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G ILE* 3.9 6.6 - - + +
308G PHE* 3.4 37.5 - - + -
331G PHE* 2.6 25.7 + - + +
332G GLY 3.3 5.8 - - - +
333G VAL 3.2 0.2 - - - -
334G LEU* 1.3 72.5 - - - +
336G MET* 1.3 57.8 + - - +
338G GLY* 5.0 0.2 - - - -
339G ALA* 2.8 25.1 + - - +
401G PHE* 3.3 18.7 - - + -
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Residues in contact with MET 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G LEU* 3.7 23.8 - - + -
301G PHE* 3.3 38.8 - - + +
304G ILE* 4.1 8.0 - - - +
305G LEU* 4.0 13.2 - - + -
332G GLY 3.0 11.4 + - - +
333G VAL 3.0 7.8 + - - +
335G ALA* 1.3 72.4 - - - +
337G PHE* 1.3 84.1 + - + +
338G GLY 2.9 0.9 - - - -
339G ALA* 2.8 20.8 + - - +
340G ILE* 3.3 8.5 + - - +
503G SMA 3.3 61.7 - - - +
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Residues in contact with PHE 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G LEU* 5.8 4.7 - - + -
165G LEU* 4.5 14.8 - - + -
166G PHE* 4.6 20.9 - + - -
333G VAL* 3.1 41.5 + - + +
334G LEU* 4.4 3.4 - - - +
336G MET* 1.3 95.6 - - + +
338G GLY* 1.3 56.5 + - - +
340G ILE* 3.1 12.1 + - + +
341G LEU* 2.8 29.6 + - - +
503G SMA 3.5 41.1 - - - -
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Residues in contact with GLY 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G LEU 2.7 23.5 + - - -
335G ALA 3.8 0.4 - - - -
337G PHE* 1.3 69.9 - - - +
339G ALA* 1.3 64.1 + - - +
340G ILE 2.9 2.4 + - - -
341G LEU* 2.9 11.6 + - - -
342G VAL* 2.8 30.6 + - - +
401G PHE* 3.9 9.9 - - - -
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Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301G PHE* 4.5 9.9 - - + -
304G ILE* 3.8 20.2 - - + -
335G ALA 2.8 13.6 + - - +
336G MET* 2.8 12.2 + - - +
338G GLY* 1.3 75.3 - - - +
340G ILE* 1.3 58.6 + - - +
342G VAL* 3.2 11.2 - - - +
343G MET* 3.9 1.6 + - - +
400G TRP* 2.9 35.9 + - - +
401G PHE* 3.6 20.8 - - + -
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Residues in contact with ILE 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G MET* 3.8 21.9 - - + +
136G TYR* 4.5 9.2 - - + -
137G LEU* 4.9 13.2 - - + -
140G MET* 3.9 15.9 - - + -
301G PHE* 3.2 35.7 - - + -
336G MET 3.8 7.2 - - - +
337G PHE* 3.1 12.7 + - + +
338G GLY 2.9 0.4 - - - -
339G ALA* 1.3 76.5 - - - +
341G LEU* 1.3 66.4 + - - +
343G MET* 2.9 28.8 + - + +
344G ALA 3.2 4.3 + - - -
503G SMA 3.9 28.3 - - - -
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Residues in contact with LEU 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337G PHE 2.8 20.4 + - - +
338G GLY* 2.9 10.7 + - - +
340G ILE* 1.3 74.6 - - - +
342G VAL* 1.3 66.3 + - + +
344G ALA* 3.0 19.1 + - + +
345G LEU* 3.2 36.0 + - + +
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Residues in contact with VAL 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G GLY* 2.8 22.8 + - - +
339G ALA* 3.2 21.1 - - - +
341G LEU* 1.3 73.9 - - + +
343G MET* 1.3 67.8 + - - +
345G LEU* 2.8 32.2 + - + +
346G VAL* 3.0 10.2 + - - -
349G LEU* 4.7 4.2 - - + +
400G TRP* 4.0 10.5 - - + +
401G PHE* 4.1 20.2 - - + -
404G PHE* 3.9 32.3 - - + -
405G LEU* 4.3 22.0 - - + -
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Residues in contact with MET 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 6.5 0.2 - - + -
112G ILE* 4.3 26.5 - - + -
116G LEU* 4.8 4.3 - - + -
129G TRP* 3.2 17.9 + - + -
133G MET* 3.9 22.7 - - + -
136G TYR* 4.4 19.7 - - + -
301G PHE* 4.7 10.3 - - + -
339G ALA 4.1 6.5 - - - +
340G ILE* 2.9 23.2 + - + +
342G VAL* 1.3 80.9 - - - +
344G ALA* 1.3 54.9 + - - +
346G VAL* 2.9 27.6 - - - +
400G TRP* 4.2 20.6 - - + -
404G PHE* 3.9 26.7 - - + -
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Residues in contact with ALA 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G TRP* 3.6 15.9 + - - +
130G ILE* 5.2 3.5 - - + +
133G MET* 3.9 27.6 - - + +
340G ILE 3.2 1.8 + - - +
341G LEU* 3.0 21.2 + - + +
343G MET* 1.3 80.8 - - - +
345G LEU* 1.3 61.9 + - + +
346G VAL 3.2 0.4 - - - -
347G PRO* 3.0 16.6 - - - +
348G TRP* 3.6 7.6 - - - -
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Residues in contact with LEU 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341G LEU* 3.3 41.5 - - + +
342G VAL* 2.8 14.1 + - + +
344G ALA* 1.3 76.1 - - + +
346G VAL* 1.3 51.0 + - - +
347G PRO* 3.0 6.9 - - - +
348G TRP* 2.6 48.8 + - + +
349G LEU* 3.2 23.2 + - + -
405G LEU* 6.6 0.7 - - + -
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Residues in contact with VAL 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.1 6.3 - - + -
121G TYR* 3.7 30.4 - - + -
129G TRP* 3.4 21.3 - - + +
342G VAL 3.0 5.8 + - - -
343G MET 2.9 22.7 - - - +
345G LEU* 1.3 75.9 - - - +
347G PRO* 1.3 72.8 - - + +
348G TRP 3.0 0.7 + - - -
349G LEU* 3.7 8.5 - - - +
350G ASP* 3.1 20.8 + - - +
404G PHE* 4.0 20.2 - - + -
408G LEU* 4.0 20.6 - - + -
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Residues in contact with PRO 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G TYR* 3.7 33.8 - - + +
122G LYS* 5.3 4.6 - - - +
123G ALA 5.9 0.3 + - - -
126G GLU* 4.1 15.4 - - + +
129G TRP* 3.7 21.5 - - + -
344G ALA 3.0 12.6 - - - +
345G LEU 3.0 7.2 - - - +
346G VAL* 1.3 97.6 - - + +
348G TRP* 1.3 80.4 + - + +
350G ASP* 3.8 11.5 - - - +
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Residues in contact with TRP 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G GLU* 4.4 23.0 + - + +
130G ILE* 3.9 29.8 - - + -
344G ALA 3.6 18.4 - - - -
345G LEU* 2.6 45.0 + - + +
347G PRO* 1.3 90.7 - - + +
349G LEU* 1.3 68.8 - - + +
350G ASP 3.3 4.0 - - - +
351G THR* 4.7 8.0 - - - +
18J TRP* 4.6 12.9 - + - -
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Residues in contact with LEU 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G VAL* 4.7 9.2 - - + +
345G LEU* 3.2 25.9 + - + +
346G VAL* 3.3 6.5 + - - +
348G TRP* 1.3 87.0 - - + +
350G ASP* 1.3 61.6 + - - +
351G THR* 3.2 9.2 + - - +
404G PHE* 2.9 43.3 - - + +
405G LEU* 3.5 25.1 - - + -
408G LEU* 4.4 4.0 - - + -
409G PRO* 3.3 33.2 - - + +
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Residues in contact with ASP 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G TYR* 2.9 29.9 + - + +
122G LYS* 3.3 13.0 - - + +
346G VAL 3.1 17.1 + - - +
347G PRO 3.8 12.4 - - - +
348G TRP 4.5 1.5 - - - -
349G LEU* 1.3 76.0 - - - +
351G THR* 1.3 59.5 + - - +
352G SER* 3.0 31.0 + - - +
360G ARG* 3.1 23.0 + - - -
363G PHE* 4.1 0.2 - - - -
408G LEU* 4.1 23.5 - - + +
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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