Contacts of the helix formed by residues 327 - 350 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O PRO* 3.7 24.9 - - + +
315P VAL* 4.8 2.5 - - - -
319P ASN* 4.0 15.7 - - - +
324P GLY 3.1 12.7 + - - +
325P ILE 3.1 6.9 + - - -
326P ILE* 1.3 74.5 - - - +
328P ALA* 1.3 65.6 + - - +
329P LYS* 3.1 19.7 + - - +
330P PHE* 3.1 13.7 + - - +
331P PHE* 2.9 24.1 + - - +
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Residues in contact with ALA 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O PRO* 4.1 13.7 - - + +
168O PRO* 6.1 0.7 - - + -
308P PHE 4.2 9.5 - - - +
309P THR 3.8 6.7 - - - +
310P ALA* 3.6 39.2 - - + +
315P VAL* 4.0 12.0 - - + +
327P ASP* 1.3 76.2 - - - +
329P LYS* 1.3 66.6 + - - +
331P PHE* 2.8 9.0 + - - +
332P GLY* 2.7 22.3 + - - -
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Residues in contact with LYS 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130O THR 2.8 18.9 + - - +
131O HIS* 2.6 47.9 + - + +
132O LEU* 4.6 4.7 - - + -
166O PRO* 3.9 16.5 + - - +
168O PRO* 4.1 14.7 - - + +
164P GLY 5.2 1.1 - - - -
167P GLY 4.8 5.2 + - - -
168P ALA* 4.2 31.4 - - + +
305P LEU* 5.4 0.3 - - - +
327P ASP* 3.3 13.6 - - - +
328P ALA* 1.3 82.1 - - - +
330P PHE* 1.3 58.9 + - + +
332P GLY* 3.0 13.0 + - - -
333P VAL* 3.1 16.1 + - + +
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Residues in contact with PHE 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168P ALA* 3.4 28.0 - - + +
169P ILE* 4.0 15.3 - - + -
170P PRO* 3.5 34.3 - - + -
325P ILE* 4.3 7.0 - - + +
326P ILE* 4.3 22.9 - - + -
327P ASP* 3.1 12.9 + - - +
329P LYS* 1.3 78.4 - - + +
331P PHE* 1.3 59.9 + - - +
333P VAL* 3.7 13.0 - - + -
334P LEU* 2.8 76.7 + - + +
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Residues in contact with PHE 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P PHE* 3.3 53.4 - + + -
314P VAL* 3.8 32.1 - - + -
315P VAL* 4.0 10.8 - - + -
318P ALA* 4.3 14.8 - - + -
326P ILE* 4.1 19.0 - - + +
327P ASP 2.9 15.6 + - - +
328P ALA* 2.8 13.2 + - - +
330P PHE* 1.3 75.0 - - - +
332P GLY* 1.3 53.7 + - - +
334P LEU* 2.9 13.8 + - + +
335P ALA* 2.6 39.6 + - + +
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Residues in contact with GLY 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131O HIS* 6.4 0.2 - - - -
305P LEU* 3.6 37.8 - - - +
308P PHE* 4.5 5.4 - - - -
328P ALA 2.7 12.5 + - - -
329P LYS 3.4 4.5 - - - -
331P PHE* 1.3 80.1 - - - +
333P VAL* 1.3 61.8 + - - +
335P ALA* 3.2 8.6 + - - +
336P MET* 3.0 18.4 + - - +
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Residues in contact with VAL 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131O HIS* 6.1 0.9 - - - +
132O LEU* 5.3 2.7 - - + -
165P LEU* 4.1 32.1 - - + +
168P ALA* 3.5 28.5 - - + -
169P ILE* 6.0 2.2 - - + +
305P LEU* 3.8 9.2 - - + +
329P LYS* 3.1 11.7 + - + +
330P PHE* 3.5 17.7 - - + +
331P PHE 3.2 0.2 - - - -
332P GLY* 1.3 75.1 - - - +
334P LEU* 1.3 66.1 + - + +
336P MET* 3.0 14.3 + - - +
337P PHE* 3.1 40.0 + - + -
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Residues in contact with LEU 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P ILE* 4.4 16.4 - - + -
330P PHE* 2.8 65.0 + - + +
331P PHE* 3.3 11.2 - - + +
333P VAL* 1.3 76.4 - - + +
335P ALA* 1.3 54.1 + - - +
337P PHE* 4.3 4.2 - - + +
338P GLY* 2.7 35.7 + - - -
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Residues in contact with ALA 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304P ILE* 3.9 7.0 - - + +
308P PHE* 3.4 37.5 - - + -
331P PHE* 2.6 25.4 + - + +
332P GLY 3.4 5.8 - - - +
333P VAL 3.1 0.2 - - - -
334P LEU* 1.3 72.2 - - - +
336P MET* 1.3 57.7 + - - +
339P ALA* 2.8 25.1 + - - +
401P PHE* 3.3 19.0 - - + -
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Residues in contact with MET 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P LEU* 3.8 22.9 - - + -
301P PHE* 3.4 37.9 - - + +
304P ILE* 4.2 7.6 - - - +
305P LEU* 3.9 12.3 - - + -
332P GLY 3.0 10.7 + - - +
333P VAL* 3.0 8.3 + - - +
335P ALA* 1.3 73.3 - - - +
337P PHE* 1.3 86.4 + - + +
338P GLY 2.9 0.7 - - - -
339P ALA* 2.8 21.2 + - - +
340P ILE* 3.3 7.7 + - - +
503P SMA 3.3 60.3 - - - +
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Residues in contact with PHE 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 5.8 4.9 - - + -
165P LEU* 4.5 14.4 - - + -
166P PHE* 4.6 18.2 - + - -
333P VAL* 3.1 40.3 + - + +
334P LEU* 4.3 4.0 - - + +
336P MET* 1.3 94.4 - - + +
338P GLY* 1.3 56.8 + - - +
340P ILE* 3.1 13.3 + - + +
341P LEU* 2.8 28.8 + - - +
503P SMA 3.7 43.1 - - - -
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Residues in contact with GLY 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P LEU 2.7 24.7 + - - -
335P ALA 3.8 0.4 - - - -
337P PHE* 1.3 70.4 - - - +
339P ALA* 1.3 66.0 + - - +
340P ILE 2.9 0.3 + - - -
341P LEU* 3.0 12.3 + - - +
342P VAL* 2.8 29.9 + - - +
401P PHE* 3.9 9.9 - - - -
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Residues in contact with ALA 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301P PHE* 4.5 9.2 - - + -
304P ILE* 3.8 17.5 - - + -
335P ALA 2.8 14.3 + - - +
336P MET* 2.8 15.3 + - - +
338P GLY* 1.3 71.1 - - - +
340P ILE* 1.3 59.0 + - - +
342P VAL* 3.2 12.0 - - - +
343P MET* 3.9 1.7 + - - +
400P TRP* 2.9 38.4 + - + +
401P PHE* 3.6 21.0 - - + -
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Residues in contact with ILE 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P MET* 3.8 21.9 - - + +
136P TYR* 4.6 9.2 - - + -
137P LEU* 5.0 13.7 - - + -
140P MET* 4.0 14.1 - - + -
301P PHE* 3.2 35.7 - - + -
336P MET 3.8 8.5 - - - +
337P PHE* 3.1 13.4 + - + +
338P GLY 2.9 0.6 - - - -
339P ALA* 1.3 77.4 - - - +
341P LEU* 1.3 68.5 + - - +
343P MET* 2.9 29.0 + - + +
344P ALA 3.2 4.2 + - - -
503P SMA 3.8 29.2 - - - -
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Residues in contact with LEU 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337P PHE 2.8 20.0 + - - +
338P GLY* 3.5 10.8 - - - +
340P ILE* 1.3 75.4 - - - +
342P VAL* 1.3 66.2 + - + +
344P ALA* 2.9 20.4 + - + +
345P LEU* 3.1 36.2 + - + +
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Residues in contact with VAL 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P GLY* 2.8 22.2 + - - +
339P ALA* 3.2 20.0 - - - +
341P LEU* 1.3 73.4 - - + +
343P MET* 1.3 66.6 + - - +
345P LEU* 2.8 34.1 + - + +
346P VAL* 3.0 10.2 + - - -
349P LEU* 4.7 3.8 - - + +
400P TRP* 4.1 6.3 - - + +
401P PHE* 4.1 20.4 - - + -
404P PHE* 3.9 35.9 - - + -
405P LEU* 4.3 22.0 - - + -
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Residues in contact with MET 343 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P TYR* 6.5 0.2 - - + -
112P ILE* 4.3 24.7 - - + -
116P LEU* 4.9 5.6 - - + -
129P TRP* 3.2 17.5 + - + -
133P MET* 4.0 22.0 - - + -
136P TYR* 4.4 19.3 - - + -
301P PHE* 4.7 10.1 - - + -
339P ALA 4.1 6.1 - - - +
340P ILE* 2.9 23.5 + - + +
342P VAL* 1.3 81.1 - - - +
344P ALA* 1.3 55.9 - - - +
346P VAL* 2.9 26.3 - - - +
400P TRP* 4.2 20.9 - - + -
404P PHE* 3.9 25.8 - - + -
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Residues in contact with ALA 344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P TRP* 3.6 13.5 + - - +
130P ILE* 5.2 3.1 - - + +
133P MET* 3.9 29.8 - - + +
340P ILE 3.2 3.2 + - - +
341P LEU* 2.9 22.3 + - + +
343P MET* 1.3 78.4 - - - +
345P LEU* 1.3 60.8 + - + +
346P VAL 3.2 0.7 - - - -
347P PRO* 3.1 16.1 - - - +
348P TRP* 3.6 8.8 - - - -
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Residues in contact with LEU 345 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341P LEU* 3.3 42.4 - - + +
342P VAL* 2.8 13.3 + - + +
344P ALA* 1.3 78.2 - - + +
346P VAL* 1.3 51.8 + - - +
347P PRO* 3.0 6.3 - - - -
348P TRP* 2.7 48.0 + - + +
349P LEU* 3.2 23.3 + - + -
405P LEU* 6.5 0.9 - - + -
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Residues in contact with VAL 346 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P LEU* 4.1 5.8 - - + -
121P TYR* 3.7 29.1 - - + -
129P TRP* 3.4 21.3 - - + +
342P VAL 3.0 6.0 + - - -
343P MET 2.9 26.0 - - - +
345P LEU* 1.3 77.4 - - - +
347P PRO* 1.3 73.1 - - + +
348P TRP 3.0 1.5 + - - -
349P LEU* 4.2 8.3 - - - +
350P ASP* 3.1 20.8 + - - +
404P PHE* 4.0 23.8 - - + -
408P LEU* 4.1 16.6 - - + -
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Residues in contact with PRO 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P TYR* 3.7 32.8 - - + +
122P LYS* 5.2 5.8 - - - +
123P ALA 5.8 0.2 + - - -
126P GLU* 4.2 15.6 - - + +
129P TRP* 3.7 22.2 - - + -
344P ALA 3.1 10.5 - - - +
345P LEU 3.0 7.4 - - - +
346P VAL* 1.3 99.5 - - + +
348P TRP* 1.3 80.4 + - + +
350P ASP* 3.9 11.1 - - - +
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Residues in contact with TRP 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M TRP* 4.8 12.5 - + - -
126P GLU* 4.4 22.2 + - + +
130P ILE* 3.8 29.8 - - + -
344P ALA 3.6 18.6 - - - -
345P LEU* 2.7 46.1 + - + +
347P PRO* 1.3 89.6 - - + +
349P LEU* 1.3 69.1 + - + +
350P ASP 3.3 4.5 - - - +
351P THR* 4.7 8.0 - - - +
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Residues in contact with LEU 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342P VAL* 4.7 9.4 - - + +
345P LEU* 3.2 27.4 + - + +
346P VAL* 3.3 5.8 + - - +
348P TRP* 1.3 85.1 - - + +
350P ASP* 1.3 61.2 + - - +
351P THR* 3.2 9.2 + - - +
404P PHE* 2.8 43.7 - - + +
405P LEU* 3.5 23.6 - - + -
408P LEU* 4.5 3.8 - - + -
409P PRO* 3.2 32.2 - - + +
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Residues in contact with ASP 350 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P TYR* 2.9 29.4 + - + +
122P LYS* 3.1 22.8 - - + +
346P VAL 3.1 17.5 + - - +
347P PRO 3.9 11.4 - - - +
348P TRP 4.5 1.1 - - - -
349P LEU* 1.3 77.3 - - - +
351P THR* 1.3 59.1 + - - +
352P SER* 3.0 29.5 + - - +
360P ARG* 3.1 13.1 + - - -
408P LEU* 3.6 26.7 - - + +
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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