Contacts of the helix formed by residues 327 - 350 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315M VAL* 4.9 2.0 - - - -
319M ASN* 4.4 12.3 - - - +
324M GLY 3.6 10.6 + - - +
325M ILE 2.7 15.0 + - - +
326M ILE* 1.3 74.2 - - - +
328M ALA* 1.3 66.0 + - - +
329M LYS* 3.0 21.2 + - - +
330M PHE* 3.1 12.5 + - - +
331M PHE* 2.9 21.0 + - - +
168R PRO* 4.0 22.9 - - + +
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Residues in contact with ALA 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M PHE 4.2 11.2 - - - +
309M THR 3.8 6.3 - - - +
310M ALA* 3.5 41.5 - - + +
315M VAL* 4.2 10.7 - - + +
327M ASP* 1.3 75.8 - - - +
329M LYS* 1.3 64.8 + - - +
331M PHE* 2.9 9.1 + - - +
332M GLY* 2.7 23.0 + - - -
166R PRO* 4.1 13.2 - - + +
168R PRO* 6.2 0.4 - - + -
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Residues in contact with LYS 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLY 5.3 0.9 - - - -
167M GLY 4.9 6.5 + - - -
168M ALA* 4.5 24.0 - - + +
305M LEU* 5.3 0.7 - - - +
327M ASP* 3.0 13.2 + - - +
328M ALA* 1.3 81.9 - - - +
330M PHE* 1.3 61.7 - - + +
332M GLY* 3.1 9.0 + - - -
333M VAL* 3.1 16.0 + - + +
130R THR 3.2 17.4 + - - +
131R HIS* 2.6 57.7 + - + +
132R LEU* 4.4 9.9 - - + -
166R PRO* 4.0 9.8 + - - +
168R PRO* 4.3 13.4 - - + +
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Residues in contact with PHE 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M ALA* 3.4 30.5 - - + +
169M ILE* 3.9 15.0 - - + -
170M PRO* 3.5 35.0 - - + -
325M ILE* 4.7 3.6 - - + +
326M ILE* 4.3 22.7 - - + -
327M ASP* 3.1 15.8 + - - +
329M LYS* 1.3 76.4 - - - +
331M PHE* 1.3 60.5 + - - +
333M VAL* 4.2 13.2 - - + -
334M LEU* 2.8 76.6 + - + +
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Residues in contact with PHE 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M PHE* 3.3 45.3 - + + -
314M VAL* 3.9 24.9 - - + -
315M VAL* 3.4 23.8 - - + -
318M ALA* 4.0 29.6 - - + -
326M ILE* 4.0 8.5 - - + +
327M ASP 2.9 19.7 + - - +
328M ALA* 2.9 8.9 + - - +
330M PHE* 1.3 75.1 - - - +
332M GLY* 1.3 52.5 + - - +
334M LEU* 2.9 13.5 + - + +
335M ALA* 2.6 40.4 + - + +
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Residues in contact with GLY 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305M LEU* 3.5 38.7 - - - +
308M PHE* 4.5 4.7 - - - -
328M ALA 2.7 16.1 + - - -
329M LYS 3.1 4.5 + - - -
331M PHE* 1.3 77.0 - - - +
333M VAL* 1.3 60.6 + - - +
335M ALA* 3.4 8.2 + - - +
336M MET* 3.0 18.0 + - - +
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Residues in contact with VAL 333 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M LEU* 4.1 31.9 - - + +
168M ALA* 3.5 25.1 - - + -
169M ILE* 6.0 2.2 - - + +
305M LEU* 3.8 8.7 - - + +
329M LYS* 3.1 14.1 + - + +
330M PHE* 3.5 18.2 - - + +
332M GLY* 1.3 75.5 - - - +
334M LEU* 1.3 64.3 + - + +
336M MET* 2.9 14.4 + - - +
337M PHE* 3.1 40.6 + - + -
131R HIS* 6.2 0.7 - - - +
132R LEU* 5.3 3.8 - - + -
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Residues in contact with LEU 334 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326M ILE* 4.4 16.2 - - + -
330M PHE* 2.8 67.5 + - + +
331M PHE* 3.3 12.3 - - + +
333M VAL* 1.3 74.0 - - + +
335M ALA* 1.3 54.4 + - - +
337M PHE* 4.3 4.2 - - - +
338M GLY* 2.7 36.0 + - - -
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Residues in contact with ALA 335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304M ILE* 3.9 7.1 - - + +
308M PHE* 3.4 37.2 - - + -
331M PHE* 2.6 24.8 + - + +
332M GLY 3.4 5.8 - - - +
334M LEU* 1.3 74.3 - - - +
336M MET* 1.3 58.1 + - - +
338M GLY* 5.0 0.4 - - - -
339M ALA* 2.9 25.5 + - - +
401M PHE* 3.2 19.2 - - + -
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Residues in contact with MET 336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M LEU* 3.8 22.7 - - + -
301M PHE* 3.3 38.5 - - + +
304M ILE* 4.1 7.8 - - - +
305M LEU* 4.0 12.1 - - + -
332M GLY 3.0 11.3 + - - +
333M VAL* 2.9 8.7 + - - +
335M ALA* 1.3 72.1 - - - +
337M PHE* 1.3 86.1 + - + +
338M GLY 3.0 0.9 - - - -
339M ALA* 2.8 20.7 + - - +
340M ILE* 3.3 9.3 + - - +
503M SMA 3.2 60.3 - - - +
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Residues in contact with PHE 337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M LEU* 5.4 6.7 - - + -
165M LEU* 4.6 14.4 - - + -
166M PHE* 4.6 15.5 - + - -
333M VAL* 3.1 41.3 + - + +
334M LEU* 4.3 3.4 - - - +
336M MET* 1.3 93.7 - - + +
338M GLY* 1.3 50.3 + - - +
340M ILE* 3.1 12.9 + - + +
341M LEU* 2.8 35.6 + - - +
503M SMA 3.8 44.6 - - + -
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Residues in contact with GLY 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334M LEU 2.7 24.7 + - - -
335M ALA 3.8 0.7 - - - -
337M PHE* 1.3 69.3 - - - +
339M ALA* 1.3 64.0 + - - +
340M ILE 2.9 2.4 + - - -
341M LEU* 2.9 11.7 + - - -
342M VAL* 2.8 31.2 + - - +
401M PHE* 3.9 10.1 - - - -
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Residues in contact with ALA 339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301M PHE* 4.5 9.4 - - + -
304M ILE* 3.8 20.4 - - + -
335M ALA 2.9 14.3 + - - +
336M MET* 2.8 12.2 + - - +
338M GLY* 1.3 75.1 - - - +
340M ILE* 1.3 58.7 + - - +
342M VAL* 3.2 12.1 - - - +
343M MET* 3.9 1.6 + - - +
400M TRP* 2.9 37.1 + - - +
401M PHE* 3.6 19.2 - - + -
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Residues in contact with ILE 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M MET* 3.8 22.5 - - + +
136M TYR* 4.6 8.7 - - + -
137M LEU* 5.1 12.8 - - + -
140M MET* 3.9 16.8 - - + -
301M PHE* 3.2 36.1 - - + -
336M MET 3.7 7.6 - - - +
337M PHE* 3.1 15.0 + - + +
338M GLY 2.9 0.8 - - - -
339M ALA* 1.3 75.9 - - - +
341M LEU* 1.3 68.5 + - - +
343M MET* 2.9 29.3 + - + +
344M ALA 3.2 4.0 + - - -
503M SMA 3.9 27.8 - - - -
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Residues in contact with LEU 341 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337M PHE 2.8 19.3 + - - +
338M GLY* 3.5 10.3 - - - +
340M ILE* 1.3 75.0 - - - +
342M VAL* 1.3 65.7 + - + +
344M ALA* 2.9 19.0 + - + +
345M LEU* 3.1 37.7 + - + +
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Residues in contact with VAL 342 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338M GLY* 2.8 22.2 + - - +
339M ALA* 3.2 20.6 - - - +
341M LEU* 1.3 74.9 - - + +
343M MET* 1.3 68.1 + - - +
345M LEU* 2.8 33.4 + - + +
346M VAL* 3.0 10.6 + - - -
349M LEU* 4.7 3.3 - - + +
400M TRP* 4.0 5.8 - - + +
401M PHE* 4.1 20.6 - - + -
404M PHE* 3.9 36.6 - - + -
405M LEU* 4.3 21.8 - - + -
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Residues in contact with MET 343 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M TYR* 6.5 0.2 - - + -
112M ILE* 4.2 26.5 - - + -
116M LEU* 4.8 8.5 - - + -
129M TRP* 3.2 18.7 + - + -
133M MET* 4.0 21.1 - - + -
136M TYR* 4.5 19.7 - - + -
301M PHE* 4.7 10.5 - - + -
339M ALA 4.1 5.8 - - - +
340M ILE* 2.9 22.4 + - + +
342M VAL* 1.3 80.7 - - - +
344M ALA* 1.3 55.1 + - - +
346M VAL* 2.9 27.2 - - - +
400M TRP* 4.2 20.4 - - + -
404M PHE* 4.0 24.0 - - + -
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Residues in contact with ALA 344 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M TRP* 3.6 15.0 + - - +
130M ILE* 5.2 3.6 - - + +
133M MET* 3.9 28.7 - - + +
340M ILE 3.2 3.6 + - - +
341M LEU* 2.9 22.3 + - + +
343M MET* 1.3 79.1 - - - +
345M LEU* 1.3 61.0 + - + +
346M VAL 3.2 0.7 - - - -
347M PRO* 3.0 16.3 - - - +
348M TRP* 3.6 8.5 - - - -
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Residues in contact with LEU 345 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341M LEU* 3.3 40.2 - - + +
342M VAL* 2.8 12.6 + - + +
344M ALA* 1.3 78.4 - - + +
346M VAL* 1.3 51.4 + - - +
347M PRO* 3.0 7.2 - - - -
348M TRP* 2.6 48.2 + - + +
349M LEU* 3.2 24.0 + - + -
405M LEU* 6.5 0.9 - - + -
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Residues in contact with VAL 346 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M LEU* 4.1 5.4 - - + -
121M TYR* 3.6 29.2 - - + -
129M TRP* 3.4 21.3 - - + +
342M VAL 3.0 6.0 + - - -
343M MET 2.9 25.8 - - - +
345M LEU* 1.3 75.7 - - - +
347M PRO* 1.3 74.7 - - + +
348M TRP 3.0 1.3 + - - -
349M LEU* 3.7 8.5 - - - +
350M ASP* 3.2 19.4 + - - +
403M TYR* 5.8 0.2 - - + -
404M PHE* 4.0 17.9 - - + -
408M LEU* 3.8 21.8 - - + -
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Residues in contact with PRO 347 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M TYR* 3.7 33.2 - - + +
122M LYS* 5.1 6.1 - - - +
123M ALA 5.8 0.2 + - - -
126M GLU* 4.2 15.4 - - + +
129M TRP* 3.7 22.4 - - + -
344M ALA 3.0 13.0 - - - +
345M LEU 3.0 7.6 - - - +
346M VAL* 1.3 96.8 - - + +
348M TRP* 1.3 81.2 + - + +
350M ASP* 3.8 11.8 - - - +
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Residues in contact with TRP 348 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M GLU* 4.4 22.8 + - + +
130M ILE* 3.8 30.5 - - + -
344M ALA 3.6 18.6 - - - -
345M LEU* 2.6 50.8 + - + +
347M PRO* 1.3 91.1 - - + +
349M LEU* 1.3 69.5 + - + +
350M ASP 3.3 4.0 - - - +
351M THR* 4.7 8.0 - - - +
18P TRP* 4.7 11.2 - + - -
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Residues in contact with LEU 349 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M VAL* 4.7 8.5 - - + +
345M LEU* 3.2 27.0 + - + +
346M VAL* 3.4 6.9 + - - +
348M TRP* 1.3 85.7 - - + +
350M ASP* 1.3 61.0 + - - +
351M THR* 3.2 8.8 + - - +
404M PHE* 2.8 43.1 - - + +
405M LEU* 3.5 23.8 - - + -
408M LEU* 4.3 5.8 - - + -
409M PRO* 3.3 31.6 - - + +
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Residues in contact with ASP 350 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M TYR* 2.9 28.4 + - + -
122M LYS* 3.1 23.2 - - + +
346M VAL 3.2 16.9 + - - +
347M PRO 3.8 12.5 - - - +
348M TRP 4.5 1.5 - - - -
349M LEU* 1.3 77.7 - - - +
351M THR* 1.3 59.4 + - - +
352M SER* 3.0 30.1 + - - +
360M ARG* 3.1 13.6 + - - -
363M PHE* 4.0 0.2 - - - -
408M LEU* 3.7 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) + - + + + + + -
------------------------------------------------------------
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