Contacts of the helix formed by residues 318 - 340 (chain P) in PDB entry 1PP9
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 ARG 318 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P TYR* 5.4 2.2 + - - -
308P HIS* 4.0 7.9 + - - -
310P SER* 3.3 29.3 + - - +
312P GLN* 3.4 37.6 + - - +
313P ARG 3.8 5.7 + - - -
314P SER 3.2 31.4 + - - -
315P MET* 2.9 30.4 + - - +
316P MET 3.3 0.8 + - - -
317P PHE* 1.3 79.0 - - - +
319P PRO* 1.3 60.3 - - - +
321P SER* 3.0 24.6 + - - -
322P GLN* 2.9 31.6 + - - +
366P MET 5.5 1.8 + - - -
370P GLY* 4.9 3.6 - - - -
373P GLU* 3.0 29.3 + - + +
20S TYR* 3.9 3.6 - - - +
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Residues in contact with PRO 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P PHE 3.3 11.4 - - - +
318P ARG* 1.3 85.2 - - - +
320P LEU* 1.3 67.9 + - + +
322P GLN* 3.2 4.8 + - + +
323P CYS* 3.1 28.7 + - - -
19S TRP* 5.1 5.8 - - + -
20S TYR* 3.7 24.5 - - + -
23S ALA* 3.6 41.5 - - + +
24S ALA* 3.7 1.8 - - - +
47T ARG* 3.8 26.1 - - + +
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Residues in contact with LEU 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319P PRO* 1.3 80.8 - - + +
321P SER* 1.3 62.7 + - - +
323P CYS* 3.2 9.7 + - - +
324P LEU* 3.1 27.2 + - + +
369P ALA* 4.3 12.1 - - + +
372P ILE* 3.7 29.6 - - + -
373P GLU* 3.3 27.9 + - + +
376P LEU* 4.5 8.1 - - + -
19S TRP* 5.0 16.2 - - + -
20S TYR* 4.4 9.0 - - + -
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Residues in contact with SER 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315P MET* 3.6 15.9 - - - +
318P ARG* 3.0 35.9 + - - -
320P LEU* 1.3 73.3 - - - +
322P GLN* 1.3 57.5 + - - +
324P LEU* 3.4 5.9 + - - +
325P PHE* 2.9 27.9 + - - +
366P MET* 4.2 6.4 + - - +
369P ALA* 4.0 14.1 - - - +
370P GLY 4.3 1.6 + - - -
373P GLU* 2.8 34.1 + - - -
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Residues in contact with GLN 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P TYR* 3.2 30.2 + - + +
315P MET* 2.7 27.0 + - + +
316P MET* 3.0 19.0 + - - +
318P ARG 2.9 16.7 + - - +
319P PRO 3.5 6.7 - - - +
320P LEU 3.2 0.2 - - - -
321P SER* 1.3 75.1 - - - +
323P CYS* 1.3 67.1 + - - +
325P PHE* 3.0 7.8 + - - +
326P TRP* 3.0 34.0 + - + -
3007P PEE 3.9 6.4 + - - +
44T CYS* 5.7 2.3 - - - +
47T ARG* 2.9 45.4 + - + +
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Residues in contact with CYS 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319P PRO 3.1 18.8 + - - -
320P LEU* 3.2 10.7 + - - +
322P GLN* 1.3 77.3 - - - +
324P LEU* 1.3 64.2 + - + +
326P TRP* 3.4 2.8 + - - +
327P ALA* 3.1 21.3 + - - +
46T LEU 4.4 5.4 - - - -
47T ARG* 4.0 33.7 - - - -
51T PRO* 4.1 6.8 - - + +
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Residues in contact with LEU 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320P LEU* 3.1 11.2 + - + +
321P SER* 3.8 7.2 - - - +
322P GLN 3.2 0.2 - - - -
323P CYS* 1.3 74.6 - - + +
325P PHE* 1.3 66.0 + - - +
327P ALA* 3.2 7.9 + - + +
328P LEU* 3.0 22.3 + - - +
361P LEU* 3.8 22.3 - - + +
365P LEU* 3.5 32.3 - - + +
366P MET* 3.9 18.2 - - + +
369P ALA* 3.4 33.7 - - + -
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Residues in contact with PHE 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P GLY* 3.7 24.2 - - - -
102P LEU* 4.3 12.1 - - + -
103P TYR* 3.6 33.4 - + + -
315P MET* 3.8 18.4 - - + -
321P SER 2.9 14.1 + - - +
322P GLN* 3.0 9.4 + - - +
324P LEU* 1.3 78.1 - - - +
326P TRP* 1.3 83.7 + + - +
328P LEU* 3.2 11.8 + - + +
329P VAL* 3.1 40.3 + - + +
366P MET* 3.6 12.7 - - + +
3007P PEE 3.6 37.0 - - + -
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Residues in contact with TRP 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P TYR* 4.3 9.7 + - - -
322P GLN* 3.0 31.8 + - + +
323P CYS 4.0 0.7 - - - +
325P PHE* 1.3 102.5 - + - +
327P ALA* 1.3 59.3 - - - +
329P VAL* 3.3 11.4 + - + +
330P ALA* 2.8 30.0 + - - +
3007P PEE 3.4 85.9 + - + -
47T ARG* 3.4 28.2 - - - +
48T VAL* 3.5 27.6 - - + +
51T PRO* 3.5 12.5 - - + +
52T PHE* 3.7 25.2 - + + -
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Residues in contact with ALA 327 (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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323P CYS 3.1 14.3 + - - +
324P LEU* 3.5 14.8 - - + +
325P PHE 3.2 0.2 - - - -
326P TRP* 1.3 76.0 - - - +
328P LEU* 1.3 60.0 + - - +
330P ALA* 3.7 1.8 - - - +
331P ASP* 2.8 30.1 + - - +
357P LEU* 5.1 5.1 - - + +
361P LEU* 4.0 14.9 - - + +
51T PRO* 3.7 16.8 - - + +
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Residues in contact with LEU 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P LEU* 5.0 16.4 - - + -
324P LEU 3.0 12.1 + - - +
325P PHE* 3.4 15.9 - - + +
327P ALA* 1.3 77.8 - - - +
329P VAL* 1.3 57.3 + - + +
331P ASP* 3.1 4.6 + - + +
332P LEU* 2.9 38.0 + - + +
358P TYR* 3.5 43.5 - - + +
361P LEU* 3.6 21.7 - - + +
362P ILE* 4.1 21.3 - - + -
366P MET* 4.4 16.4 - - + -
3007P PEE 5.3 5.4 - - + -
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Residues in contact with VAL 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P PHE* 3.1 41.4 + - + +
326P TRP* 3.7 14.6 - - + +
328P LEU* 1.3 75.2 - - + +
330P ALA* 1.3 65.1 + - - +
332P LEU* 3.2 10.2 + - - +
333P LEU* 3.0 21.7 + - - +
3007P PEE 3.8 57.3 - - + +
52T PHE* 3.7 18.4 - - + -
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Residues in contact with ALA 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P TRP 2.8 16.8 + - - +
327P ALA* 3.7 4.5 - - - +
329P VAL* 1.3 76.9 - - - +
331P ASP* 1.3 57.7 + - - +
333P LEU* 3.1 6.8 + - - +
334P THR* 2.8 31.0 + - - -
51T PRO* 3.5 34.5 - - + +
52T PHE* 3.9 18.1 - - + -
55T PHE* 4.2 6.3 - - + -
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Residues in contact with ASP 331 (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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327P ALA 2.8 19.2 + - - +
328P LEU* 3.4 9.9 - - + +
329P VAL 3.1 0.2 - - - -
330P ALA* 1.3 75.2 - - - +
332P LEU* 1.3 60.5 + - - +
334P THR* 3.1 8.3 + - - -
335P LEU* 2.9 29.3 + - - +
354P ALA* 2.7 47.8 - - - +
357P LEU* 3.6 23.5 - - + +
358P TYR* 3.3 22.2 + - - +
361P LEU* 4.6 1.6 - - + -
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Residues in contact with LEU 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276P PHE* 3.9 32.6 - - + +
328P LEU* 2.9 28.4 + - + +
329P VAL* 3.2 6.5 + - - +
331P ASP* 1.3 75.0 - - - +
333P LEU* 1.3 58.8 + - - +
335P LEU* 3.4 7.2 + - + +
336P THR* 2.8 33.9 + - - -
358P TYR* 3.6 31.6 - - + -
3007P PEE 3.6 65.5 - - + -
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Residues in contact with LEU 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329P VAL 3.0 12.7 + - - +
330P ALA 3.2 8.5 - - - +
331P ASP 3.1 0.2 - - - -
332P LEU* 1.3 77.6 - - - +
334P THR* 1.3 59.9 + - - +
336P THR* 3.3 11.8 + - + -
337P TRP* 3.0 22.7 + - + +
3007P PEE 4.2 26.0 - - + +
52T PHE* 4.1 24.9 - - + -
55T PHE* 3.8 38.4 - - + -
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Residues in contact with THR 334 (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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330P ALA 2.8 17.1 + - - -
331P ASP* 3.1 14.1 + - - +
333P LEU* 1.3 77.4 - - - +
335P LEU* 1.3 57.8 + - - +
337P TRP* 3.2 12.6 + - + +
338P ILE* 2.8 28.1 + - + +
350P ILE* 4.0 22.4 - - + -
354P ALA* 3.9 18.8 - - + -
55T PHE* 3.2 26.1 - - - +
58T VAL* 5.1 6.4 - - + +
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Residues in contact with LEU 335 (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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275P LEU 3.8 1.0 - - - +
276P PHE* 4.0 14.1 - - + +
279P ALA* 3.2 25.6 - - + +
280P ILE* 3.9 25.6 - - + -
331P ASP* 2.9 25.0 + - - +
332P LEU* 3.8 17.9 - - + +
334P THR* 1.3 76.2 - - - +
336P THR* 1.3 57.3 + - - +
338P ILE* 4.4 2.9 - - + -
339P GLY* 2.9 25.1 + - - -
351P GLY* 3.9 6.3 - - - +
354P ALA* 3.6 32.3 - - + +
355P SER* 3.5 24.0 - - - +
358P TYR* 4.4 6.5 - - + -
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Residues in contact with THR 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272P TRP* 4.3 13.7 + - + +
275P LEU* 3.7 35.8 - - + +
276P PHE* 3.9 12.1 + - - +
332P LEU 2.8 24.3 + - - -
333P LEU* 3.6 13.2 - - + -
335P LEU* 1.3 76.0 - - - +
337P TRP* 1.3 64.4 + - - +
339P GLY 3.3 7.6 + - - -
340P GLY* 3.5 7.4 + - - -
3007P PEE 3.5 20.3 - - + +
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Residues in contact with TRP 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333P LEU* 3.0 14.1 + - + +
334P THR* 3.5 22.0 - - + +
336P THR* 1.3 76.5 - - - +
338P ILE* 1.3 80.9 + - + +
340P GLY* 3.0 13.3 + - - -
341P GLN* 3.4 31.4 + - + +
347P TYR* 3.5 23.1 - + - -
350P ILE* 4.0 24.9 - - + -
55T PHE* 4.2 17.3 - + + -
58T VAL* 3.8 13.7 - - + -
59T TYR* 3.4 62.6 - + - -
62T GLY* 4.5 1.6 - - - -
63T THR* 3.9 5.1 + - - -
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Residues in contact with ILE 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P ALA* 4.4 9.9 - - + +
282P ARG* 2.9 22.8 + - - +
283P SER* 5.7 0.4 - - - +
334P THR* 2.8 21.6 + - + +
335P LEU* 3.8 6.7 - - - +
337P TRP* 1.3 101.2 - - + +
339P GLY* 1.3 58.1 + - - +
340P GLY 3.0 0.2 - - - -
341P GLN* 2.9 20.6 + - - +
347P TYR* 3.9 46.4 - - + +
350P ILE* 3.8 21.3 - - + -
351P GLY* 3.9 17.3 - - - +
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Residues in contact with GLY 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LYS* 4.5 4.7 - - - +
275P LEU* 3.3 27.8 - - - +
278P TYR* 3.2 28.7 - - - -
279P ALA* 3.9 4.5 - - - +
282P ARG* 3.9 9.8 + - - -
335P LEU 2.9 16.5 + - - -
336P THR 3.3 3.3 + - - -
337P TRP 3.2 0.6 - - - -
338P ILE* 1.3 74.9 - - - +
340P GLY* 1.3 57.4 + - - +
341P GLN 3.3 0.6 + - - -
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Residues in contact with GLY 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LYS* 4.1 29.0 + - - +
275P LEU* 4.0 9.8 - - - +
336P THR 3.5 6.2 + - - -
337P TRP 3.0 9.6 + - - -
339P GLY* 1.3 76.9 - - - +
341P GLN* 1.3 71.1 + - - +
342P PRO* 4.4 1.6 - - - +
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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