Contacts of the helix formed by residues 319 - 341 (chain P) in PDB entry 3H1I
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 319 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P LEU 5.6 0.8 + - - -
106P GLY 6.1 0.4 - - - +
108P TYR* 5.1 5.1 + - - -
309P HIS* 4.8 7.7 + - - -
310P LYS 5.8 0.4 - - - +
311P SER* 3.0 42.9 - - - +
313P GLN* 3.7 13.4 + - - +
314P ARG 4.1 12.0 + - - -
315P THR 3.5 17.3 + - - +
316P MET* 3.0 44.6 + - - +
317P THR 3.5 0.6 + - - -
318P PHE* 1.3 82.8 - - - +
320P PRO* 1.3 71.2 - - - +
321P LEU 2.8 4.0 + - - -
322P SER* 2.9 27.7 + - - -
323P GLN* 2.9 14.5 + - - +
367P PHE 5.6 1.6 + - - -
371P GLY* 4.7 4.4 - - - -
374P GLU* 2.8 24.8 + - + +
20S TYR* 3.4 4.7 - - - +
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Residues in contact with PRO 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318P PHE* 3.7 5.8 - - - +
319P ARG* 1.3 86.5 - - - +
321P LEU* 1.3 73.9 + - + +
323P GLN* 3.3 17.4 - - + +
324P THR* 3.0 25.3 + - - -
19S TRP* 6.2 2.9 - - + -
20S TYR* 3.6 24.9 - - + +
23S ALA* 4.2 22.4 - - + +
24S ALA* 4.2 10.1 - - - -
47T LYS* 4.2 23.3 - - - +
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Residues in contact with LEU 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319P ARG 2.8 1.4 + - - -
320P PRO* 1.3 85.6 - - + +
322P SER* 1.3 68.8 + - - +
324P THR* 3.2 10.5 + - + +
325P LEU* 3.1 17.0 + - - +
370P ILE* 3.4 33.9 - - + +
373P LEU* 4.9 8.7 - - + -
374P GLU* 3.3 16.6 - - + +
377P MET* 4.4 23.1 - - + -
19S TRP* 5.1 14.6 - - + -
20S TYR* 4.1 13.0 - - + -
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Residues in contact with SER 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316P MET* 3.8 16.8 - - - -
319P ARG* 2.9 38.1 + - - -
321P LEU* 1.3 73.9 - - - +
323P GLN* 1.3 65.2 + - - +
325P LEU* 2.7 11.4 + - - +
326P PHE* 2.7 21.5 + - - +
367P PHE* 3.9 8.4 + - - -
370P ILE* 3.9 8.8 - - - +
371P GLY* 4.7 2.4 - - - -
374P GLU* 2.8 27.0 + - - -
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Residues in contact with GLN 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P TYR* 3.0 30.4 + - + -
316P MET* 3.1 32.1 + - + +
317P THR 3.3 15.2 + - - -
319P ARG 2.9 9.2 + - - +
320P PRO* 3.3 17.6 - - + +
322P SER* 1.3 75.3 - - - +
324P THR* 1.3 64.5 + - - +
326P PHE* 2.8 27.5 + - - +
327P TRP* 3.0 18.8 + - + -
3007P PEE 4.2 2.2 + - - -
44T GLN* 3.5 17.7 + - - -
47T LYS* 3.4 33.5 - - + +
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Residues in contact with THR 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320P PRO 3.0 8.9 + - - -
321P LEU* 3.6 14.4 - - + +
323P GLN* 1.3 78.8 - - - +
325P LEU* 1.3 67.2 + - + +
327P TRP* 3.8 1.9 + - - +
328P LEU* 3.1 23.5 + - + +
46T PHE 4.9 1.9 + - - -
47T LYS* 4.0 31.3 + - - +
50T PRO* 5.9 1.2 - - - +
51T PRO* 4.9 5.1 - - + +
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Residues in contact with LEU 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321P LEU 3.1 10.0 + - - +
322P SER* 2.7 15.7 + - - +
324P THR* 1.3 77.2 - - + +
326P PHE* 1.3 63.2 + - - +
328P LEU* 2.9 34.1 + - + +
329P LEU* 2.9 11.6 + - - +
362P ILE* 3.7 21.8 - - + -
366P LEU* 3.3 43.5 - - + -
367P PHE* 3.8 21.3 - - + +
370P ILE* 3.7 24.2 - - + -
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Residues in contact with PHE 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P GLY* 4.1 3.4 - - - -
103P LEU* 3.9 28.9 - - + -
104P TYR* 3.6 32.3 - + + -
316P MET* 3.7 29.8 - - + -
322P SER 2.7 13.6 + - - +
323P GLN* 2.8 9.6 + - - +
325P LEU* 1.3 70.3 - - - +
327P TRP* 1.3 85.9 + + - +
329P LEU* 2.7 28.0 + - + +
330P VAL* 2.9 29.7 + - + +
367P PHE* 3.7 11.3 - - - -
3007P PEE 3.8 44.9 - - + -
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Residues in contact with TRP 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P TYR* 4.7 9.1 - - - -
323P GLN* 3.0 36.4 + - + +
324P THR 4.1 1.6 - - - +
326P PHE* 1.3 82.9 - + - +
328P LEU* 1.3 67.5 + - - +
330P VAL* 3.1 23.2 + - + +
331P ALA* 2.9 24.9 + - - +
3007P PEE 3.3 93.0 + - + -
44T GLN* 5.0 2.0 - - - +
47T LYS* 4.0 17.7 - - + +
48T VAL* 3.5 24.1 - - + +
51T PRO* 3.9 18.1 - - + +
52T PHE* 3.9 22.8 - + + -
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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
----------------------------------------------------------
324P THR* 3.1 16.6 + - + +
325P LEU* 2.9 31.1 + - + +
327P TRP* 1.3 77.0 - - - +
329P LEU* 1.3 49.9 + - - +
331P ALA* 3.3 3.3 + - + +
332P ASN* 2.6 35.9 + - + +
358P SER* 5.8 2.0 - - - +
362P ILE* 4.3 11.9 - - + -
366P LEU* 5.7 2.5 - - + -
51T PRO* 3.5 28.2 - - + +
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Residues in contact with LEU 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P LEU* 3.8 29.4 - - + -
325P LEU 2.9 9.7 + - - +
326P PHE* 2.7 21.1 + - + +
328P LEU* 1.3 68.7 - - - +
330P VAL* 1.3 68.5 + - + +
332P ASN* 3.0 17.1 + - - +
333P LEU* 3.0 17.3 + - + +
359P TYR* 4.1 26.7 - - + +
362P ILE* 3.7 32.7 - - + +
363P LEU* 3.8 22.2 - - + -
367P PHE* 4.3 5.8 - - + -
3007P PEE 4.9 13.9 - - + -
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Residues in contact with VAL 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P PHE* 2.9 47.3 + - + +
327P TRP* 3.1 17.9 + - + +
329P LEU* 1.3 74.8 - - + +
331P ALA* 1.3 57.8 + - - +
333P LEU* 2.8 34.8 + - - +
334P LEU* 2.9 10.8 + - + +
3007P PEE 4.0 48.7 - - + +
52T PHE* 3.9 20.9 - - + -
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Residues in contact with ALA 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P TRP 2.9 13.4 + - - +
328P LEU* 3.5 5.6 - - + +
330P VAL* 1.3 80.5 - - - +
332P ASN* 1.3 58.1 + - - +
334P LEU* 3.0 11.7 + - + +
335P ILE* 2.7 37.8 + - + +
51T PRO* 4.3 18.2 - - + +
52T PHE* 3.4 25.8 - - + -
55T ALA* 4.7 7.9 - - + -
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Residues in contact with ASN 332 (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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328P LEU* 2.6 20.1 + - + +
329P LEU* 3.0 16.7 + - - +
331P ALA* 1.3 73.3 - - - +
333P LEU* 1.3 54.2 + - - +
335P ILE* 3.3 12.1 - - - +
336P LEU* 3.0 27.3 + - - +
355P ALA* 3.1 19.3 + - - +
358P SER* 3.0 22.6 + - - +
359P TYR* 2.7 48.3 - - - +
362P ILE* 3.9 6.3 - - + +
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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
----------------------------------------------------------
277P PHE* 4.7 20.1 - - + +
281P ILE* 6.2 0.4 - - + -
329P LEU* 3.0 20.6 + - + +
330P VAL* 2.8 9.2 + - - +
332P ASN* 1.3 73.0 - - - +
334P LEU* 1.3 65.0 + - - +
335P ILE 2.8 5.6 + - - -
336P LEU* 2.9 12.0 + - + +
337P THR* 2.8 27.0 + - - -
359P TYR* 3.5 34.8 - - + -
3007P PEE 3.5 71.1 - - + -
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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
----------------------------------------------------------
330P VAL* 2.9 7.2 + - + +
331P ALA* 3.3 15.5 - - + +
333P LEU* 1.3 76.7 - - - +
335P ILE* 1.3 62.3 + - + +
337P THR* 3.7 8.0 - - + +
338P TRP* 3.5 15.4 + - - +
3007P PEE 4.6 39.3 - - + +
52T PHE* 4.3 27.6 - - + -
55T ALA* 6.0 4.7 - - + -
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Residues in contact with ILE 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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331P ALA* 2.7 20.4 + - + +
332P ASN* 3.3 18.2 - - - +
333P LEU 2.8 0.4 + - - -
334P LEU* 1.3 75.3 - - - +
336P LEU* 1.3 68.7 + - - +
337P THR 2.9 1.1 - - - -
338P TRP* 2.7 43.5 + - + +
339P ILE* 3.1 10.7 + - + +
351P ILE* 4.9 7.6 - - + -
355P ALA* 4.2 17.3 - - + -
55T ALA* 3.6 34.1 - - + -
58T LEU* 4.6 16.4 - - + -
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Residues in contact with LEU 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P PHE* 4.2 13.2 - - + +
280P ALA* 3.3 25.8 - - + +
281P ILE* 3.6 22.4 - - + -
332P ASN* 3.0 28.8 + - - +
333P LEU* 2.9 17.9 + - + +
335P ILE* 1.3 80.6 - - - +
337P THR* 1.3 61.8 - - - +
339P ILE* 3.4 6.9 + - - +
340P GLY 3.1 16.8 + - - -
352P GLY* 4.8 2.7 - - - +
355P ALA* 3.6 27.4 - - + +
356P SER* 3.6 27.8 - - - +
359P TYR* 4.1 12.8 - - + -
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Residues in contact with THR 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P TRP* 4.8 6.9 + - + +
276P LEU* 3.9 21.5 - - + +
277P PHE* 3.7 28.6 + - - +
333P LEU 2.8 13.9 + - - -
334P LEU* 3.7 13.7 - - + +
335P ILE 2.8 0.6 + - - -
336P LEU* 1.3 73.4 - - - +
338P TRP* 1.3 72.3 + - - +
340P GLY* 2.8 13.9 + - - -
341P SER* 3.2 7.0 + - - -
3007P PEE 3.9 20.9 - - + +
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Residues in contact with TRP 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P LEU 3.5 9.0 + - - +
335P ILE* 2.7 24.7 + - + +
337P THR* 1.3 76.9 - - - +
339P ILE* 1.3 84.9 + - + +
341P SER* 2.6 43.0 + - - -
342P GLN* 3.3 26.4 + - + +
348P PHE* 3.4 28.0 - + - -
351P ILE* 4.0 19.3 - - + -
58T LEU* 3.6 27.4 - - + -
59T TYR* 2.9 55.9 - + + -
62T GLY* 4.4 1.8 - - - -
63T THR* 4.0 4.2 + - - -
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Residues in contact with ILE 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ALA* 4.6 8.7 - - + +
283P ARG* 2.7 32.4 + - - +
284P SER* 5.7 1.6 - - - +
335P ILE* 3.1 15.2 + - + +
336P LEU* 3.4 10.8 - - - +
338P TRP* 1.3 113.4 - - + +
340P GLY* 1.3 51.7 + - - +
342P GLN* 2.6 29.7 + - - +
348P PHE* 3.9 37.0 - - + +
349P ILE* 5.8 0.9 - - - -
351P ILE* 3.9 10.8 - - + -
352P GLY* 4.2 19.5 - - - -
355P ALA* 5.7 0.2 - - + -
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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
----------------------------------------------------------
270P LYS* 3.5 8.8 - - - +
276P LEU* 4.2 13.9 - - - -
279P TYR* 3.4 36.9 - - - -
280P ALA* 4.2 4.7 - - - +
283P ARG* 3.8 8.7 + - - -
336P LEU 3.1 6.8 + - - -
337P THR 2.8 15.7 + - - -
339P ILE* 1.3 75.3 - - - +
341P SER* 1.3 55.5 + - - -
342P GLN 3.0 5.0 + - - -
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Residues in contact with SER 341 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P LYS* 3.9 21.9 - - - +
276P LEU* 4.1 19.8 - - - +
337P THR* 3.2 3.7 + - - -
338P TRP* 2.6 27.0 + - - -
340P GLY* 1.3 70.1 - - - -
342P GLN* 1.3 73.7 + - - -
343P PRO* 4.2 0.7 - - - +
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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