Contacts of the helix formed by residues 319 - 342 (chain C) in PDB entry 3H1J
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU 5.8 0.2 + - - -
104C TYR 5.0 0.4 + - - -
108C TYR* 4.8 4.2 + - - -
309C HIS* 4.4 6.3 + - - -
311C SER* 3.0 41.6 + - - -
313C GLN* 3.8 13.2 + - - +
314C ARG 4.2 8.9 + - - -
315C THR 3.2 23.7 + - - +
316C MET* 3.1 36.1 + - - +
317C THR 3.5 0.4 - - - -
318C PHE* 1.3 83.0 - - - +
320C PRO* 1.3 62.1 - - - +
321C LEU 3.3 2.0 - - - -
322C SER* 3.1 22.7 + - - -
323C GLN* 2.9 31.1 + - - +
367C PHE* 5.6 3.0 + - - -
371C GLY* 4.5 6.5 - - - -
374C GLU* 3.1 31.4 + - + +
20F TYR* 3.8 5.6 - - - +
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Residues in contact with PRO 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE 3.6 8.7 - - - +
319C ARG* 1.3 86.4 - - - +
321C LEU* 1.3 71.6 + - + +
323C GLN* 3.3 6.5 + - - +
324C THR* 3.2 23.4 + - - -
19F TRP* 5.1 2.9 - - + -
20F TYR* 3.9 24.5 - - + -
23F ALA* 4.1 22.7 - - + +
24F ALA* 4.1 9.0 - - - -
47G LYS* 3.8 31.9 - - - +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ARG 3.3 0.6 - - - -
320C PRO* 1.3 80.5 - - + +
322C SER* 1.3 68.7 + - - +
324C THR* 3.0 16.8 + - - -
325C LEU* 3.1 12.8 + - - +
370C ILE* 3.4 22.8 - - + +
373C LEU* 4.6 12.8 - - + -
374C GLU* 3.2 25.4 - - + +
377C MET* 4.2 21.8 - - + -
19F TRP* 4.3 21.3 - - + -
20F TYR* 4.5 2.0 - - + -
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C MET* 3.8 23.7 - - - +
319C ARG* 3.1 30.8 + - - -
321C LEU* 1.3 75.3 - - - +
323C GLN* 1.3 57.6 + - - +
325C LEU* 3.4 8.2 + - - +
326C PHE* 2.9 29.5 + - - +
367C PHE* 3.7 9.8 + - - -
370C ILE* 4.1 7.8 - - - +
371C GLY* 4.9 1.2 - - - -
374C GLU* 2.7 28.8 + - - -
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Residues in contact with GLN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C TYR* 3.3 24.2 + - + +
316C MET* 2.6 30.9 + - + +
317C THR* 3.0 19.4 + - - +
319C ARG 2.9 16.1 + - - +
320C PRO* 3.4 8.5 - - - +
321C LEU 3.1 0.4 - - - -
322C SER* 1.3 76.8 - - - +
324C THR* 1.3 60.6 + - - +
326C PHE* 3.3 6.6 + - - +
327C TRP* 3.0 35.2 + - + +
2007C PEE 4.3 1.8 + - - -
24F ALA 5.7 0.2 + - - -
44G GLN* 3.3 12.7 + - - +
47G LYS* 2.9 45.2 + - + +
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Residues in contact with THR 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C PRO 3.2 9.2 + - - -
321C LEU* 3.0 9.4 + - - -
323C GLN* 1.3 75.2 - - - +
325C LEU* 1.3 70.4 + - - +
326C PHE 3.1 0.2 + - - -
327C TRP* 3.2 2.6 + - - +
328C LEU* 2.9 36.4 + - + +
46G PHE 5.3 0.7 + - - -
47G LYS* 4.2 27.5 + - - +
50G PRO* 6.3 0.7 - - + -
51G PRO* 4.7 6.1 - - + +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C LEU 3.1 11.3 + - - +
322C SER* 3.6 8.1 - - - +
324C THR* 1.3 79.3 - - - +
326C PHE* 1.3 63.1 + - - +
328C LEU* 3.2 18.8 - - + +
329C LEU* 3.0 21.5 + - - +
362C ILE* 3.4 26.5 - - + +
366C LEU* 3.5 30.5 - - + -
367C PHE* 3.4 47.1 - - + +
370C ILE* 3.7 18.2 - - + -
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Residues in contact with PHE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLY* 4.0 8.7 - - - -
103C LEU* 4.3 21.5 - - + -
104C TYR* 3.7 34.5 - + + -
316C MET* 4.0 16.6 - - + -
322C SER 2.9 14.5 + - - +
323C GLN* 3.3 9.4 - - - +
324C THR 3.0 0.2 - - - -
325C LEU* 1.3 77.2 - - - +
327C TRP* 1.3 81.2 + + - +
329C LEU* 3.0 9.7 + - + +
330C VAL* 3.0 42.9 + - + +
367C PHE* 3.7 9.1 - + + -
2007C PEE 3.8 51.4 - - + -
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Residues in contact with TRP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C TYR* 4.5 7.9 - - - -
323C GLN* 3.0 28.3 + - + +
324C THR 4.0 1.6 - - - +
326C PHE* 1.3 97.7 - + - +
328C LEU* 1.3 64.3 + - - +
330C VAL* 3.6 18.0 - - + +
331C ALA* 3.1 22.7 + - - +
2007C PEE 3.2 86.6 - - + -
44G GLN* 4.6 8.3 - - - +
47G LYS* 4.0 16.4 - - + +
48G VAL* 3.6 22.7 - - + +
51G PRO* 3.6 22.2 - - + +
52G PHE* 4.1 23.7 - + + -
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C THR* 2.9 19.9 + - + +
325C LEU* 3.2 27.1 - - + +
327C TRP* 1.3 78.4 - - - +
329C LEU* 1.3 51.8 + - - +
331C ALA* 3.2 4.6 + - + +
332C ASN* 2.7 36.2 + - + +
362C ILE* 4.5 11.9 - - + -
366C LEU* 5.7 2.7 - - + -
51G PRO* 3.2 31.6 - - + +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 4.0 19.7 - - + -
325C LEU 3.0 8.4 + - - +
326C PHE* 3.0 12.7 + - + +
328C LEU* 1.3 81.3 - - - +
330C VAL* 1.3 63.1 + - + +
332C ASN* 3.0 9.9 + - - +
333C LEU* 3.0 27.1 + - + +
359C TYR* 3.8 33.4 - - + +
362C ILE* 3.9 29.1 - - + +
363C LEU* 3.8 25.4 - - + -
367C PHE* 4.3 6.1 - - + -
2007C PEE 4.6 16.6 - - + -
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Residues in contact with VAL 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C PHE* 3.0 42.3 + - + +
327C TRP* 3.7 13.9 - - + +
328C LEU 3.2 0.4 - - - -
329C LEU* 1.3 76.0 - - + +
331C ALA* 1.3 57.7 + - - +
333C LEU* 3.1 13.4 + - - +
334C LEU* 3.0 24.5 + - + +
2007C PEE 4.2 52.2 - - + +
52G PHE* 3.7 22.4 - - + -
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C TRP 3.1 10.7 + - - +
328C LEU* 3.6 7.0 - - + +
330C VAL* 1.3 72.2 - - - +
332C ASN* 1.3 56.2 + - - +
334C LEU* 3.1 7.5 + - - +
335C ILE* 2.7 41.5 + - + +
51G PRO* 3.6 21.3 - - + +
52G PHE* 3.4 30.9 - - + -
55G ALA* 4.1 8.7 - - + -
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Residues in contact with ASN 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU* 2.7 18.3 + - + +
329C LEU* 3.0 18.6 + - + +
331C ALA* 1.3 73.0 - - - +
333C LEU* 1.3 53.6 + - - +
335C ILE* 3.2 13.7 - - - +
336C LEU* 2.9 31.0 + - - +
355C ALA* 3.1 21.6 - - - +
358C SER* 2.6 31.2 + - - +
359C TYR* 2.9 28.6 - - - +
362C ILE* 3.5 9.6 - - + +
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Residues in contact with LEU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PHE* 4.2 24.9 - - + +
329C LEU* 3.0 21.9 + - + +
330C VAL* 3.5 9.6 - - - +
332C ASN* 1.3 70.4 - - - +
334C LEU* 1.3 57.7 + - - +
335C ILE 3.0 1.3 - - - -
336C LEU* 3.0 11.4 + - + +
337C THR* 2.7 38.8 + - - -
359C TYR* 3.6 32.3 - - + -
2007C PEE 3.8 69.3 - - + -
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Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C VAL* 3.0 13.0 + - + +
331C ALA* 3.2 11.0 - - + +
333C LEU* 1.3 75.5 - - - +
335C ILE* 1.3 64.2 + - + +
337C THR* 3.4 10.7 + - + -
338C TRP* 3.0 21.5 + - - +
2007C PEE 4.4 30.4 - - + +
52G PHE* 4.2 26.9 - - + -
55G ALA* 5.5 6.1 - - + -
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Residues in contact with ILE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ALA* 2.7 21.1 + - + +
332C ASN* 3.2 12.8 - - - +
334C LEU* 1.3 73.8 - - + +
336C LEU* 1.3 67.0 + - - +
338C TRP* 2.9 16.6 + - + +
339C ILE* 2.8 31.8 + - + +
351C ILE* 4.4 13.7 - - + -
355C ALA* 4.0 19.7 - - + -
55G ALA* 3.8 28.5 - - + +
58G LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU 4.2 0.3 - - - +
277C PHE* 4.1 16.4 - - + +
280C ALA* 3.3 21.6 - - + +
281C ILE* 4.0 20.0 - - + -
332C ASN* 2.9 32.3 + - - +
333C LEU* 3.5 17.3 - - + +
335C ILE* 1.3 75.9 - - - +
337C THR* 1.3 57.3 + - - +
339C ILE* 3.3 3.7 + - - +
340C GLY* 2.9 25.5 + - - -
352C GLY* 4.0 6.3 - - - +
355C ALA* 3.5 22.7 - - + +
356C SER* 3.5 21.5 - - - +
359C TYR* 4.0 21.5 - - + -
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Residues in contact with THR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TRP* 4.4 11.3 + - + +
276C LEU* 3.8 35.8 - - + +
277C PHE* 3.9 12.8 + - - +
333C LEU 2.7 18.2 + - - -
334C LEU* 3.5 14.6 - - + -
336C LEU* 1.3 72.8 - - - +
338C TRP* 1.3 66.2 + - - +
340C GLY* 3.1 9.9 + - - -
341C SER* 3.4 8.5 + - - -
2007C PEE 3.8 22.2 - - + +
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Residues in contact with TRP 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C LEU 3.0 13.1 + - - +
335C ILE* 2.9 21.7 + - + +
337C THR* 1.3 75.7 - - - +
339C ILE* 1.3 86.8 + - + +
341C SER* 2.7 28.6 + - - -
342C GLN* 3.4 24.1 + - + +
348C PHE* 3.3 33.0 - + - -
351C ILE* 3.9 21.5 - - + -
58G LEU* 3.7 28.3 - - + -
59G TYR* 3.2 52.1 - + + -
62G GLY* 4.1 2.0 - - - -
63G THR* 3.8 4.9 + - - -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 4.1 11.4 - - + +
283C ARG* 2.8 24.1 + - - +
335C ILE* 2.8 26.7 + - + +
336C LEU* 3.4 11.0 - - - +
338C TRP* 1.3 93.7 - - + +
340C GLY* 1.3 58.6 + - - +
342C GLN* 2.8 25.2 + - - +
348C PHE* 3.6 39.7 - - + +
349C ILE* 6.0 0.4 - - - -
351C ILE* 3.9 15.0 - - + -
352C GLY* 4.0 24.9 - - - +
355C ALA* 5.6 0.2 - - + -
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Residues in contact with GLY 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LYS* 3.6 7.6 - - - +
276C LEU* 3.8 13.2 - - - +
279C TYR* 3.1 36.7 - - - -
280C ALA* 3.8 8.2 - - - +
283C ARG* 3.7 9.0 + - - -
336C LEU 2.9 17.6 + - - -
337C THR 3.1 5.9 + - - -
339C ILE* 1.3 73.9 - - - +
341C SER* 1.3 58.3 + - - +
342C GLN 3.5 0.2 + - - -
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Residues in contact with SER 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LYS* 4.1 19.8 - - - +
276C LEU* 4.1 14.3 - - - +
337C THR 3.4 6.6 + - - -
338C TRP* 2.7 24.6 + - - -
340C GLY* 1.3 75.1 - - - +
342C GLN* 1.3 76.2 + - - +
343C PRO* 4.2 1.7 - - - +
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Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LYS* 4.1 3.0 - - - -
283C ARG* 2.8 37.4 + - - -
338C TRP* 3.4 34.8 + - + +
339C ILE* 2.8 9.1 + - - +
341C SER* 1.3 94.5 + - - +
343C PRO* 1.3 67.9 - - - +
348C PHE* 3.3 46.5 - - + -
59G TYR* 5.3 0.9 - - - -
66G PHE* 5.7 2.0 - - - -
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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