Contacts of the helix formed by residues 325 - 346 (chain C) in PDB entry 2I2X
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 THR 325 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C VAL* 3.4 27.7 - - + +
316C GLU 2.8 29.4 + - - +
317C TYR* 3.5 15.9 - - + -
318C HIS* 2.9 23.2 + - - +
320C GLU* 3.9 23.7 + - - +
323C GLY 3.5 1.2 + - - -
324C THR* 1.3 71.4 - - - +
326C VAL* 1.3 68.9 + - + +
328C CYS* 3.5 2.1 + - - -
329C TRP* 3.1 35.5 + - - -
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.7 10.7 - - + +
44C ASN 4.5 4.5 - - - +
45C TYR* 3.5 33.4 - - + -
65C ILE* 3.9 8.5 - - + +
68C ASP* 3.9 9.2 - - + -
69C VAL* 3.7 25.6 - - + +
315C VAL* 4.5 0.9 - - + -
317C TYR* 3.8 16.6 - - + -
324C THR* 3.0 25.1 - - + -
325C THR* 1.3 92.9 - - + +
327C GLN* 1.3 50.7 + - - +
330C SER* 2.8 36.8 + - - -
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Residues in contact with GLN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP* 2.9 46.3 + - + +
71C GLU* 4.7 7.1 - - - +
72C ARG* 3.6 45.4 + - + +
323C GLY* 3.7 3.8 - - - -
324C THR* 2.7 43.3 + - + +
326C VAL* 1.3 77.2 - - - +
328C CYS* 1.3 65.3 + - - +
330C SER* 3.2 5.3 + - - -
331C GLU* 3.0 27.2 + - - +
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Residues in contact with CYS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 2.9 55.7 + - - +
293A CYS* 4.0 4.7 - - - +
329A TRP* 4.6 3.8 - - + -
72C ARG* 4.3 2.2 - - - +
320C GLU* 3.9 20.6 - - + -
322C GLY 4.1 9.4 - - - -
323C GLY 3.8 13.9 - - - -
324C THR 2.9 18.6 + - - -
325C THR* 3.8 6.1 - - - +
327C GLN* 1.3 78.9 - - - +
329C TRP* 1.3 67.9 + - + +
331C GLU* 3.8 0.2 - - - +
332C THR* 3.3 11.4 + - - -
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Residues in contact with TRP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 5.9 4.1 - - + -
328A CYS* 4.5 6.3 - - + -
329A TRP* 3.7 47.8 - + - +
332A THR* 4.2 9.0 - - + -
43C ILE* 4.0 5.8 - - + -
290C THR* 3.5 41.9 - - + +
292C THR* 3.4 25.6 - - - -
293C CYS* 3.3 34.9 - - + +
312C ASN* 4.0 17.3 - - + +
315C VAL* 3.9 19.8 - - + +
320C GLU* 5.8 2.6 + - - +
325C THR* 3.1 29.7 + - - +
328C CYS* 1.3 77.6 - - + +
330C SER* 1.3 66.6 + - - +
332C THR* 3.3 4.5 + - - +
333C LEU* 2.9 26.9 + - - +
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Residues in contact with SER 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PRO* 4.5 2.7 - - - +
43C ILE* 3.7 26.4 - - - +
69C VAL* 4.6 8.0 + - - +
72C ARG* 4.5 6.2 - - - +
73C MET* 4.3 18.6 - - - +
81C ILE* 5.0 2.5 - - - -
326C VAL 2.8 25.7 + - - -
327C GLN* 3.2 8.5 + - - -
329C TRP* 1.3 76.5 - - - +
331C GLU* 1.3 60.7 + - - +
333C LEU* 3.3 7.2 + - - +
334C ALA* 2.9 33.2 + - - +
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Residues in contact with GLU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 5.5 0.2 - - - -
292A THR* 3.5 22.2 - - + +
296A SER* 2.7 26.0 + - - -
297A ASP* 3.1 33.4 + - - +
72C ARG* 2.9 20.5 + - + +
73C MET* 5.4 0.2 - - - -
76C VAL* 3.7 7.0 - - - +
78C PHE* 4.2 13.9 - - + -
327C GLN 3.0 18.3 + - - +
328C CYS 3.8 4.0 - - - +
330C SER* 1.3 78.1 + - - +
332C THR* 1.3 60.6 + - - +
334C ALA* 3.4 1.9 + - - +
335C TYR* 3.0 44.1 + - + -
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Residues in contact with THR 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 2.7 33.9 + - + +
290A THR* 4.3 11.0 - - - +
292A THR* 2.9 16.8 + - - -
329A TRP* 4.2 7.6 - - + -
332A THR* 4.9 5.4 - - + -
290C THR* 3.5 29.2 - - + +
328C CYS 3.3 2.8 + - - -
329C TRP* 3.3 8.7 + - - -
331C GLU* 1.3 75.7 - - - +
333C LEU* 1.3 65.3 + - - +
335C TYR* 3.3 4.6 + - - +
336C ASP* 3.0 34.8 + - - +
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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
----------------------------------------------------------
41C PRO* 3.8 13.9 - - + -
42C GLU 3.6 28.3 - - - +
43C ILE* 4.2 9.2 - - + +
290C THR* 3.6 21.5 - - + +
310C TRP* 3.5 26.4 - - + +
311C SER 3.4 26.7 - - - +
312C ASN* 3.6 17.3 - - + +
329C TRP 2.9 21.9 + - - +
330C SER* 3.8 4.5 - - - +
332C THR* 1.3 75.5 - - - +
334C ALA* 1.3 57.2 + - - +
336C ASP* 3.2 4.4 + - - +
337C CYS* 2.9 32.2 + - - -
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Residues in contact with ALA 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PRO* 3.7 12.3 - - + +
73C MET* 3.6 13.7 - - + -
78C PHE* 3.5 44.5 - - + -
330C SER 2.9 18.1 + - - +
331C GLU 3.7 0.2 - - - +
333C LEU* 1.3 75.1 - - - +
335C TYR* 1.3 59.4 + - - +
337C CYS* 3.4 4.5 + - - +
338C ALA* 2.8 26.5 + - - +
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Residues in contact with TYR 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 3.7 31.2 - - + -
297A ASP* 2.6 22.3 + - - -
298A VAL* 3.1 5.9 - - - -
299A MET 3.1 7.3 + - - -
300A GLY* 3.0 32.0 + - - -
301A ASN* 2.8 33.4 - - - +
360A ASP* 3.4 18.8 - - - -
363A ARG* 3.8 12.9 - - - -
76C VAL* 3.5 9.7 - - + +
78C PHE* 3.8 10.1 - + - -
331C GLU* 3.0 52.6 + - + +
332C THR 3.8 1.6 - - - +
334C ALA* 1.3 75.6 - - - +
336C ASP* 1.3 65.5 + - - +
338C ALA* 2.9 11.7 + - + +
339C LEU 3.0 3.6 + - - -
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Residues in contact with ASP 336 (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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289A LYS* 2.6 44.7 + - - +
289C LYS* 4.0 13.0 - - - -
290C THR* 2.7 27.7 + - - -
304C MET* 4.5 8.1 - - - +
310C TRP* 2.7 28.1 + - + +
332C THR* 3.0 19.9 + - - +
333C LEU 3.2 4.0 + - - +
335C TYR* 1.3 76.9 - - - +
337C CYS* 1.3 62.1 + - - +
339C LEU* 3.4 5.9 + - - +
340C MET* 3.3 26.4 + - - +
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Residues in contact with CYS 337 (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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39C THR* 3.1 28.6 + - - +
40C ILE 3.4 11.9 - - - -
41C PRO* 3.4 33.2 - - + -
310C TRP* 3.7 18.4 - - - -
333C LEU 2.9 15.7 + - - +
334C ALA 3.6 8.1 - - - +
336C ASP* 1.3 77.5 - - - +
338C ALA* 1.3 57.5 + - - +
340C MET* 3.2 4.7 + - - -
341C ASN* 2.8 37.5 + - - +
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Residues in contact with ALA 338 (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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301A ASN* 4.2 0.2 - - - +
359A SER* 3.9 9.9 - - - +
363A ARG* 3.8 25.1 - - - +
12B VAL* 4.5 11.9 - - + +
78C PHE* 4.9 3.8 - - + -
334C ALA 2.8 14.7 + - - +
335C TYR* 2.9 12.3 + - + +
337C CYS* 1.3 75.0 - - - +
339C LEU* 1.3 59.2 + - - +
341C ASN* 3.3 8.7 + - - +
342C THR* 2.8 35.5 + - - -
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Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 4.5 12.8 - - - +
301A ASN* 3.8 15.1 + - + +
304A MET* 5.3 2.9 - - + -
339A LEU* 4.4 23.6 - - + -
352A LEU* 4.4 7.9 - - + -
355A LEU* 3.9 13.5 - - + +
356A MET* 3.7 43.5 - - + +
359A SER* 4.7 1.6 - - - -
289C LYS* 6.2 0.2 - - - +
335C TYR 3.0 9.7 + - - +
336C ASP* 3.5 11.4 - - - +
338C ALA* 1.3 75.1 - - - +
340C MET* 1.3 64.1 + - + +
342C THR* 3.2 6.8 + - - -
343C ALA* 3.0 22.0 + - - +
352C LEU* 4.2 16.6 - - + +
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Residues in contact with MET 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.2 47.2 - - + -
39C THR* 3.8 17.5 - - + +
304C MET* 4.0 26.9 - - - +
307C CYS* 3.6 33.7 - - - -
310C TRP* 4.5 6.1 - - + -
336C ASP 3.3 19.2 + - - +
337C CYS* 3.2 21.9 + - - +
339C LEU* 1.3 82.1 - - + +
341C ASN* 1.3 58.4 + - - +
343C ALA* 3.1 1.9 + - - +
344C LEU* 2.9 24.5 + - - +
352C LEU* 4.2 7.9 - - + -
356C MET* 4.6 4.9 - - - -
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Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS 5.6 1.4 + - - -
12B VAL* 4.3 21.4 + - + +
37C GLY 5.7 0.7 - - - +
38C TYR* 3.6 18.5 - - + +
39C THR* 2.8 49.2 + - - +
79C PRO* 5.6 6.1 - - - +
337C CYS* 2.8 23.3 + - - +
338C ALA* 3.9 7.3 - - - +
340C MET* 1.3 74.3 - - - +
342C THR* 1.4 58.2 + - - +
344C LEU* 3.2 9.0 + - + +
345C GLU* 2.9 37.3 + - + +
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Residues in contact with THR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.7 30.3 - - + +
358A LEU* 3.8 18.2 - - + -
359A SER* 3.3 17.8 - - - +
4B PHE* 3.6 31.9 - - + -
12B VAL* 4.0 4.4 - - - +
338C ALA 2.8 23.6 + - - -
339C LEU 3.2 5.8 + - - -
341C ASN* 1.4 75.0 - - - +
343C ALA* 1.3 64.2 + - - +
345C GLU* 3.4 0.9 + - - -
346C THR* 3.0 27.0 + - - +
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.9 17.8 - - + +
19C PHE* 4.0 0.7 - - + -
339C LEU 3.0 8.0 + - - +
340C MET 3.1 8.5 + - - +
342C THR* 1.3 76.9 - - - +
344C LEU* 1.3 61.2 + - - +
346C THR* 3.4 0.4 + - - -
347C LYS 3.0 2.9 + - - -
348C ASN 2.8 32.0 + - - +
349C ASP* 3.2 21.7 + - - +
352C LEU* 3.7 27.8 - - + -
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR* 4.4 0.2 - - + -
19C PHE* 3.5 35.4 - - + +
20C GLY* 4.4 2.0 - - - -
21C VAL* 3.9 17.7 - - + -
37C GLY* 3.8 29.2 - - - +
38C TYR* 4.3 2.7 - - - +
340C MET 2.9 18.2 + - - +
341C ASN* 3.2 22.0 + - - +
343C ALA* 1.3 74.4 - - - +
345C GLU* 1.3 68.0 + - - +
347C LYS* 3.0 22.5 + - - +
349C ASP* 3.8 27.0 - - + +
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Residues in contact with GLU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.0 9.4 - - + -
5B THR* 6.1 0.3 - - - +
8B SER* 2.7 48.2 + - - +
11B LYS* 3.3 39.2 + - - +
12B VAL* 3.7 20.6 - - + +
37C GLY 4.1 7.8 - - - +
38C TYR* 5.9 0.3 - - - +
341C ASN* 2.9 22.8 + - - +
342C THR 3.4 4.0 + - - +
344C LEU* 1.3 77.6 - - - +
346C THR* 1.3 59.3 + - - +
347C LYS* 3.4 12.1 + - - +
12O ALA* 6.0 2.1 - - - +
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Residues in contact with THR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.4 10.4 - - - +
358A LEU* 3.6 30.1 - - + -
2B LEU* 4.6 13.2 - - + +
3B ASP 4.1 11.9 - - - +
4B PHE* 4.2 6.3 - - + -
342C THR* 3.0 18.8 + - + +
343C ALA 3.5 2.1 + - - -
344C LEU 3.1 0.6 - - - -
345C GLU* 1.3 80.1 - - - +
347C LYS* 1.3 69.7 + - - +
348C ASN* 2.9 24.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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