Contacts of the helix formed by residues 309 - 331 (chain C) in PDB entry 1I43
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 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B HIS* 4.0 8.7 + - - +
309B THR* 4.0 19.2 + - - +
313B ARG* 3.9 24.2 - - + -
392B CYS* 3.7 22.2 - - - -
266C HIS* 4.4 4.7 - - - -
306C GLY 3.2 11.8 + - - -
308C LYS* 1.3 83.1 - - - +
310C LEU* 1.3 63.5 + - - +
311C HIS* 3.5 6.7 - - - -
312C LEU* 3.3 13.1 + - + -
313C ARG* 2.9 36.6 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 4.4 5.8 - - + -
126C LEU* 4.0 27.6 - - + -
241C THR* 4.9 4.7 - - + -
242C PRO* 4.8 2.7 - - + -
243C LEU* 3.6 20.0 - - + -
262C PHE* 3.7 19.5 - - + +
263C LEU* 4.0 21.5 - - + +
307C MET* 3.0 24.1 + - + +
308C LYS 3.5 0.4 - - - -
309C THR* 1.3 74.6 - - - +
311C HIS* 1.3 68.0 + - - +
313C ARG* 2.8 29.5 + - - +
314C VAL* 2.8 39.8 + - + +
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Residues in contact with HIS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLN* 5.2 2.7 - - - -
428B VAL* 3.1 44.8 + - + +
430B ASP* 4.8 10.3 - - - +
57C ASP* 6.0 0.2 - - + -
58C GLY* 3.4 37.6 + - - +
61C ALA* 5.1 1.4 - - - +
62C ILE* 3.9 7.8 - - + +
243C LEU* 3.5 20.8 - - + +
307C MET 5.0 0.6 + - - -
308C LYS 3.5 15.2 - - - -
309C THR* 4.2 0.2 - - - -
310C LEU* 1.3 80.5 + - - +
312C LEU* 1.3 78.2 + - + +
314C VAL* 4.0 0.3 - - - +
315C GLN* 2.9 45.3 + - - +
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.5 40.8 - - + +
313B ARG* 4.0 13.5 - - + +
316B GLN* 3.9 28.3 - - + +
428B VAL* 3.3 32.1 - - + -
309C THR* 3.5 12.6 - - + +
310C LEU 3.1 0.6 - - - -
311C HIS* 1.3 102.2 - - + +
313C ARG* 1.3 67.5 + - - +
315C GLN* 3.6 13.0 - - - +
316C GLN* 3.3 15.1 + - - +
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Residues in contact with ARG 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.9 25.4 - - + -
312B LEU* 3.7 12.1 - - + -
262C PHE* 2.8 25.9 + - - +
263C LEU 3.6 6.9 + - - -
264C GLY 4.2 0.7 - - - -
265C GLY* 3.3 17.4 - - - -
266C HIS* 4.4 4.1 - - - -
306C GLY 2.8 21.9 + - - -
309C THR* 2.9 28.6 + - - +
310C LEU* 2.8 38.6 + - - +
312C LEU* 1.3 74.5 - - - +
314C VAL* 1.3 68.7 + - - +
316C GLN* 3.0 5.4 + - - +
317C GLN* 2.9 37.4 + - - +
390C GLY 4.3 5.4 + - - -
392C CYS* 4.0 15.9 - - - -
428C VAL* 4.2 7.9 - - + -
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ALA 5.2 0.2 - - - +
241C THR* 4.3 15.3 - - + +
243C LEU* 3.5 28.0 - - + -
244C ASN* 4.0 17.7 - - - +
262C PHE* 5.5 6.7 - - + -
310C LEU* 2.8 39.8 + - + +
311C HIS 4.0 1.1 - - - +
313C ARG* 1.3 72.7 - - + +
315C GLN* 1.3 63.2 + - - +
317C GLN* 3.8 10.0 - - - +
318C ASN* 2.8 46.1 + - - +
359C GLY* 6.0 0.4 - - - -
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLN* 5.2 5.2 + - - +
430B ASP* 5.4 4.9 + - - -
311C HIS* 2.9 34.8 + - - +
312C LEU* 3.6 17.7 - - - +
313C ARG 3.2 0.2 + - - -
314C VAL* 1.3 77.7 - - - +
316C GLN* 1.3 63.5 + - - +
318C ASN* 3.4 9.1 + - - +
319C SER* 3.4 22.6 + - - -
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Residues in contact with GLN 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B HIS* 5.2 2.6 + - - -
312B LEU* 3.8 23.3 - - + +
315B GLN* 5.0 7.7 + - - +
312C LEU 3.3 9.5 + - - +
313C ARG 3.0 7.9 + - - +
315C GLN* 1.3 77.1 - - - +
317C GLN* 1.3 66.0 + - - +
319C SER* 3.2 7.7 + - - -
320C THR* 3.0 35.4 + - - +
427C GLY 5.0 0.2 - - - +
428C VAL* 3.5 26.0 + - + +
429C GLU 3.4 23.8 + - - -
430C ASP* 4.5 7.9 + - - +
431C PHE* 4.5 4.6 - - - +
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Residues in contact with GLN 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C PHE* 3.4 36.4 - - + -
313C ARG* 2.9 31.7 + - - +
314C VAL* 3.8 5.5 + - - +
316C GLN* 1.3 73.9 - - - +
318C ASN* 1.3 65.0 + - - +
320C THR* 3.9 4.4 - - - -
321C ALA* 2.9 28.6 + - - +
360C GLY* 3.8 15.9 - - - +
390C GLY* 3.7 10.3 + - - +
391C GLY 4.0 10.5 + - - -
392C CYS* 6.1 0.2 - - - -
426C PHE* 2.7 27.8 + - - +
427C GLY 3.5 22.3 + - - +
428C VAL* 4.3 7.9 - - + -
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Residues in contact with ASN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ASN* 2.9 31.6 + - - +
314C VAL* 2.8 28.5 + - - +
315C GLN* 3.4 8.9 - - - +
317C GLN* 1.3 77.9 - - - +
319C SER* 1.3 62.0 + - - +
322C LEU* 3.3 23.4 + - - +
339C TYR* 3.5 6.1 + - - -
357C GLY* 3.6 9.0 - - - -
358C PHE 4.1 5.8 + - - +
359C GLY* 3.0 34.7 + - - -
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLN 3.4 10.4 + - - -
316C GLN* 3.2 10.1 + - - -
317C GLN 3.2 0.8 - - - -
318C ASN* 1.3 74.3 - - - +
320C THR* 1.3 68.6 + - - +
321C ALA 3.1 1.6 - - - -
322C LEU* 2.9 8.1 + - - +
323C ARG* 2.9 49.5 + - - +
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Residues in contact with THR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C GLN* 3.0 31.5 + - - +
317C GLN* 3.9 4.7 - - - -
319C SER* 1.3 78.0 - - - +
321C ALA* 1.3 57.4 + - - +
323C ARG* 4.2 2.5 + - - +
324C MET* 3.0 38.2 + - + +
426C PHE* 3.7 22.0 - - + -
427C GLY 5.1 2.2 + - - -
429C GLU 4.6 2.9 + - - -
431C PHE* 4.0 30.1 - - + +
434C LEU* 3.7 28.9 - - + -
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Residues in contact with ALA 321 (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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317C GLN 2.9 18.0 + - - +
318C ASN 4.0 0.2 - - - +
320C THR* 1.3 75.8 - - - +
322C LEU* 1.3 55.2 + - - +
324C MET* 3.7 0.7 - - - +
325C ALA* 2.8 36.6 + - - +
339C TYR* 3.6 11.7 - - + +
359C GLY 3.4 21.3 - - - +
360C GLY* 3.5 14.1 - - - +
362C VAL* 3.7 12.5 - - + +
426C PHE* 3.8 12.5 - - + -
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ASN 3.3 15.7 + - - +
319C SER* 2.9 7.1 + - - +
321C ALA* 1.3 77.7 - - - +
323C ARG* 1.3 68.2 + - + +
325C ALA* 3.0 13.8 + - - +
326C GLU* 3.1 30.7 + - - +
339C TYR* 3.7 28.2 + - + +
341C GLY* 4.0 24.0 - - - +
342C LEU* 4.8 3.8 - - + -
358C PHE* 4.9 11.0 - - + -
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Residues in contact with ARG 323 (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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319C SER* 2.9 37.7 + - - +
320C THR* 5.4 1.6 + - - +
322C LEU* 1.3 79.7 - - + +
324C MET* 1.3 62.6 + - - +
326C GLU* 3.3 13.0 + - - +
327C ILE* 3.1 28.4 + - + +
431C PHE* 3.0 58.9 - - + +
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Residues in contact with MET 324 (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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320C THR* 3.0 26.0 + - + +
321C ALA 3.8 0.9 - - - +
323C ARG* 1.3 74.4 - - - +
325C ALA* 1.3 60.2 + - - +
327C ILE* 4.3 14.4 - - + -
328C LEU* 2.9 50.0 + - + +
426C PHE* 3.5 29.4 - - + -
431C PHE* 3.4 28.7 - - + -
434C LEU* 5.5 0.2 - - + -
435C LYS* 3.6 26.7 - - + +
438C ILE* 3.5 30.5 - - + -
439C LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 325 (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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321C ALA 2.8 14.5 + - - +
322C LEU 3.2 9.4 - - - +
324C MET* 1.3 77.1 - - - +
326C GLU* 1.3 53.6 + - - +
328C LEU* 3.1 10.7 + - - +
329C GLU* 2.7 35.2 + - - +
337C VAL* 4.0 11.0 - - + +
339C TYR* 4.1 23.6 - - + -
342C LEU* 4.0 18.8 - - + -
362C VAL* 4.4 6.5 - - + +
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Residues in contact with GLU 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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322C LEU* 3.1 23.5 + - + +
323C ARG* 3.7 12.6 - - - +
325C ALA* 1.3 78.4 - - - +
327C ILE* 1.3 64.2 - - + +
329C GLU* 3.0 8.0 + - - +
330C ALA* 3.0 24.7 + - - +
342C LEU* 3.6 22.7 - - + +
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Residues in contact with ILE 327 (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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323C ARG* 3.1 11.3 + - + +
324C MET* 3.7 20.4 - - + +
326C GLU* 1.3 79.8 - - + +
328C LEU* 1.3 65.6 + - + +
330C ALA* 3.5 6.7 + - - +
331C HIS* 3.2 21.8 + - + +
431C PHE* 3.9 17.5 - - + -
435C LYS* 3.7 31.4 - - + +
439C LEU* 4.5 23.1 - - + -
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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
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324C MET* 2.9 36.3 + - + +
325C ALA* 3.3 4.3 - - - +
327C ILE* 1.3 79.2 - - + +
329C GLU* 1.3 63.2 + - - +
331C HIS* 2.9 20.7 + - + +
334C VAL* 3.2 21.5 - - + +
337C VAL* 3.8 11.7 - - + -
362C VAL* 4.3 14.1 - - + -
364C PHE* 3.5 39.5 - - + -
426C PHE* 4.8 6.5 - - + -
438C ILE* 3.9 16.4 - - + -
439C LEU* 6.4 0.4 - - + -
442C LEU* 3.8 27.6 - - + -
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ALA 2.7 16.7 + - - +
326C GLU* 3.0 10.6 + - - +
328C LEU* 1.3 72.5 - - - +
330C ALA* 1.3 63.1 + - + +
331C HIS 3.4 5.7 + - - +
334C VAL* 4.4 6.1 - - - +
336C HIS* 5.7 1.0 + - - -
337C VAL* 3.6 25.2 + - + +
342C LEU* 3.6 23.3 - - + +
343C GLN 5.4 0.7 + - - -
344C SER* 2.8 34.0 + - - -
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Residues in contact with ALA 330 (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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326C GLU 3.0 14.6 + - - +
327C ILE* 3.8 7.0 - - - +
329C GLU* 1.3 75.8 - - + +
331C HIS* 1.3 64.2 + - - +
332C PRO* 3.5 5.4 - - - +
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Residues in contact with HIS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ILE* 3.2 12.6 + - + +
328C LEU* 2.9 18.2 + - + +
329C GLU 3.8 2.4 - - - +
330C ALA* 1.3 79.3 - - - +
332C PRO* 1.3 78.9 - - + +
333C LYS* 3.0 51.2 + - + +
334C VAL* 3.3 25.9 + - + +
439C LEU* 3.9 22.8 + - + +
442C LEU* 3.8 35.1 - - + +
443C ASP* 5.1 7.3 + - - -
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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
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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