Contacts of the helix formed by residues 309 - 331 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I HIS* 4.2 8.5 + - - +
309I THR* 4.0 16.4 + - - +
313I ARG* 3.9 23.8 - - + -
392I CYS* 3.9 19.7 - - - -
428I VAL* 5.2 0.4 - - + -
266L HIS* 4.4 4.9 - - - -
306L GLY 3.5 5.4 + - - -
307L MET 3.0 0.2 - - - -
308L LYS* 1.3 85.1 - - - +
310L LEU* 1.3 64.0 + - - +
311L HIS* 3.5 7.0 - - - -
312L LEU* 3.4 13.2 + - + -
313L ARG* 2.9 43.1 + - - +
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Residues in contact with LEU 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L ALA* 4.4 5.8 - - + -
126L LEU* 3.9 24.2 - - + -
241L THR* 4.7 6.3 - - + -
242L PRO* 4.7 3.6 - - + -
243L LEU* 3.9 19.3 - - + -
262L PHE* 3.8 17.9 - - + +
263L LEU* 3.9 25.1 - - + -
307L MET* 3.2 22.8 + - + +
308L LYS 3.6 0.2 - - - -
309L THR* 1.3 76.6 - - - +
311L HIS* 1.3 62.0 + - - +
313L ARG* 2.9 29.6 + - - +
314L VAL* 2.8 48.3 + - + +
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Residues in contact with HIS 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLN* 5.2 3.6 - - - -
428I VAL* 3.0 45.0 + - + +
429I GLU* 4.8 0.2 - - - -
430I ASP* 4.9 9.4 - - - +
57L ASP* 5.8 0.2 - - + -
58L GLY* 3.4 35.9 + - - +
61L ALA* 4.9 2.4 - - + +
62L ILE* 3.9 8.3 - - + -
243L LEU* 3.3 23.9 - - + +
308L LYS 3.6 14.3 - - - -
309L THR* 4.3 0.7 - - - -
310L LEU* 1.3 79.8 + - - +
312L LEU* 1.3 84.2 + - + +
314L VAL* 4.0 0.2 - - - +
315L GLN* 2.9 39.7 + - + +
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Residues in contact with LEU 312 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I LEU* 3.8 26.1 - - + +
313I ARG* 3.7 28.9 - - + +
316I GLN* 4.0 28.9 - - + +
428I VAL* 3.4 29.6 - - + -
309L THR* 3.7 13.2 - - + +
310L LEU 3.1 0.6 - - - -
311L HIS* 1.3 108.8 + - + +
313L ARG* 1.3 64.9 + - - +
315L GLN* 3.6 11.7 - - - +
316L GLN* 3.4 13.7 + - - +
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Residues in contact with ARG 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I THR* 3.9 26.0 - - + -
312I LEU* 3.7 12.6 - - + -
262L PHE* 2.7 31.9 + - - +
263L LEU 3.4 8.3 + - - -
264L GLY 4.5 0.4 - - - -
265L GLY* 3.2 17.4 - - - -
266L HIS* 4.4 4.5 - - - -
306L GLY 2.8 22.7 + - - -
309L THR* 2.9 28.8 + - - +
310L LEU* 2.9 29.3 + - - +
312L LEU* 1.3 73.8 - - - +
314L VAL* 1.3 67.3 + - - +
316L GLN* 3.0 6.6 + - - +
317L GLN* 2.9 35.3 + - - +
390L GLY 4.1 6.1 + - - -
391L GLY 6.3 0.2 - - - -
392L CYS* 4.2 15.0 - - - +
428L VAL* 4.3 6.5 - - + -
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Residues in contact with VAL 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241L THR* 4.1 15.5 - - + +
243L LEU* 3.8 17.7 - - + -
244L ASN* 4.0 17.7 - - - +
262L PHE* 5.3 9.2 - - + -
310L LEU* 2.8 48.8 + - + +
311L HIS 4.0 2.9 - - - +
313L ARG* 1.3 71.5 - - + +
315L GLN* 1.3 65.0 + - - +
317L GLN* 3.0 11.3 + - + +
318L ASN* 2.8 43.4 + - - +
359L GLY* 6.2 0.2 - - - -
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Residues in contact with GLN 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLN* 5.4 5.1 + - - +
430I ASP* 5.5 4.6 + - - -
311L HIS* 2.9 34.1 + - - +
312L LEU* 3.6 13.0 - - - +
314L VAL* 1.3 77.5 - - - +
316L GLN* 1.3 61.0 + - - +
318L ASN* 3.6 9.0 + - - +
319L SER* 3.4 21.7 + - - -
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Residues in contact with GLN 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I HIS* 5.0 3.0 + - - -
312I LEU* 4.1 20.5 - - + +
315I GLN* 5.5 5.2 + - - +
312L LEU 3.4 8.9 + - - +
313L ARG 3.0 8.9 + - - +
315L GLN* 1.3 77.0 - - - +
317L GLN* 1.3 67.4 + - - +
319L SER* 3.2 7.8 + - - -
320L THR* 3.1 32.7 + - - +
427L GLY 4.9 0.2 - - - +
428L VAL* 3.3 40.0 + - + +
429L GLU 3.3 14.5 + - - -
430L ASP* 4.5 7.3 + - - +
431L PHE* 4.6 3.0 - - - +
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Residues in contact with GLN 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262L PHE* 3.4 35.2 - - + -
313L ARG* 2.9 32.9 + - - +
314L VAL* 3.6 6.7 + - + +
316L GLN* 1.3 75.8 - - - +
318L ASN* 1.3 63.5 + - - +
320L THR* 4.1 3.3 - - - -
321L ALA* 2.9 28.6 + - - +
360L GLY* 3.7 16.4 - - - +
390L GLY* 3.5 15.2 + - - +
391L GLY 4.2 4.0 + - - -
426L PHE* 2.7 31.0 + - - +
427L GLY* 3.2 21.9 + - - +
428L VAL* 4.3 7.4 - - + -
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Residues in contact with ASN 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244L ASN* 2.8 33.8 + - - +
314L VAL* 2.8 25.9 + - - +
315L GLN* 3.6 8.3 - - - +
317L GLN* 1.3 78.0 - - - +
319L SER* 1.3 63.2 + - - +
322L LEU* 3.2 22.7 + - - +
339L TYR* 3.5 4.2 + - - -
356L THR 5.2 0.2 + - - -
357L GLY* 3.6 9.0 - - - -
358L PHE 4.1 5.4 - - - +
359L GLY* 3.0 33.9 + - - -
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Residues in contact with SER 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315L GLN 3.4 11.9 + - - -
316L GLN* 3.2 11.6 + - - -
318L ASN* 1.3 74.7 - - - +
320L THR* 1.3 70.4 + - - +
321L ALA 2.9 1.6 + - - -
322L LEU* 2.9 15.9 + - - +
323L ARG* 2.9 36.9 + - - +
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Residues in contact with THR 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316L GLN* 3.1 29.3 + - - +
317L GLN* 4.1 3.8 - - - -
319L SER* 1.3 76.6 - - - +
321L ALA* 1.3 57.9 + - - +
323L ARG* 4.0 4.0 + - - +
324L MET* 2.9 36.3 + - + +
426L PHE* 3.7 21.1 - - + -
427L GLY 5.4 2.3 + - - -
429L GLU 4.6 2.9 + - - -
431L PHE* 3.9 32.2 - - + +
434L LEU* 3.7 28.7 - - + +
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Residues in contact with ALA 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317L GLN 2.9 21.3 + - - +
319L SER 2.9 0.6 + - - -
320L THR* 1.3 77.8 - - - +
322L LEU* 1.3 57.0 + - - +
324L MET* 3.8 0.5 - - - +
325L ALA* 2.9 30.5 + - - +
339L TYR* 3.5 11.2 - - + +
359L GLY 3.1 22.0 - - - +
360L GLY* 3.6 13.2 - - - +
362L VAL* 3.5 12.8 - - + +
426L PHE* 3.9 12.1 - - + -
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Residues in contact with LEU 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318L ASN 3.2 15.1 + - - +
319L SER* 2.9 10.1 + - - +
321L ALA* 1.3 76.2 - - - +
323L ARG* 1.3 66.8 + - + +
325L ALA* 3.1 13.0 + - - +
326L GLU* 3.2 30.2 + - - +
339L TYR* 3.6 30.0 + - + +
341L GLY* 4.1 20.6 - - - +
342L LEU* 4.6 4.0 - - + +
358L PHE* 4.8 11.4 - - + -
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Residues in contact with ARG 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L SER* 2.9 36.0 + - - +
320L THR* 4.0 3.0 + - - +
322L LEU* 1.3 82.9 - - + +
324L MET* 1.3 62.2 + - - +
326L GLU* 3.4 11.6 + - - +
327L ILE* 3.2 28.4 + - + +
431L PHE* 3.0 57.8 - - + +
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Residues in contact with MET 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320L THR* 2.9 21.5 + - + +
321L ALA 3.9 1.1 - - - +
323L ARG* 1.3 74.3 - - - +
325L ALA* 1.3 55.3 + - - +
327L ILE* 3.3 13.6 + - + +
328L LEU* 2.8 56.8 + - + +
426L PHE* 3.5 31.4 - - + -
431L PHE* 3.5 28.0 - - + -
434L LEU* 5.5 0.2 - - + -
435L LYS* 3.7 26.0 - - + +
438L ILE* 3.4 31.4 - - + -
439L LEU* 5.7 2.2 - - + -
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Residues in contact with ALA 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321L ALA 2.9 18.6 + - - +
322L LEU 3.1 6.5 + - - +
324L MET* 1.3 76.4 - - - +
326L GLU* 1.3 57.6 + - - +
328L LEU* 3.2 5.0 + - - +
329L GLU* 2.8 29.1 + - - +
337L VAL* 3.9 9.1 - - + +
339L TYR* 3.9 30.7 - - + -
342L LEU* 4.0 13.2 - - + -
362L VAL* 4.2 13.0 - - + +
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Residues in contact with GLU 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322L LEU* 3.2 26.2 + - + +
323L ARG* 3.7 11.8 - - - +
324L MET 3.3 0.2 - - - -
325L ALA* 1.3 76.5 - - - +
327L ILE* 1.3 64.8 + - + +
329L GLU* 2.9 17.5 + - - +
330L ALA* 2.9 15.4 + - - +
342L LEU* 3.7 20.4 - - + +
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Residues in contact with ILE 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323L ARG* 3.2 15.4 + - + +
324L MET* 3.6 20.0 - - + +
326L GLU* 1.3 76.8 - - + +
328L LEU* 1.3 62.2 + - + +
330L ALA* 3.5 6.5 + - - +
331L HIS* 3.2 21.6 + - + +
431L PHE* 3.9 15.5 - - + -
435L LYS* 3.9 29.4 - - + +
439L LEU* 4.3 26.9 - - + -
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Residues in contact with LEU 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324L MET* 2.8 39.9 + - + +
325L ALA 3.5 4.5 - - - +
327L ILE* 1.3 73.2 - - + +
329L GLU* 1.3 66.3 + - - +
331L HIS* 3.0 11.5 + - + +
334L VAL* 3.1 40.8 - - + +
337L VAL* 3.8 11.4 - - + -
362L VAL* 4.5 12.3 - - + -
364L PHE* 3.8 37.9 - - + -
426L PHE* 4.7 7.2 - - + -
438L ILE* 4.0 24.2 - - + -
439L LEU* 6.2 0.7 - - + -
442L LEU* 4.1 10.1 - - + -
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Residues in contact with GLU 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325L ALA 2.8 14.0 + - - +
326L GLU* 2.9 11.8 + - - +
328L LEU* 1.3 78.7 - - - +
330L ALA* 1.3 62.2 + - + +
331L HIS 3.2 7.3 + - - +
334L VAL* 4.5 5.6 - - - +
336L HIS* 5.8 1.0 - - - -
337L VAL* 3.6 21.9 + - + +
342L LEU* 3.8 22.0 - - + +
343L GLN 5.3 1.2 + - - -
344L SER* 2.7 33.3 + - - -
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Residues in contact with ALA 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326L GLU 2.9 13.9 + - - +
327L ILE* 3.9 6.5 - - - +
329L GLU* 1.3 75.7 - - + +
331L HIS* 1.3 63.5 + - - +
332L PRO* 3.6 4.9 - - - +
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Residues in contact with HIS 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327L ILE* 3.2 12.2 + - + +
328L LEU* 3.0 16.3 + - + +
329L GLU 3.6 3.8 - - - +
330L ALA* 1.3 79.3 - - - +
332L PRO* 1.3 81.9 - - + +
333L LYS* 3.0 47.7 + - + +
334L VAL* 3.3 25.8 + - + +
439L LEU* 4.0 19.3 + - + +
442L LEU* 3.5 38.2 - - + +
443L ASP* 5.3 5.1 + - - -
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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