Contacts of the helix formed by residues 343 - 367 (chain D) in PDB entry 2YPT
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 GLY 343 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D HIS 3.4 4.0 + - - -
340D TRP 3.3 10.4 + - - -
341D LYS 3.2 5.6 + - - -
342D LEU* 1.3 78.6 - - - +
344D HIS* 1.3 57.5 + - - +
345D THR* 3.3 3.4 - - - -
346D VAL* 3.5 11.8 + - - +
347D LYS* 3.0 30.0 + - - +
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Residues in contact with HIS 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D HIS* 2.8 43.4 + - + +
342D LEU* 3.6 29.3 - - + +
343D GLY* 1.3 75.0 - - - +
345D THR* 1.3 63.8 + - - +
348D ASN* 3.1 25.1 + - - +
414D PHE* 3.1 66.1 + + + -
417D GLN* 2.8 37.6 + - + -
418D ALA 4.2 1.3 - - - -
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D HIS* 3.4 21.7 + - - +
340D TRP* 4.2 8.0 + - - +
343D GLY* 5.1 0.9 - - - -
344D HIS* 1.3 76.4 - - - +
346D VAL* 1.4 61.1 + - - +
348D ASN* 3.4 8.0 + - - +
349D ILE* 3.3 36.2 + - + +
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Residues in contact with VAL 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLY* 3.5 13.4 + - - +
345D THR* 1.4 74.9 - - - +
347D LYS* 1.4 63.8 + - - +
349D ILE* 3.3 15.3 + - + +
350D ILE* 3.2 35.8 + - + +
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Residues in contact with LYS 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLY 3.0 18.6 + - - +
344D HIS 3.9 4.7 - - - +
346D VAL* 1.4 74.8 - - - +
348D ASN* 1.4 56.4 + - - +
350D ILE* 3.3 13.2 + - - +
351D ILE* 3.1 38.1 + - + +
414D PHE* 4.0 20.2 - - + -
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Residues in contact with ASN 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D HIS 3.1 19.0 + - - +
345D THR* 3.6 7.4 - - - +
346D VAL 3.3 0.2 - - - -
347D LYS* 1.4 71.9 - - - +
349D ILE* 1.4 60.2 + - + +
351D ILE* 3.6 11.7 + - - +
352D SER* 3.1 26.9 + - - -
407D LEU* 5.8 4.4 - - + +
410D LEU* 5.8 1.6 - - + -
414D PHE* 4.8 6.2 - - + -
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Residues in contact with ILE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D VAL* 6.5 1.1 - - + -
345D THR* 3.3 31.9 - - + +
346D VAL* 3.3 11.8 + - - +
348D ASN* 1.4 73.2 - - + +
350D ILE* 1.4 60.5 + - + +
352D SER* 2.7 25.3 + - - +
353D GLN* 3.0 31.1 + - + +
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D VAL* 3.2 27.2 + - + +
347D LYS* 3.3 12.5 + - - +
349D ILE* 1.4 76.0 - - + +
351D ILE* 1.4 60.5 + - + +
353D GLN* 4.1 3.9 - - - +
354D MET* 3.2 32.4 + - + +
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Residues in contact with ILE 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LYS* 3.1 25.8 + - + +
348D ASN* 3.8 8.3 - - - +
350D ILE* 1.4 78.2 - - + +
352D SER* 1.4 57.9 + - - +
354D MET* 3.2 20.6 + - + +
355D ASN* 2.9 28.9 + - + +
403D LEU* 5.3 9.2 - - + -
407D LEU* 3.8 30.1 - - + -
410D LEU* 3.8 33.2 - - + -
414D PHE* 5.4 0.4 - - + -
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D ASN 3.1 14.2 + - - -
349D ILE* 2.7 26.7 + - - +
351D ILE* 1.4 78.4 - - - +
353D GLN* 1.4 69.7 + - - +
355D ASN* 3.7 12.0 + - - +
356D SER* 3.3 25.3 + - - -
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Residues in contact with GLN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TRP* 2.8 32.5 + - + +
204D THR* 4.6 1.4 + - - -
205D LEU* 3.4 50.3 + - + +
208D SER* 3.7 28.5 + - - -
349D ILE* 3.0 30.4 + - + +
350D ILE* 4.4 4.0 - - - +
352D SER* 1.4 88.4 + - - +
354D MET* 1.3 62.1 + - - +
355D ASN 3.4 0.4 - - - -
356D SER* 3.1 16.6 + - - -
357D PHE* 3.3 5.4 + - - +
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Residues in contact with MET 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ILE* 3.2 25.5 + - + +
351D ILE* 3.2 22.2 + - + +
353D GLN* 1.3 74.0 - - - +
355D ASN* 1.4 63.4 + - - +
357D PHE* 3.6 6.4 + - - +
358D LEU* 3.2 23.0 + - - +
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Residues in contact with ASN 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D ILE* 2.9 17.6 + - + +
352D SER* 3.7 12.7 + - - +
353D GLN 3.4 0.2 - - - -
354D MET* 1.4 74.5 - - - +
356D SER* 1.4 63.2 + - - +
358D LEU* 3.3 4.5 + - - +
359D CYS* 2.9 33.4 + - - +
399D TYR* 2.8 41.7 + - - +
400D ASN* 5.0 1.0 - - - +
403D LEU* 3.4 25.0 - - + +
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Residues in contact with SER 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D TRP* 3.1 25.8 + - - -
204D THR* 4.8 4.7 + - - -
352D SER 3.3 13.0 + - - -
353D GLN* 3.1 15.8 + - - -
355D ASN* 1.4 80.3 - - - +
357D PHE* 1.4 58.7 + - - +
359D CYS* 3.7 6.9 - - - +
360D PHE* 2.9 44.0 + - - -
392D PHE* 5.9 0.7 - - - -
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Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 4.3 19.2 - + - -
198D ILE* 4.2 21.8 - - + -
201D TRP* 3.4 57.0 - + + +
353D GLN 3.3 8.3 + - - +
354D MET* 3.9 7.0 - - - +
355D ASN 3.3 0.4 - - - -
356D SER* 1.4 77.9 + - - +
358D LEU* 1.4 62.7 + - - +
360D PHE* 3.5 1.2 + - - +
361D PHE* 3.0 35.6 + + + +
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D MET 3.2 12.4 + - - +
355D ASN* 3.3 6.9 + - - +
357D PHE* 1.4 81.8 - - - +
359D CYS* 1.4 59.8 + - - +
361D PHE* 3.7 9.5 - - + +
362D LEU* 3.2 48.3 + - + +
399D TYR* 3.6 38.6 - - + +
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Residues in contact with CYS 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D ASN* 2.9 38.9 + - - +
356D SER* 3.7 7.9 - - - +
357D PHE 3.3 0.2 - - - -
358D LEU* 1.4 73.5 - - - +
360D PHE* 1.4 59.3 + - - +
362D LEU* 3.4 1.8 + - - -
363D PHE* 2.9 26.5 + - - +
392D PHE* 3.6 23.3 - - + -
396D PHE* 3.3 33.6 - - + -
399D TYR* 3.7 18.4 - - - -
400D ASN* 4.6 4.3 - - - -
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Residues in contact with PHE 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 4.0 19.5 - - + -
189D ILE* 4.7 4.9 - - + -
196D PHE* 6.0 0.2 - + - -
197D PHE* 3.3 35.0 - - + +
200D ALA* 3.8 33.4 - - + -
201D TRP* 4.0 14.8 - - + -
204D THR* 3.9 24.0 - - + -
356D SER* 2.9 36.6 + - - +
357D PHE 4.1 2.7 - - - +
359D CYS* 1.4 69.4 - - - +
361D PHE* 1.4 59.2 + - - +
363D PHE* 3.4 14.5 + + - +
364D ALA 3.0 23.0 + - - -
388D LEU* 4.5 12.8 - - + -
392D PHE* 4.1 23.3 - + - -
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Residues in contact with PHE 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 3.6 36.7 - + + -
357D PHE* 3.0 26.9 + + + +
358D LEU* 3.7 10.3 - - + +
360D PHE* 1.4 76.1 - - - +
362D LEU* 1.4 78.5 + - + +
364D ALA* 3.3 5.7 + - - +
365D VAL* 3.2 45.3 + - + +
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Residues in contact with LEU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D LEU* 3.2 38.5 + - + +
359D CYS* 5.0 1.1 - - - -
361D PHE* 1.4 90.2 - - + +
363D PHE* 1.4 59.4 + - - +
365D VAL* 3.4 12.3 + - + +
366D LEU* 3.0 38.5 + - + +
396D PHE* 3.6 31.2 - - + -
399D TYR* 6.2 4.0 - - + -
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Residues in contact with PHE 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ILE* 4.3 12.3 - - + -
196D PHE* 4.0 19.1 - + - -
359D CYS 2.9 18.2 + - - +
360D PHE* 3.5 15.9 - + - +
361D PHE 3.2 0.2 - - - -
362D LEU* 1.4 74.1 - - - +
364D ALA* 1.3 56.9 + - - +
366D LEU 3.1 0.9 + - - -
367D ILE* 2.7 67.8 + - + +
384D THR 4.5 2.5 - - - -
387D GLY 3.5 26.7 - - - -
388D LEU* 3.6 28.7 - - + -
391D ILE* 3.7 28.9 - - + -
392D PHE* 3.5 27.6 - + + -
396D PHE* 4.0 0.2 - - - -
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Residues in contact with ALA 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ASP 5.7 0.9 - - - +
196D PHE* 3.7 29.6 - - + -
197D PHE* 3.7 27.6 - - + -
360D PHE 3.0 13.7 + - - +
361D PHE 3.3 9.8 + - - +
363D PHE* 1.3 76.0 - - - +
365D VAL* 1.4 60.8 + - + +
367D ILE* 3.4 12.9 - - - +
368D GLY 4.7 1.0 + - - -
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Residues in contact with VAL 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D PHE* 3.2 40.8 + - + +
362D LEU* 3.6 16.2 - - + +
363D PHE 3.2 0.6 - - - -
364D ALA* 1.4 78.7 - - + +
366D LEU* 1.4 63.7 + - + +
367D ILE 3.6 0.4 + - - -
368D GLY* 4.4 4.7 + - - -
369D ARG* 5.0 2.8 + - - +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D LEU* 3.0 27.0 + - + +
365D VAL* 1.4 84.0 - - + +
367D ILE* 1.4 63.4 + - - +
368D GLY 3.2 2.5 - - - -
369D ARG* 3.3 32.2 + - + +
372D LEU* 5.4 2.9 - - - +
373D PHE* 5.3 0.5 - - - -
391D ILE* 3.8 34.2 - - + +
395D ILE* 5.2 9.4 - - + -
396D PHE* 4.4 10.8 - - + -
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Residues in contact with ILE 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ILE* 4.4 14.8 - - + -
196D PHE* 3.8 20.2 - - + -
363D PHE* 2.7 50.6 + - + +
364D ALA 3.4 18.4 - - - +
366D LEU* 1.4 72.3 - - - +
368D GLY* 1.3 62.8 + - - +
369D ARG 3.4 0.5 + - - -
373D PHE* 3.6 30.6 - - + -
382D GLN* 5.6 1.2 - - - +
384D THR* 4.9 13.0 - - + +
387D GLY* 5.4 1.3 - - - -
391D ILE* 3.9 10.1 - - + -
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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