Contacts of the helix formed by residues 343 - 367 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B HIS 3.4 3.7 + - - -
340B TRP 3.3 10.2 + - - -
341B LYS 3.2 6.0 + - - -
342B LEU* 1.3 78.8 - - - +
344B HIS* 1.3 58.6 + - - +
345B THR* 3.3 3.1 - - - -
346B VAL* 3.5 11.8 + - - +
347B LYS* 3.0 30.2 + - - +
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Residues in contact with HIS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B HIS* 2.8 43.0 + - + +
342B LEU* 3.6 29.2 - - + +
343B GLY* 1.3 74.2 - - - +
345B THR* 1.4 63.8 + - - +
347B LYS 3.6 0.2 + - - -
348B ASN* 3.1 24.8 + - - +
414B PHE* 3.1 66.5 + + + -
417B GLN* 2.8 37.8 + - + -
418B ALA 4.2 1.3 - - - -
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.3 35.7 - - + -
339B HIS* 3.4 8.7 + - - +
340B TRP* 4.2 4.2 + - - -
343B GLY* 5.1 0.7 - - - -
344B HIS* 1.4 76.2 - - - +
346B VAL* 1.4 60.0 + - - +
348B ASN* 3.4 8.5 + - - +
349B ILE* 3.4 19.6 + - - +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY* 3.5 13.2 + - - +
345B THR* 1.4 75.5 - - - +
347B LYS* 1.4 65.0 + - - +
349B ILE* 3.3 8.5 + - - +
350B ILE* 3.2 22.0 + - - +
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY 3.0 17.9 + - - +
344B HIS 3.9 4.5 - - - +
346B VAL* 1.4 74.8 - - - +
348B ASN* 1.4 56.5 + - - +
350B ILE* 3.3 8.0 + - - +
351B ILE* 3.1 38.2 + - + +
414B PHE* 4.0 21.1 - - + -
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B HIS 3.1 17.3 + - - +
345B THR* 3.6 7.6 - - - +
346B VAL 3.3 0.2 - - - -
347B LYS* 1.4 71.9 - - - +
349B ILE* 1.4 60.7 + - - +
351B ILE* 3.6 12.3 + - - +
352B SER* 3.2 27.0 + - - -
407B LEU* 5.9 3.4 - - + +
410B LEU* 5.9 1.3 - - + -
414B PHE* 4.9 6.0 - - + -
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR 3.4 8.1 + - - +
346B VAL* 3.3 12.2 + - - +
348B ASN* 1.4 74.8 - - - +
350B ILE* 1.4 59.8 + - - +
352B SER* 2.7 24.1 + - - +
353B GLN* 3.0 24.0 + - + +
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B VAL 3.2 13.1 + - - +
347B LYS* 3.6 12.8 - - - +
349B ILE* 1.4 75.7 - - - +
351B ILE* 1.4 59.4 + - + +
353B GLN* 3.8 3.3 + - - +
354B MET* 3.2 27.5 + - - +
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 3.1 26.5 + - + +
348B ASN* 3.8 7.9 - - - +
349B ILE 3.3 0.2 - - - -
350B ILE* 1.4 75.1 - - + +
352B SER* 1.4 57.8 + - - +
354B MET* 3.2 20.9 + - + +
355B ASN* 2.9 29.4 + - + +
403B LEU* 5.3 9.6 - - + -
407B LEU* 3.8 29.8 - - + -
410B LEU* 3.8 33.4 - - + -
414B PHE* 5.4 0.4 - - + -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN 3.2 13.3 + - - -
349B ILE* 2.7 25.6 + - - +
351B ILE* 1.4 78.5 - - - +
353B GLN* 1.4 69.1 + - - +
355B ASN* 3.7 12.2 + - - +
356B SER* 3.3 25.3 + - - -
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 2.8 32.5 + - + -
204B THR* 4.6 1.4 + - - -
205B LEU* 3.4 49.2 + - + +
208B SER* 3.7 28.3 + - - -
349B ILE* 3.0 22.3 + - + +
350B ILE* 4.4 3.8 - - - +
352B SER* 1.4 86.7 + - - +
354B MET* 1.3 63.6 + - - +
355B ASN 3.4 0.2 - - - -
356B SER* 3.1 16.5 + - - -
357B PHE* 3.3 4.9 + - - +
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Residues in contact with MET 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TRP* 5.9 0.2 - - - -
350B ILE 3.2 19.3 + - - +
351B ILE* 3.2 22.8 + - + +
353B GLN* 1.3 74.0 - - - +
355B ASN* 1.4 63.5 + - - +
357B PHE* 3.6 6.4 + - - +
358B LEU* 3.2 22.7 + - - +
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Residues in contact with ASN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ILE* 2.9 17.8 + - + +
352B SER* 3.7 12.3 + - - +
353B GLN 3.4 0.2 - - - -
354B MET* 1.4 75.2 - - - +
356B SER* 1.4 62.3 + - - +
358B LEU* 3.4 4.9 + - - +
359B CYS* 2.9 33.4 + - - +
399B TYR* 2.8 42.3 + - - +
400B ASN* 5.1 1.2 - - - +
403B LEU* 3.4 25.4 - - + +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 3.1 22.4 + - - -
204B THR* 4.8 4.8 + - - -
352B SER 3.3 13.2 + - - -
353B GLN* 3.1 18.9 + - - -
355B ASN* 1.4 80.9 - - - +
357B PHE* 1.4 58.7 + - - +
359B CYS* 3.7 6.9 - - - +
360B PHE* 2.9 44.1 + - - -
392B PHE* 5.9 1.1 - - - -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 4.1 28.4 - + - -
198B ILE* 4.4 12.6 - - + -
201B TRP* 3.5 56.8 - + + +
353B GLN 3.3 8.3 + - - +
354B MET* 3.9 7.4 - - - +
355B ASN 3.3 0.4 - - - -
356B SER* 1.4 77.4 + - - +
358B LEU* 1.4 63.9 + - - +
360B PHE* 3.5 1.4 + - - +
361B PHE* 3.0 34.5 + + + +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B MET 3.2 12.4 + - - +
355B ASN* 3.4 7.2 + - - +
357B PHE* 1.4 80.6 - - - +
359B CYS* 1.4 55.8 + - - +
361B PHE* 3.6 9.5 + - + +
362B LEU* 3.2 51.0 + - + +
399B TYR* 3.6 38.6 - - + +
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Residues in contact with CYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASN* 2.9 38.5 + - - +
356B SER* 3.7 7.4 - - - +
358B LEU* 1.4 74.8 - - - +
360B PHE* 1.4 59.3 + - - +
362B LEU* 3.4 2.0 + - - -
363B PHE* 2.9 26.9 + - - +
392B PHE* 3.6 23.1 - - + -
396B PHE* 3.3 33.6 - - + -
399B TYR* 3.7 17.9 - - - -
400B ASN* 4.7 4.3 - - - -
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Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.0 17.5 - - + -
196B PHE* 5.9 0.7 - + - -
197B PHE* 3.3 33.9 - - + +
200B ALA* 3.8 32.5 - - + -
201B TRP* 4.0 13.2 - - + -
204B THR* 4.0 24.0 - - + -
356B SER* 2.9 37.6 + - - +
357B PHE 4.1 2.7 - - - +
359B CYS* 1.4 68.3 - - - +
361B PHE* 1.4 59.2 + - - +
363B PHE* 3.4 17.0 + + - +
364B ALA 3.0 23.0 + - - -
388B LEU* 4.5 15.5 - - + -
392B PHE* 4.1 24.0 - + - -
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Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PHE* 3.6 40.0 - + + -
357B PHE* 3.0 26.0 + + + +
358B LEU* 3.7 10.3 - - + +
360B PHE* 1.4 74.9 - - - +
362B LEU* 1.4 78.8 + - + +
364B ALA* 3.3 6.1 + - - +
365B VAL* 3.2 44.9 + - + +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B LEU* 3.2 38.5 + - + +
359B CYS* 5.0 1.1 - - - -
361B PHE* 1.4 90.0 - - + +
363B PHE* 1.4 59.7 + - - +
365B VAL* 3.4 11.2 + - + +
366B LEU* 3.0 38.7 + - + +
396B PHE* 3.6 31.4 - - + -
399B TYR* 6.2 3.6 - - + -
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ILE* 5.3 6.5 - - + -
196B PHE* 4.0 19.3 - + - -
359B CYS 2.9 17.9 + - - +
360B PHE* 3.5 18.4 - + - +
361B PHE 3.2 0.2 - - - -
362B LEU* 1.4 74.1 - - - +
364B ALA* 1.4 56.9 + - - +
366B LEU 3.1 0.5 + - - -
367B ILE* 2.7 68.0 + - + +
384B THR* 4.6 4.7 - - + -
387B GLY 3.5 26.5 - - - -
388B LEU* 3.6 28.5 - - + -
391B ILE* 3.7 29.4 - - + -
392B PHE* 3.5 28.0 - + + -
396B PHE* 4.0 0.4 - - - -
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ASP 5.8 0.4 - - - +
196B PHE* 3.7 31.1 - - + -
197B PHE* 3.7 24.9 - - + -
360B PHE 3.0 14.1 + - - +
361B PHE 3.5 9.4 - - - +
363B PHE* 1.4 75.8 - - - +
365B VAL* 1.4 61.0 + - + +
367B ILE* 3.4 13.0 - - - +
368B GLY 4.7 1.0 + - - -
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 3.2 41.2 + - + +
362B LEU* 3.6 16.2 - - + +
363B PHE 3.2 0.4 - - - -
364B ALA* 1.4 78.6 - - + +
366B LEU* 1.4 65.1 + - + +
367B ILE 3.6 0.4 + - - -
368B GLY* 4.4 4.7 + - - -
369B ARG* 5.0 2.8 + - - +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.0 26.7 + - + +
365B VAL* 1.4 83.2 - - + +
367B ILE* 1.4 62.5 + - - +
368B GLY 3.2 2.9 - - - -
369B ARG* 3.3 31.6 + - + +
372B LEU* 5.3 3.1 - - - +
373B PHE* 5.2 0.3 - - - -
391B ILE* 3.8 34.9 - - + +
395B ILE* 5.2 9.0 - - + -
396B PHE* 4.4 10.8 - - + -
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 5.9 1.6 - - + -
196B PHE* 3.9 22.7 - - + -
363B PHE* 2.7 50.2 + - + +
364B ALA 3.4 18.6 - - - +
366B LEU* 1.4 71.9 - - - +
368B GLY* 1.3 63.6 + - - +
369B ARG 3.4 0.7 + - - -
373B PHE* 3.6 30.1 - - + -
382B GLN* 5.6 1.2 - - - +
384B THR* 4.9 19.7 - - + +
387B GLY* 5.4 1.3 - - - -
391B ILE* 3.9 9.6 - - + -
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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) + - + + + + + -
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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