Contacts of the helix formed by residues 366 - 389 (chain B) in PDB entry 5U3Y
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 ASN 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 5.5 3.3 - - + +
274B PHE* 6.2 2.6 - - + -
277B ASP* 3.0 13.7 + - - +
364B LEU* 5.2 0.4 - - - -
365B MET* 1.3 83.4 - - + +
367B VAL* 1.3 62.0 + - - +
368B PRO* 3.6 9.9 - - - +
369B ARG* 3.2 38.4 + - + +
370B VAL* 3.2 26.5 + - + +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLY 3.8 16.2 - - - +
364B LEU* 3.9 38.4 - - + +
365B MET 3.2 4.7 + - - +
366B ASN* 1.3 71.8 - - - +
368B PRO* 1.3 73.7 - - + +
370B VAL* 3.1 3.1 + - - +
371B GLU* 2.9 46.9 + - - +
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Residues in contact with PRO 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B MET 5.0 1.3 - - - +
366B ASN* 3.6 11.2 - - - +
367B VAL* 1.3 95.4 - - + +
369B ARG* 1.3 61.6 + - - +
371B GLU* 3.5 12.4 + - - +
372B ALA* 3.0 24.8 + - - +
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Residues in contact with ARG 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 4.5 12.5 + - - +
272B SER* 4.7 14.8 + - - -
273B LEU* 3.6 23.5 - - + +
366B ASN* 3.2 36.4 + - + +
367B VAL 3.2 0.6 - - - -
368B PRO* 1.3 79.2 - - - +
370B VAL* 1.3 61.2 + - - +
372B ALA* 3.3 12.2 + - - +
373B ILE* 3.0 49.3 + - + +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.1 27.8 - - + -
277B ASP* 5.1 2.9 - - + +
281B LEU* 4.1 12.3 - - + -
357B LEU* 4.0 6.5 - - + -
358B CYS 3.7 39.5 - - - +
359B GLY* 3.8 0.9 - - - +
364B LEU* 4.1 22.9 - - + -
366B ASN 3.2 13.9 + - - +
367B VAL 3.1 6.5 + - - +
369B ARG* 1.3 72.9 - - - +
371B GLU* 1.3 60.8 + - - +
373B ILE* 3.1 7.9 + - - +
374B GLN* 2.7 28.6 + - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLY* 4.0 16.0 - - - +
360B ASP* 4.9 6.3 - - - +
367B VAL* 2.9 39.2 + - + +
368B PRO* 3.8 10.2 - - - +
370B VAL* 1.3 76.1 - - - +
372B ALA* 1.3 58.7 + - - +
374B GLN* 3.3 14.7 + - - +
375B ASP* 2.9 29.7 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B PRO 3.0 18.7 + - - +
369B ARG* 3.6 15.3 - - - +
370B VAL 3.2 0.4 - - - -
371B GLU* 1.3 75.4 - - - +
373B ILE* 1.3 63.8 + - - +
375B ASP* 3.3 7.0 + - - +
376B THR* 3.0 26.4 + - - -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 5.1 2.7 - - + -
269B SER* 3.5 46.7 - - - +
273B LEU* 4.0 13.0 - - + -
357B LEU* 3.5 39.3 - - + -
369B ARG* 3.0 39.7 + - - +
370B VAL* 3.5 5.8 - - - +
372B ALA* 1.3 73.9 - - - +
374B GLN* 1.3 66.5 + - - +
376B THR* 3.1 8.5 + - - -
377B ILE* 3.0 26.6 + - + +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 4.1 11.3 + - - +
357B LEU 3.0 24.6 + - - +
358B CYS* 3.8 24.8 - - - +
359B GLY* 3.5 14.2 + - - -
360B ASP* 5.2 4.0 + - - +
370B VAL 2.7 17.6 + - - +
371B GLU* 3.5 10.9 - - - +
373B ILE* 1.3 72.7 - - - +
375B ASP* 1.3 57.7 + - - +
377B ILE* 3.2 9.3 + - - +
378B LEU* 2.9 47.5 + - + +
403B MET* 5.8 5.1 - - - -
407B ARG* 4.8 4.4 - - - +
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Residues in contact with ASP 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU 2.9 17.2 + - - +
372B ALA* 3.6 7.9 - - - +
373B ILE 3.2 0.4 - - - -
374B GLN* 1.3 77.5 - - - +
376B THR* 1.3 57.9 + - - +
378B LEU* 3.3 12.5 + - - +
379B ARG* 2.5 76.2 + - - +
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Residues in contact with THR 376 (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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175B LEU* 3.8 21.6 - - + +
178B PHE* 4.2 23.1 - - + -
372B ALA 3.0 15.1 + - - -
373B ILE* 3.1 9.4 + - - -
375B ASP* 1.3 76.0 + - - +
377B ILE* 1.3 57.8 + - - +
379B ARG* 3.5 10.4 + - - +
380B ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 377 (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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178B PHE* 3.7 25.8 - - + -
182B ILE* 4.6 3.1 - - + -
267B ILE* 5.9 0.2 - - + -
350B LEU* 3.5 34.2 - - + +
353B ALA* 3.8 19.1 - - + +
354B ALA* 3.7 15.5 - - + +
357B LEU* 3.3 39.7 - - + -
373B ILE* 3.0 17.9 + - + +
374B GLN* 3.6 7.0 - - - +
376B THR* 1.3 76.6 - - - +
378B LEU* 1.3 57.0 + - - +
380B ALA* 3.2 3.3 + - - +
381B LEU* 2.7 28.2 + - + +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 4.1 10.3 - - + -
374B GLN* 2.9 42.1 + - + +
375B ASP* 3.3 12.1 + - - +
377B ILE* 1.3 73.5 - - - +
379B ARG* 1.3 66.3 + - - +
381B LEU* 3.2 6.8 + - + +
382B GLU* 2.9 20.8 + - - +
396B PHE* 3.5 23.0 - - + -
400B LEU* 3.9 29.2 - - + -
403B MET* 3.9 23.8 - - + -
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.5 12.8 - - + -
375B ASP* 2.5 47.2 + - - +
376B THR* 3.7 9.6 - - - +
378B LEU* 1.3 76.3 - - + +
380B ALA* 1.3 56.7 + - - +
382B GLU* 3.2 8.3 + - - +
383B PHE* 2.9 30.0 + - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.0 23.9 - - + +
178B PHE* 4.3 10.3 - - + -
179B SER* 3.2 23.4 + - - +
350B LEU* 3.8 8.1 - - + +
376B THR 2.9 17.4 + - - +
377B ILE* 3.2 6.5 + - - +
379B ARG* 1.3 75.0 - - - +
381B LEU* 1.3 58.2 + - - +
383B PHE* 3.6 4.0 - - - +
384B HIS* 2.8 30.8 + - - +
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Residues in contact with LEU 381 (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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347B ASP* 4.1 13.5 - - - +
350B LEU* 3.7 30.9 - - + +
351B PHE* 4.4 19.1 - - + -
354B ALA* 5.3 0.4 - - + -
377B ILE* 2.7 20.7 + - + +
378B LEU* 3.2 9.8 + - + +
380B ALA* 1.3 73.0 - - - +
382B GLU* 1.3 57.5 + - - +
384B HIS* 3.0 2.7 + - + +
385B LEU* 2.8 59.2 + - + +
396B PHE* 4.2 15.9 - - + -
399B LEU* 4.5 10.8 - - + -
400B LEU* 6.2 0.2 - - + -
403B MET* 4.4 22.4 - - + -
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Residues in contact with GLU 382 (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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378B LEU 2.9 17.4 + - - +
379B ARG* 3.7 6.5 - - - +
381B LEU* 1.3 75.3 - - - +
383B PHE* 1.3 65.4 + - - +
384B HIS 3.2 0.2 + - - -
385B LEU* 3.2 5.1 + - - +
386B GLN* 3.0 39.0 + - + +
396B PHE* 3.4 47.1 - - + +
397B PRO* 5.7 0.3 - - - +
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Residues in contact with PHE 383 (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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175B LEU* 4.4 18.4 - - + -
176B LYS* 3.6 47.3 - - + -
179B SER* 5.4 5.8 - - - -
379B ARG 2.9 17.0 + - - +
380B ALA* 3.6 9.2 - - - +
382B GLU* 1.3 77.1 - - - +
384B HIS* 1.3 70.5 + - + +
386B GLN* 3.4 21.7 + - - +
387B ALA* 3.4 19.0 + - + +
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Residues in contact with HIS 384 (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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179B SER* 5.3 5.1 - - - +
346B SER* 2.8 48.3 + - - -
347B ASP* 3.0 24.9 + - - -
350B LEU* 3.6 15.5 - - + +
380B ALA 2.8 21.5 + - - +
381B LEU* 3.0 5.4 + - + +
383B PHE* 1.3 80.4 - - + +
385B LEU* 1.3 61.9 + - + +
387B ALA* 3.1 7.0 + - + +
388B ASN* 2.8 44.2 + - + +
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Residues in contact with LEU 385 (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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343B LEU* 4.6 0.4 - - + -
347B ASP* 3.9 28.5 - - + +
381B LEU* 2.8 42.5 + - + +
382B GLU* 3.9 3.8 - - - +
384B HIS* 1.3 72.5 - - + +
386B GLN* 1.3 57.7 + - - +
388B ASN* 4.4 1.6 - - - +
389B HIS* 2.9 37.3 + - + +
395B LEU* 3.8 27.4 - - + -
396B PHE* 4.0 29.4 - - + +
399B LEU* 3.7 27.6 - - + -
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Residues in contact with GLN 386 (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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382B GLU* 3.0 30.8 + - + +
383B PHE* 3.5 19.1 - - - +
384B HIS 3.1 0.2 - - - -
385B LEU* 1.3 78.3 - - - +
387B ALA* 1.3 60.8 + - - +
389B HIS 5.0 0.9 - - - -
390B PRO* 3.3 26.1 - - - +
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Residues in contact with ALA 387 (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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383B PHE* 3.4 16.0 + - + +
384B HIS* 3.1 10.6 + - + +
386B GLN* 1.3 79.1 - - - +
388B ASN* 1.3 63.2 + - - +
390B PRO* 3.4 12.4 - - - +
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Residues in contact with ASN 388 (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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344B ASP* 2.9 27.9 + - - +
346B SER* 3.2 8.2 + - - -
347B ASP* 2.8 29.2 + - - +
384B HIS* 2.8 31.8 + - + +
387B ALA* 1.3 74.4 - - + +
389B HIS* 1.3 69.5 + - + +
390B PRO* 3.4 6.1 - - - +
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Residues in contact with HIS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU 4.6 3.1 + - - -
342B GLU* 3.3 30.0 - - + +
343B LEU* 4.4 1.3 - - - -
344B ASP* 4.8 2.2 - - + -
347B ASP* 2.6 31.6 + - - -
385B LEU* 2.9 27.3 + - + +
386B GLN* 5.0 0.3 - - - -
388B ASN* 1.3 97.2 + - + +
390B PRO* 1.3 66.9 - - - +
391B ASP 3.1 2.9 - - - -
392B ALA* 3.0 32.8 + - + +
395B LEU* 3.9 16.8 - - + +
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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