Contacts of the helix formed by residues 376 - 396 (chain B) in PDB entry 5D3Y
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 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ASN* 3.7 10.3 - - - +
374B ALA* 3.2 5.0 - - - +
375B LYS* 1.3 100.8 - - + +
377B ALA* 1.3 63.7 + - - +
378B GLU* 3.4 8.8 + - - +
379B GLU* 3.0 25.9 + - + +
380B LYS* 3.1 19.9 + - - +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 3.9 30.1 - - + +
264A ASN* 5.8 6.5 - - - +
357B ASN* 3.6 20.0 + - - +
376B THR* 1.3 73.2 - - - +
378B GLU* 1.3 57.4 + - - +
380B LYS* 3.3 7.2 + - - +
381B GLN* 3.0 29.2 + - - +
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 4.3 12.4 + - - +
376B THR* 3.3 7.7 + - - +
377B ALA* 1.3 78.9 - - - +
379B GLU* 1.3 59.6 + - - +
381B GLN* 3.3 6.6 + - + +
382B LYS* 2.9 44.7 + - + +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 5.4 0.5 - - - +
275B GLN 4.9 2.6 - - - +
276B GLY* 4.6 11.4 - - - -
277B THR 5.4 4.3 + - - +
278B LEU* 4.9 3.1 - - + -
374B ALA* 3.8 16.2 - - + -
375B LYS* 4.6 6.7 - - + +
376B THR* 3.0 25.8 + - + +
378B GLU* 1.3 76.4 - - - +
380B LYS* 1.3 64.3 + - - +
382B LYS* 3.3 30.3 + - - +
383B TRP* 3.0 47.9 + - + +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN* 5.1 12.9 - - - +
340B ASN* 2.7 30.5 + - - +
341B VAL 3.0 12.5 + - - -
342B GLU* 5.2 0.4 - - - +
343B ASP* 4.7 4.0 + - - -
357B ASN* 3.5 30.0 - - - +
358B GLY 2.8 23.5 + - - +
359B TRP* 3.7 25.4 - - + -
374B ALA* 3.6 1.2 - - + +
376B THR 3.1 13.3 + - - +
377B ALA* 3.3 10.5 + - - +
379B GLU* 1.3 75.1 - - - +
381B GLN* 1.3 67.7 + - - +
383B TRP* 3.1 5.0 + - - +
384B LEU* 2.9 38.8 + - + +
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Residues in contact with GLN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 5.5 2.8 - - - +
377B ALA 3.0 17.4 + - - +
378B GLU* 3.7 7.6 - - - +
379B GLU 3.3 0.2 - - - -
380B LYS* 1.3 80.0 - - - +
382B LYS* 1.3 61.4 + - - +
384B LEU* 4.5 16.2 - - - +
385B ASP* 2.9 63.3 + - - +
388B ILE* 6.2 0.2 - - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.6 31.5 - - + +
378B GLU* 2.9 34.4 + - + +
379B GLU* 3.4 35.0 - - - +
380B LYS 3.3 0.2 - - - -
381B GLN* 1.3 75.8 - - - +
383B TRP* 1.3 56.8 + - - +
385B ASP* 3.9 5.0 - - - +
386B ALA* 2.9 30.5 + - - +
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Residues in contact with TRP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.3 35.6 - - + +
276B GLY* 3.7 23.5 - - - -
278B LEU* 3.7 24.2 - - + +
291B PHE* 3.4 40.4 - + + -
293B LEU* 3.9 25.6 - - + -
298B LEU* 4.1 12.3 - - + -
359B TRP* 3.5 37.5 - + + -
379B GLU* 3.0 42.2 + - + -
380B LYS 3.1 2.6 + - - +
382B LYS* 1.3 75.0 - - - +
384B LEU* 1.3 66.0 + - - +
386B ALA* 3.3 1.2 + - - +
387B ILE* 3.0 42.7 + - + +
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Residues in contact with LEU 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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338B VAL* 4.0 20.9 - - + -
340B ASN* 4.2 11.9 - - + +
359B TRP* 3.8 31.2 - - + +
380B LYS* 2.9 53.4 + - + +
381B GLN* 4.0 17.7 - - - +
383B TRP* 1.3 76.2 - - - +
385B ASP* 1.3 63.8 + - - +
387B ILE* 3.4 5.4 + - + +
388B ILE* 3.0 35.0 + - + +
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLN* 2.9 52.8 + - - +
382B LYS* 3.9 4.8 - - - +
384B LEU* 1.3 76.9 - - - +
386B ALA* 1.3 57.1 + - - +
388B ILE* 3.3 14.7 + - - +
389B ARG* 2.9 51.0 + - - +
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Residues in contact with ALA 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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273B LEU* 5.1 7.8 - - + +
274B LEU* 3.9 24.2 - - + -
293B LEU* 3.7 14.6 - - + +
382B LYS 2.9 20.6 + - - +
383B TRP 3.3 3.6 + - - +
385B ASP* 1.3 76.8 - - - +
387B ILE* 1.3 57.6 + - - +
389B ARG* 3.3 8.7 + - - +
390B GLU* 2.9 29.6 + - - +
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Residues in contact with ILE 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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293B LEU* 4.0 18.4 - - + -
298B LEU* 5.9 2.9 - - + -
336B MET* 4.1 17.0 - - + -
338B VAL* 3.9 37.2 - - + -
359B TRP* 4.3 18.4 - - - +
361B ILE* 4.3 6.7 - - + -
383B TRP* 3.0 36.3 + - + +
384B LEU* 3.7 8.5 - - + +
386B ALA* 1.3 71.4 - - - +
388B ILE* 1.3 69.2 + - + +
390B GLU* 3.4 5.4 + - - +
391B ARG* 3.0 37.3 + - - +
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Residues in contact with ILE 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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381B GLN* 6.2 0.2 - - - +
384B LEU* 3.0 28.2 + - + +
385B ASP* 3.3 16.6 + - - +
387B ILE* 1.3 80.1 - - + +
389B ARG* 1.3 59.3 + - + +
391B ARG* 3.0 11.5 + - - +
392B GLU* 2.9 55.3 + - + +
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Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ASP* 2.9 37.6 + - + +
386B ALA* 3.7 7.4 - - - +
388B ILE* 1.3 78.6 - - + +
390B GLU* 1.3 57.0 + - - +
392B GLU* 3.9 10.7 - - - +
393B GLN* 2.9 31.4 + - - +
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Residues in contact with GLU 390 (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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273B LEU* 3.6 30.4 - - + +
293B LEU* 4.3 10.1 - - + -
294B PHE 3.7 10.3 - - - +
295B ASP* 4.0 5.0 - - + +
296B ASN 2.8 15.7 + - - -
333B THR* 2.7 31.4 + - - +
336B MET* 5.7 0.9 - - - +
386B ALA 2.9 17.1 + - - +
387B ILE* 3.7 7.1 - - - +
389B ARG* 1.3 75.6 - - - +
391B ARG* 1.3 65.2 + - - +
393B GLN* 3.4 6.0 + - - +
394B ARG* 2.9 54.7 + - - +
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Residues in contact with ARG 391 (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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333B THR 5.8 0.8 + - - -
336B MET* 3.9 23.8 + - - +
337B GLU* 5.1 4.2 - - - +
338B VAL* 4.0 19.4 - - - +
387B ILE* 3.0 34.4 + - - +
388B ILE* 3.0 13.7 + - + +
390B GLU* 1.3 78.0 + - - +
392B GLU* 1.3 58.8 + - + +
394B ARG* 3.2 27.1 + - - +
395B GLU* 2.9 58.2 + - - +
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Residues in contact with GLU 392 (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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388B ILE* 2.9 38.8 + - + +
389B ARG* 3.9 10.4 - - - +
391B ARG* 1.3 73.7 - - + +
393B GLN* 1.3 61.0 + - - +
395B GLU* 3.4 10.9 + - - +
396B SER* 3.0 28.6 + - - -
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Residues in contact with GLN 393 (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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295B ASP* 4.8 15.4 - - - +
389B ARG 2.9 18.7 + - - +
390B GLU* 3.8 6.0 - - - +
392B GLU* 1.3 75.2 - - - +
394B ARG* 1.3 70.8 + - - +
396B SER* 2.7 26.3 + - - +
398B LYS* 3.3 28.7 - - - +
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Residues in contact with ARG 394 (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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296B ASN* 3.5 25.1 - - - +
332B ASN* 5.7 0.4 - - - -
333B THR* 3.4 21.6 + - - -
334B GLU* 3.6 33.2 + - - +
390B GLU* 2.9 47.5 + - - +
391B ARG* 3.6 29.7 + - - +
393B GLN* 1.3 88.8 + - - +
395B GLU* 1.3 67.0 + - + +
398B LYS* 3.0 20.5 + - - +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 2.9 44.9 + - + +
392B GLU* 4.0 8.9 - - - +
394B ARG* 1.3 83.8 + - - +
396B SER* 1.3 66.3 + - - +
397B LEU* 3.8 2.6 + - - +
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Residues in contact with SER 396 (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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392B GLU 3.0 16.9 + - - -
393B GLN* 2.7 23.5 + - - +
395B GLU* 1.3 81.0 - - - +
397B LEU* 1.3 67.8 + - - +
398B LYS* 2.9 30.3 + - - +
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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