Contacts of the helix formed by residues 328 - 345 (chain B) in PDB entry 3QXY
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 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B LYS* 1.3 81.6 - - + +
329B GLU* 1.3 64.2 + - - +
330B ALA* 2.9 11.2 + - - +
331B GLU* 2.7 54.5 + - - +
332B ARG* 3.0 17.0 + - - +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS 4.1 0.8 + - - -
328B THR* 1.3 71.5 - - - +
330B ALA* 1.3 56.7 + - - +
332B ARG* 3.7 17.1 + - - +
333B HIS* 3.2 24.9 + - - +
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Residues in contact with ALA 330 (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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328B THR* 2.9 9.9 + - - +
329B GLU* 1.3 78.9 - - - +
331B GLU* 1.3 65.1 + - + +
332B ARG 3.3 0.2 - - - -
333B HIS* 3.5 8.6 + - - +
334B LEU* 3.4 17.8 + - - +
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR* 3.6 20.3 - - + +
327B LYS* 2.7 35.0 + - - +
328B THR* 2.7 43.3 + - - +
330B ALA* 1.3 70.7 - - + +
332B ARG* 1.3 66.3 + - - +
334B LEU* 3.3 15.0 + - - +
335B VAL* 3.5 15.2 + - - +
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 3.8 37.4 + - + +
324B GLN* 5.6 1.0 - - - +
326B THR* 3.4 31.5 + - - +
327B LYS* 5.3 3.7 - - - +
328B THR 3.0 20.6 + - - +
329B GLU* 3.8 15.5 - - - +
331B GLU* 1.3 74.9 - - - +
333B HIS* 1.3 66.0 + - - +
335B VAL* 3.0 18.2 + - - +
336B TYR* 3.0 31.4 + - + -
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Residues in contact with HIS 333 (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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329B GLU 3.2 16.2 + - - +
330B ALA* 3.7 9.6 - - - +
331B GLU 3.3 0.2 - - - -
332B ARG* 1.3 80.8 - - - +
334B LEU* 1.3 57.0 + - - +
336B TYR* 3.4 10.4 + - + +
337B GLU* 2.9 41.9 + - + +
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Residues in contact with LEU 334 (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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330B ALA 3.4 9.1 + - - +
331B GLU* 3.3 11.1 + - - +
332B ARG 3.2 0.8 - - - -
333B HIS* 1.3 77.4 + - - +
335B VAL* 1.3 66.5 + - + +
337B GLU* 3.1 17.0 + - + +
338B ARG* 3.0 53.7 + - + +
378B ALA* 4.4 15.9 - - + -
381B PHE* 4.4 13.9 - - + -
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Residues in contact with VAL 335 (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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319B ARG* 4.6 7.2 - - + +
322B ALA* 3.9 26.7 - - + +
323B LEU* 3.2 29.2 - - + -
326B THR* 4.2 15.9 - - + -
331B GLU 3.7 14.8 - - - +
332B ARG* 3.0 6.8 + - - +
334B LEU* 1.3 75.5 - - + +
336B TYR* 1.3 62.4 + - - +
338B ARG* 2.8 29.1 + - - +
339B TRP* 2.8 12.1 + - + +
374B LEU* 4.2 11.7 - - + -
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Residues in contact with TYR 336 (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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319B ARG* 4.0 38.2 + - - +
323B LEU* 3.4 33.3 - - + +
332B ARG* 3.0 37.1 + - + -
333B HIS* 3.7 13.2 - - + +
335B VAL* 1.3 76.3 - - - +
337B GLU* 1.3 57.0 + - - +
339B TRP* 3.6 8.5 - + + +
340B ASP* 2.9 40.5 + - - +
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Residues in contact with GLU 337 (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 HIS* 2.9 31.8 + - + +
334B LEU* 3.3 20.1 - - + +
335B VAL 3.0 0.4 - - - -
336B TYR* 1.3 79.3 - - - +
338B ARG* 1.3 59.2 + - - +
340B ASP* 3.5 9.1 + - - +
341B PHE* 3.2 17.3 + - - +
381B PHE* 3.8 24.4 - - + -
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 3.0 37.2 + - - +
335B VAL* 2.8 15.4 + - - +
337B GLU* 1.3 73.2 - - - +
339B TRP* 1.3 66.6 + - - +
341B PHE* 3.2 4.2 + - - +
342B LEU* 3.0 26.7 + - - +
373B VAL* 2.6 44.4 + - + +
374B LEU* 3.7 27.0 + - + +
376B MET* 2.8 35.3 + - - +
377B PRO 3.9 0.4 - - - -
378B ALA* 3.5 25.9 - - - +
381B PHE* 3.7 31.6 - - + +
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Residues in contact with TRP 339 (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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315B MET* 3.4 44.4 - - + -
316B VAL* 3.9 3.8 - - - -
318B VAL* 5.7 0.2 - - + -
319B ARG* 3.1 61.4 - - + +
335B VAL 2.8 12.3 + - - +
336B TYR* 3.6 12.8 - + - +
338B ARG* 1.3 73.3 - - - +
340B ASP* 1.3 78.7 + - - +
342B LEU* 2.9 15.4 + - + +
343B CYS* 2.9 39.5 + - - -
348B VAL* 3.8 28.9 - - + -
349B GLY 3.8 16.4 - - - -
350B GLU* 3.5 13.4 + - - -
370B THR* 5.4 4.5 - - + -
374B LEU* 4.8 8.0 - - + +
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Residues in contact with ASP 340 (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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336B TYR* 2.9 27.4 + - - +
337B GLU* 3.7 8.6 - - + +
339B TRP* 1.3 85.1 - - - +
341B PHE* 1.3 64.1 + - - +
343B CYS* 3.0 12.7 + - - +
344B LYS* 3.0 20.3 + - - +
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Residues in contact with PHE 341 (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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337B GLU 3.2 10.8 + - - +
338B ARG 3.5 7.6 - - - +
339B TRP 3.2 0.6 - - - -
340B ASP* 1.3 79.3 - - - +
342B LEU* 1.3 62.7 + - - +
344B LYS* 3.0 14.5 + - + +
345B LEU* 2.9 56.1 + - + +
373B VAL* 4.4 13.5 - - + -
381B PHE* 3.8 23.6 - + + -
384B LEU* 4.0 37.9 - - + -
385B LYS* 4.2 25.6 - - + -
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Residues in contact with LEU 342 (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 ARG 3.0 17.8 + - - +
339B TRP* 2.9 16.6 + - + +
341B PHE* 1.3 76.7 - - - +
343B CYS* 1.3 61.1 + - - +
345B LEU* 3.4 7.6 + - + +
346B GLU 3.1 3.3 + - - -
347B MET* 3.0 37.0 + - + +
348B VAL* 3.5 17.0 + - + -
369B THR* 3.9 14.1 - - + +
370B THR* 3.9 45.1 - - + +
373B VAL* 3.8 31.6 - - + -
374B LEU* 4.2 13.9 - - + -
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Residues in contact with CYS 343 (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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339B TRP* 2.9 44.5 + - - -
340B ASP* 3.2 12.8 - - - +
342B LEU* 1.3 74.7 - - - +
344B LYS* 1.3 60.4 + - - +
346B GLU* 2.8 21.0 + - - +
348B VAL* 3.6 23.5 - - - +
349B GLY* 4.8 4.5 - - - -
350B GLU 5.3 1.3 - - - -
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Residues in contact with LYS 344 (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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340B ASP 3.0 11.8 + - - +
341B PHE* 3.0 19.5 + - + +
343B CYS* 1.3 72.0 - - - +
345B LEU* 1.3 58.3 + - + +
346B GLU* 2.9 12.6 + - - +
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Residues in contact with LEU 345 (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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341B PHE* 2.9 50.5 + - + +
342B LEU* 3.7 11.7 - - + +
343B CYS 3.3 0.4 - - - -
344B LYS* 1.3 74.9 - - - +
346B GLU* 1.3 68.7 + - - +
347B MET* 3.3 23.5 + - + +
369B THR* 4.4 22.4 - - + -
373B VAL* 5.2 1.8 - - + -
384B LEU* 5.9 0.9 - - + -
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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
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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