Contacts of the helix formed by residues 325 - 340 (chain B) in PDB entry 1QK0
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 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ALA* 3.3 15.3 - - - +
307B ASN* 5.0 1.1 - - - -
308B GLY 3.3 15.9 - - - +
309B TRP 3.3 9.3 + - - +
310B ASN* 3.9 4.2 - - - +
311B ILE* 3.2 40.2 + - + +
323B VAL* 3.5 0.9 + - - +
324B TYR* 1.3 87.5 + - - +
326B GLU* 1.3 62.7 + - - +
327B LYS* 3.1 4.6 + - - +
328B LEU* 2.7 49.4 + - - +
329B TYR 3.3 13.7 + - - -
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS* 4.0 0.2 - - - -
267B ALA* 2.9 25.3 + - - +
301B THR* 2.8 31.5 + - - +
302B ASN* 3.7 15.8 + - + +
307B ASN* 2.7 36.1 + - + +
308B GLY 2.9 22.4 + - - +
309B TRP* 3.9 9.2 - - + -
325B ASN* 1.3 70.9 - - - +
327B LYS* 1.3 66.0 + - - +
329B TYR* 3.2 4.5 + - - +
330B ILE* 3.0 27.9 + - - +
349B THR* 3.7 29.2 - - + +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 2.9 50.5 + - + +
310B ASN* 4.1 18.5 - - + +
325B ASN* 3.6 4.3 - - - +
326B GLU* 1.3 76.8 - - - +
328B LEU* 1.3 67.3 + - + +
330B ILE* 3.4 0.7 - - - +
331B HIS* 3.1 46.3 + - + -
384B GLY 5.4 5.1 + - - -
385B ASP* 4.1 11.0 + - - -
502B NAG 4.8 10.9 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA 3.3 26.5 - - - +
323B VAL* 3.7 14.1 - - + +
324B TYR* 3.7 24.9 - - + +
325B ASN* 2.7 36.9 + - - +
327B LYS* 1.3 77.9 - - + +
329B TYR* 1.3 62.2 + - - +
331B HIS* 3.6 4.3 + - + +
332B ALA* 3.1 25.6 + - - +
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 2.7 34.7 + - + +
266B HIS* 3.9 8.7 - - - -
267B ALA* 3.8 11.2 - - + -
270B LEU* 3.3 43.5 - - + +
271B GLY* 3.8 16.8 - - - -
276B GLN* 5.5 2.5 - - + -
301B THR* 3.8 22.0 - - + -
323B VAL* 3.3 12.1 - - + +
325B ASN 3.3 11.9 + - - +
326B GLU* 3.2 24.0 + - - +
327B LYS 3.2 0.4 - - - -
328B LEU* 1.3 80.2 - - - +
330B ILE* 1.3 58.3 + - + +
332B ALA* 3.1 5.4 + - + +
333B ILE* 3.0 49.6 + - + +
347B PHE* 6.1 0.2 - + - -
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 3.9 19.5 - - + +
309B TRP* 3.8 18.2 - - + -
326B GLU 3.0 14.6 + - - +
327B LYS 3.4 10.8 - - - +
329B TYR* 1.3 76.3 - - + +
331B HIS* 1.3 65.4 + - + +
332B ALA 3.1 0.2 - - - -
333B ILE* 4.0 7.4 - - - -
334B GLY* 2.9 29.8 + - - -
347B PHE* 3.5 32.4 - - + -
349B THR* 4.4 7.0 - - - +
385B ASP* 3.7 22.7 - - - +
387B LEU* 3.5 20.6 - - + +
388B LEU* 4.1 12.1 - - + +
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Residues in contact with HIS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 3.1 43.1 + - + +
328B LEU* 3.9 5.2 - - - +
330B ILE* 1.3 85.6 - - + +
332B ALA* 1.3 57.0 + - - +
335B PRO* 3.3 21.3 - - - +
385B ASP* 2.6 32.7 + - - -
386B SER* 3.6 23.1 - - - -
387B LEU* 3.5 21.0 - - + +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 3.7 29.7 - - + +
323B VAL* 4.7 5.6 - - + -
328B LEU 3.1 18.7 + - - +
329B TYR* 3.5 6.7 - - + +
330B ILE 3.1 0.4 - - - -
331B HIS* 1.3 79.1 - - - +
333B ILE* 1.3 62.9 + - - +
334B GLY 3.4 0.4 - - - -
335B PRO* 3.8 6.6 - - - +
336B LEU* 3.4 19.4 - - - +
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 4.3 9.0 - - + +
279B ALA* 4.1 6.5 - - + -
280B ALA* 3.8 34.3 - - + +
283B PHE* 3.9 24.2 - - + -
299B LEU* 4.5 4.9 - - + -
329B TYR* 3.0 45.8 + - + +
330B ILE* 3.8 2.0 - - - +
332B ALA* 1.3 78.2 - - - +
334B GLY* 1.3 68.8 + - - +
335B PRO 3.4 0.2 - - - -
336B LEU* 3.1 8.4 + - + +
337B LEU* 2.9 24.9 + - + +
347B PHE* 3.6 26.7 - - + -
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE 2.9 17.1 + - - -
333B ILE* 1.3 77.4 - - - +
335B PRO* 1.3 67.8 - - - +
337B LEU* 3.1 17.6 + - - +
338B ALA* 3.2 10.7 + - - +
345B ALA* 5.7 1.4 - - - +
347B PHE* 3.9 18.2 - - - -
387B LEU* 4.6 6.7 - - - -
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Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS* 3.3 25.6 - - - +
332B ALA 3.8 5.6 - - - +
333B ILE 3.7 1.8 - - - -
334B GLY* 1.3 88.9 - - - +
336B LEU* 1.3 58.5 + - + +
338B ALA* 3.2 9.4 + - + +
339B ASN* 2.9 38.2 + - - +
387B LEU* 5.1 3.6 - - + -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 3.6 47.1 - - + +
277B ASP* 3.8 14.6 - - + +
280B ALA* 3.4 12.6 - - + -
332B ALA 3.4 19.7 - - - +
333B ILE* 3.1 11.3 + - - +
335B PRO* 1.3 77.3 - - + +
337B LEU* 1.3 65.4 + - - +
339B ASN* 3.1 19.7 + - + +
340B HIS* 3.0 32.2 + - + +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 3.7 31.4 - - + +
283B PHE* 4.0 18.2 - - + -
284B ALA* 4.5 0.9 - - - +
299B LEU* 3.8 24.9 - - + -
333B ILE* 2.9 18.8 + - + +
334B GLY* 3.4 6.3 - - - +
336B LEU* 1.3 76.4 - - - +
338B ALA* 1.3 62.2 + - - +
340B HIS* 3.0 13.2 + - - +
341B GLY 3.4 0.2 + - - -
342B TRP* 2.9 46.5 + - + +
345B ALA* 3.7 23.8 - - + -
347B PHE* 3.9 17.9 - - + -
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Residues in contact with ALA 338 (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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334B GLY 3.2 7.2 + - - +
335B PRO* 3.2 14.0 + - + +
337B LEU* 1.3 80.7 - - - +
339B ASN* 1.3 63.5 + - - +
340B HIS 3.3 0.5 + - - -
341B GLY* 3.3 10.7 + - - -
342B TRP 3.2 14.4 + - - +
343B SER* 4.2 19.0 + - - +
344B ASN 5.5 0.7 - - - +
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Residues in contact with ASN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO* 2.9 24.3 + - - +
336B LEU* 3.1 28.9 + - + +
338B ALA* 1.3 78.2 - - - +
340B HIS* 1.3 66.8 + - + +
341B GLY 3.3 2.6 + - - -
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Residues in contact with HIS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASP* 2.8 30.2 + - - -
280B ALA* 4.0 3.4 - - + +
281B GLN* 3.7 47.3 - - + +
284B ALA* 3.3 21.7 - - + +
288B LYS* 2.7 34.5 + - - +
336B LEU* 3.0 29.0 + - + +
337B LEU 3.0 3.2 + - - +
339B ASN* 1.3 83.2 + - + +
341B GLY* 1.3 57.4 + - - +
342B TRP 3.5 1.8 - - - -
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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
------------------------------------------------------------
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