Contacts of the helix formed by residues 325 - 338 (chain B) in PDB entry 3QKJ
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 LEU 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR* 5.1 5.6 - - + +
326B GLU* 1.4 61.1 + - - +
327B ASP* 3.3 7.5 - - - +
328B GLN* 3.3 20.1 + - - +
329B LEU* 3.0 31.6 + - - +
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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
----------------------------------------------------------
299B ARG* 6.1 5.8 - - - +
325B LEU* 1.4 76.1 - - - +
327B ASP* 1.4 60.3 + - - +
329B LEU* 3.4 10.2 + - - +
330B LYS* 3.1 27.5 + - - +
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Residues in contact with ASP 327 (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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325B LEU 3.3 5.0 - - - +
326B GLU* 1.4 78.1 - - - +
328B GLN* 1.4 62.8 + - - +
329B LEU 3.5 0.2 + - - -
330B LYS* 3.6 9.8 + - - +
331B PRO* 3.4 18.5 - - - +
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.4 39.3 + - + -
307B GLU* 5.5 0.9 - - - +
325B LEU* 3.3 20.8 + - - +
327B ASP* 1.4 77.0 - - + +
329B LEU* 1.3 62.7 + - - +
331B PRO* 3.3 17.5 - - - +
332B MET* 3.2 15.1 - - + +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 3.7 31.9 - - + -
299B ARG* 3.4 29.4 - - + +
302B MET* 4.1 10.8 - - + +
303B TYR* 3.8 32.3 - - + +
306B LEU* 4.6 9.9 - - + -
325B LEU 3.0 18.1 + - - +
326B GLU* 3.6 10.3 - - - +
328B GLN* 1.3 75.1 - - - +
330B LYS* 1.3 55.5 + - - +
332B MET* 3.0 15.3 + - + +
333B LEU* 2.8 39.7 + - + +
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Residues in contact with LYS 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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289A LEU* 5.4 0.2 - - - +
293A ASN* 3.8 30.5 + - + +
326B GLU 3.1 12.5 + - - +
327B ASP* 3.7 13.7 - - - +
329B LEU* 1.3 74.8 - - - +
331B PRO* 1.4 64.1 - - + +
333B LEU* 3.4 7.6 + - - +
334B GLU* 3.1 39.4 + - - +
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Residues in contact with PRO 331 (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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317B PHE* 3.5 34.4 - - + -
318B PRO* 5.4 7.2 - - + -
327B ASP 3.4 13.7 - - - +
328B GLN* 3.3 20.0 - - - +
330B LYS* 1.4 84.3 - - + +
332B MET* 1.4 55.9 + - - +
334B GLU* 3.8 14.4 - - - +
335B TRP* 3.0 28.6 + - - +
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Residues in contact with MET 332 (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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303B TYR* 3.3 38.4 - - + +
306B LEU* 3.8 20.7 - - + +
307B GLU* 4.0 33.9 - - - +
310B ARG* 5.2 1.1 - - - -
317B PHE* 3.6 35.2 - - + -
328B GLN* 3.2 25.1 - - + +
329B LEU* 3.0 16.6 + - + +
331B PRO* 1.4 76.0 - - - +
333B LEU* 1.3 58.4 + - - +
335B TRP* 3.3 7.4 + - + +
336B ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.0 20.6 - - + -
283B PHE* 3.8 27.8 - - + -
287B PHE* 3.9 20.9 - - + -
292B PHE* 3.5 34.8 - - + -
302B MET* 4.5 9.0 - - + -
306B LEU* 3.8 12.7 - - + +
329B LEU* 2.8 23.0 + - + +
330B LYS* 3.7 7.2 - - - +
332B MET* 1.3 74.3 - - - +
334B GLU* 1.3 59.0 + - - +
336B ALA* 3.7 1.0 - - - +
337B HIS* 2.9 32.7 + - - +
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Residues in contact with GLU 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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289A LEU* 4.2 10.9 - - + +
290A ALA* 3.6 40.8 + - + +
293A ASN* 2.9 37.3 + - - +
330B LYS* 3.1 30.6 + - - +
331B PRO* 3.8 13.4 - - - +
332B MET 3.4 0.2 - - - -
333B LEU* 1.3 74.8 - - - +
335B TRP* 1.4 57.3 + - - +
337B HIS* 3.9 2.0 - - - +
338B GLY* 3.0 27.0 + - - -
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Residues in contact with TRP 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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306B LEU* 4.0 8.5 - - + -
309B ALA* 3.7 16.6 - - + -
310B ARG* 3.7 36.3 - - + -
313B ALA* 3.8 20.4 - - + -
315B LYS* 3.5 26.0 - - + +
317B PHE* 3.5 24.5 - + + -
331B PRO 3.0 18.2 + - - +
332B MET* 3.3 12.8 + - + +
334B GLU* 1.4 75.3 - - - +
336B ALA* 1.3 59.9 + - + +
338B GLY* 3.3 8.1 + - - -
339B GLY 3.4 0.5 + - - -
340B PHE* 2.9 73.5 + + + -
341B LYS* 2.9 31.7 + - + -
342B PRO* 5.0 0.2 - - - +
343B THR* 4.9 0.4 - - - -
348B LEU* 4.2 1.3 - - + -
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Residues in contact with ALA 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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283B PHE* 3.7 28.9 - - + +
306B LEU* 3.7 27.8 - - + -
332B MET 2.9 16.3 + - - +
333B LEU 3.7 2.0 - - - +
335B TRP* 1.3 77.1 - - - +
337B HIS* 1.4 61.7 + - - +
339B GLY* 3.2 11.6 + - - -
340B PHE* 3.7 31.2 - - + -
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER 3.5 23.6 - - - -
287A PHE* 3.6 31.9 + + - +
288A ASN* 5.3 0.2 - - - -
289A LEU* 4.2 26.5 + - + +
337A HIS* 2.8 31.2 + - - -
283B PHE* 3.7 10.2 - + + -
284B SER* 3.7 25.0 + - - -
287B PHE* 4.2 19.7 - + - -
333B LEU* 2.9 21.5 + - + +
334B GLU 4.1 2.5 - - - +
336B ALA* 1.4 72.6 - - - +
338B GLY* 1.3 56.8 + - - +
339B GLY 3.3 2.8 + - - -
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Residues in contact with GLY 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 GLU 3.0 17.9 + - - -
335B TRP* 3.8 2.5 - - - -
336B ALA 3.2 0.6 - - - -
337B HIS* 1.3 76.3 - - - +
339B GLY* 1.3 56.4 + - - +
340B PHE 3.7 1.3 - - - -
341B LYS* 3.4 29.4 - - - +
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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