Contacts of the helix formed by residues 328 - 338 (chain A) 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 GLN 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A TYR* 3.6 40.0 + - + -
307A GLU* 5.5 2.6 + - - -
326A GLU 3.4 3.2 - - - +
327A ASP* 1.3 77.0 - - - +
329A LEU* 1.3 62.7 + - - +
331A PRO* 3.3 18.1 - - - +
332A MET* 3.2 16.4 - - - +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A PHE* 3.7 32.1 - - + -
299A ARG* 3.5 27.8 - - + +
302A MET* 4.1 10.8 - - + +
303A TYR* 3.8 33.0 - - + +
306A LEU* 4.5 10.3 - - + -
326A GLU* 3.4 21.0 + - - +
327A ASP 3.3 0.6 - - - -
328A GLN* 1.3 78.8 - - - +
330A LYS* 1.3 54.6 + - - +
332A MET* 3.1 15.4 + - + +
333A LEU* 2.8 40.3 + - + +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU 3.1 13.3 + - - +
327A ASP* 3.7 13.9 - - - +
329A LEU* 1.3 73.4 - - - +
331A PRO* 1.4 68.8 - - + +
333A LEU* 3.4 7.8 + - - +
334A GLU* 3.1 48.6 + - - +
289B LEU* 5.4 0.2 - - - +
293B ASN* 3.8 35.6 + - - +
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Residues in contact with PRO 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A PHE* 3.5 33.6 - - + -
318A PRO* 5.4 7.2 - - + -
327A ASP 3.4 12.3 - - - +
328A GLN* 3.3 19.3 - - - +
330A LYS* 1.4 86.9 - - + +
332A MET* 1.3 56.8 + - - +
334A GLU* 3.8 14.6 - - - +
335A TRP* 3.0 27.9 + - - +
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TYR* 3.3 39.0 - - + +
306A LEU* 3.8 21.0 - - + +
307A GLU* 4.1 35.0 - - - +
310A ARG* 5.2 1.1 - - - -
317A PHE* 3.6 32.8 - - + -
328A GLN* 3.2 25.6 - - + +
329A LEU* 3.1 17.3 + - + +
331A PRO* 1.3 75.6 - - - +
333A LEU* 1.3 58.2 + - - +
335A TRP* 3.3 7.7 + - + +
336A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 3.8 27.8 - - + -
287A PHE* 3.9 21.5 - - + -
292A PHE* 3.5 38.4 - - + -
302A MET* 4.6 3.6 - - + -
306A LEU* 3.8 13.6 - - + +
329A LEU* 2.8 25.4 + - + +
330A LYS* 3.7 6.7 - - - +
332A MET* 1.3 73.5 - - - +
334A GLU* 1.3 58.8 + - - +
336A ALA* 3.4 1.4 + - - +
337A HIS* 2.9 33.0 + - + +
289B LEU* 3.9 20.6 - - + -
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 3.1 32.3 + - - +
331A PRO* 3.8 13.5 - - - +
332A MET 3.4 0.2 - - - -
333A LEU* 1.3 75.4 - - - +
335A TRP* 1.4 55.9 + - - +
337A HIS* 3.9 2.2 - - - +
338A GLY* 3.0 26.7 + - - -
289B LEU* 4.2 10.9 - - + +
290B ALA* 3.6 40.0 + - + +
293B ASN* 2.9 38.6 + - - +
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Residues in contact with TRP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 4.0 8.7 - - + -
309A ALA* 3.7 16.2 - - + -
310A ARG* 3.7 35.7 - - + -
313A ALA* 3.8 20.0 - - + -
315A LYS* 3.5 26.9 - - + +
317A PHE* 3.5 24.7 - + + -
331A PRO 3.0 18.8 + - - +
332A MET* 3.5 12.1 - - + +
334A GLU* 1.4 72.7 - - - +
336A ALA* 1.3 63.4 + - + +
338A GLY* 3.3 8.1 + - - -
339A GLY 3.4 0.5 + - - -
340A PHE* 2.9 72.9 + + + -
341A LYS* 2.9 30.8 + - + -
343A THR* 4.9 0.4 - - - -
348A LEU* 4.2 1.1 - - + -
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 3.7 29.6 - - + +
284A SER 5.1 0.2 + - - -
306A LEU* 3.7 27.8 - - + -
332A MET 2.9 16.7 + - - +
333A LEU 3.8 1.6 - - - +
335A TRP* 1.3 77.0 - - + +
337A HIS* 1.4 62.0 + - - +
339A GLY* 3.2 11.8 + - - -
340A PHE* 3.7 30.5 - - + -
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 3.7 11.2 - + + -
284A SER* 3.7 25.3 + - - -
287A PHE* 4.2 18.8 - + - -
333A LEU 2.9 21.5 + - - +
334A GLU 4.1 2.9 - - - +
336A ALA* 1.4 72.7 - - - +
338A GLY* 1.3 57.3 + - - +
339A GLY 3.3 3.0 + - - -
284B SER 3.5 24.0 - - - -
287B PHE* 3.6 32.0 + + - -
288B ASN* 5.3 0.2 - - - -
289B LEU* 4.2 27.2 + - + +
337B HIS* 2.8 31.2 + - - -
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Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLU 3.0 17.5 + - - -
335A TRP* 3.8 2.7 - - - -
336A ALA 3.2 0.8 - - - -
337A HIS* 1.3 75.0 - - - +
339A GLY* 1.3 55.0 + - - +
340A PHE 3.7 1.8 - - - -
341A LYS* 3.5 28.6 - - - +
288B ASN* 6.6 0.2 - - - -
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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