Contacts of the helix formed by residues 301 - 312 (chain D) in PDB entry 3QNQ
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 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296D GLY 4.1 8.7 - - - +
299D GLY* 2.6 16.1 + - - -
300D ALA* 1.3 72.8 - - - +
302D LEU* 1.3 53.0 + - - +
303D ALA 2.7 4.5 + - - -
304D LEU* 2.8 13.4 + - - +
305D VAL* 2.7 49.9 + - + +
328D GLY* 5.5 3.4 - - - -
333D ASN* 3.2 44.3 + - + +
336D VAL* 4.3 15.4 - - + +
342D ILE* 4.7 6.9 - - - +
352D PHE* 5.0 0.7 - - - -
415D TYR* 4.2 3.7 + - - -
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D MET* 4.6 2.9 - - + -
296D GLY* 3.0 28.1 - - - +
300D ALA 2.6 6.0 + - - +
301D THR* 1.3 73.2 - - - +
303D ALA* 1.3 56.4 + - - +
305D VAL* 4.0 8.5 - - + +
306D VAL* 3.5 26.2 + - + +
325D ILE* 4.9 7.6 - - + +
328D GLY* 3.3 30.5 - - - +
329D ILE* 3.9 21.8 - - + +
331D ASN* 5.3 1.8 - - - +
386D ILE* 4.0 42.0 - - + -
408D PHE* 4.1 15.6 - - + -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ALA* 2.6 13.9 + - + +
302D LEU* 1.3 78.6 - - - +
304D LEU* 1.3 58.9 + - - +
305D VAL 3.1 1.1 - - - -
306D VAL* 3.3 3.2 + - - +
307D GLY* 2.9 24.8 + - - -
408D PHE* 3.7 32.3 - - + +
411D ALA* 4.3 6.7 - - + -
412D PHE* 3.8 33.3 - - - +
415D TYR* 4.9 1.3 - - + +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ALA 4.0 0.6 + - - -
301D THR* 2.8 11.5 + - - +
303D ALA* 1.3 78.0 - - - +
305D VAL* 1.3 58.5 + - + +
307D GLY* 3.2 3.1 + - - +
308D MET* 3.1 30.1 + - + +
336D VAL* 4.2 11.0 - - + -
340D MET* 4.3 14.6 - - - -
342D ILE* 3.9 28.3 - - + -
348D LEU* 5.0 7.6 - - + -
415D TYR* 3.5 52.2 - - + -
419D LEU* 4.2 32.8 - - + -
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D THR* 2.7 29.2 + - + +
302D LEU* 4.3 8.5 - - + +
304D LEU* 1.3 72.0 - - + +
306D VAL* 1.3 64.1 + - + +
307D GLY 3.1 0.2 - - - -
308D MET* 3.5 12.9 + - + +
309D LEU* 3.1 21.0 + - - +
321D GLY* 4.2 7.0 - - - +
324D SER* 3.4 22.9 - - - +
325D ILE* 3.3 31.4 - - + -
328D GLY* 5.9 1.1 - - - -
336D VAL* 3.4 34.1 - - + -
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D LEU* 3.5 20.5 + - + +
303D ALA* 3.3 10.1 + - - +
305D VAL* 1.3 79.7 - - + +
307D GLY* 1.3 64.5 + - - +
309D LEU* 3.2 16.5 + - + +
310D LEU* 3.1 42.5 + - + +
325D ILE* 5.6 2.5 - - + -
408D PHE* 4.2 18.6 - - + -
412D PHE* 4.6 13.7 - - + -
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Residues in contact with GLY 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA 2.9 13.8 + - - -
304D LEU* 3.2 6.3 + - - -
305D VAL 3.1 0.6 - - - -
306D VAL* 1.3 78.6 - - - +
308D MET* 1.3 55.6 + - - +
310D LEU* 3.8 1.3 - - - -
311D PHE* 3.0 29.0 + - - +
412D PHE* 4.2 17.0 - - - -
419D LEU* 3.2 25.4 - - - +
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Residues in contact with MET 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D LEU* 3.1 11.3 + - + +
305D VAL* 3.8 25.4 - - + -
307D GLY* 1.3 70.3 - - - +
309D LEU* 1.3 58.1 + - - +
310D LEU 2.9 11.0 + - - -
312D ALA* 3.0 31.0 + - + +
317D LEU* 3.6 26.9 - - + +
318D LYS* 4.6 6.3 - - - +
320D LEU* 3.7 13.7 - - + -
321D GLY* 3.2 31.0 - - - +
324D SER* 4.6 0.7 - - - +
336D VAL* 5.1 0.2 - - + -
340D MET* 3.3 35.7 - - + +
419D LEU* 3.5 22.2 - - + -
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D VAL 3.1 14.9 + - - +
306D VAL* 3.2 17.7 + - + +
308D MET* 1.3 75.0 - - - +
310D LEU* 1.3 69.6 + - + +
318D LYS* 5.8 3.8 - - - +
321D GLY* 4.1 19.2 - - - +
322D ARG* 4.8 8.3 - - + +
325D ILE* 3.2 34.8 - - + -
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D VAL* 3.1 32.0 + - + +
307D GLY* 4.7 0.2 - - - -
308D MET 2.9 3.6 + - - -
309D LEU* 1.3 91.0 - - + +
311D PHE* 1.3 90.0 + - + +
312D ALA 3.8 0.7 - - - -
412D PHE* 5.0 5.6 - - + -
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D GLY* 3.0 13.9 + - - +
310D LEU* 1.3 109.5 - - + +
312D ALA* 1.3 66.8 + - - +
313D ARG* 3.4 5.0 + - - +
412D PHE* 4.2 17.7 - + - -
416D LEU* 4.2 32.8 - - + -
419D LEU* 4.9 4.5 - - + -
423D ASP* 3.5 5.5 - - - +
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Residues in contact with ALA 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D GLY 3.8 1.6 + - - -
308D MET* 3.0 33.1 + - + +
310D LEU 5.5 0.3 - - - -
311D PHE* 1.3 76.9 - - - +
313D ARG* 1.3 59.2 + - - +
317D LEU* 3.8 26.5 - - + -
318D LYS* 3.2 27.8 - - - +
419D LEU* 5.0 3.1 - - + +
423D ASP* 3.2 11.2 - - + +
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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