Contacts of the helix formed by residues 333 - 340 (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 ASN 333 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D TRP* 4.9 1.7 - - - -
296D GLY 4.2 0.7 - - - +
297D GLY* 3.8 7.2 - - - -
298D SER* 3.2 30.5 + - - +
301D THR* 3.2 39.0 + - + +
324D SER* 6.2 0.7 - - - -
327D PRO* 5.5 0.4 - - - -
328D GLY* 5.3 0.4 - - - -
332D ILE* 1.3 75.7 - - - +
334D GLU* 1.3 65.8 + - - +
335D MET* 3.2 6.3 - - - +
336D VAL* 3.1 8.6 + - + +
337D THR* 3.0 31.2 + - - +
2K NAG 2.6 39.0 + - - -
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Residues in contact with GLU 334 (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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175C THR* 4.2 35.8 + - + +
176C VAL* 4.0 3.3 - - - +
177C PRO* 3.7 8.1 - - - +
245D TRP* 3.7 15.3 - - + -
250D HIS* 3.8 2.4 - - - -
332D ILE* 3.7 9.1 - - - +
333D ASN* 1.3 73.0 - - - +
335D MET* 1.3 69.1 + - - +
337D THR* 3.2 7.2 - - - +
338D PHE* 2.8 55.8 + - + +
2K NAG 2.7 42.6 + - - -
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Residues in contact with MET 335 (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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175C THR* 5.1 10.3 + - - +
320D LEU* 3.9 21.8 - - + +
323D LEU* 3.8 31.2 - - + +
324D SER* 3.1 33.4 - - - +
327D PRO* 4.6 10.8 - - + -
333D ASN* 4.6 2.0 - - - -
334D GLU* 1.3 77.6 - - - +
336D VAL* 1.3 56.4 + - - +
339D GLY* 2.9 30.8 + - - +
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Residues in contact with VAL 336 (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* 4.3 15.3 - - + +
304D LEU* 4.2 10.5 - - + -
305D VAL* 3.4 22.0 - - + -
308D MET* 5.1 1.3 - - + -
320D LEU* 5.1 2.2 - - + -
324D SER* 3.3 26.9 - - - +
333D ASN* 3.1 9.2 + - + +
334D GLU 2.9 0.6 + - - -
335D MET* 1.3 74.7 - - + +
337D THR* 1.3 67.9 + - - +
338D PHE 3.0 1.8 - - - -
340D MET* 2.8 51.6 + - + +
342D ILE* 3.2 26.9 - - + -
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Residues in contact with THR 337 (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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245D TRP* 3.9 19.5 - - + -
298D SER* 3.4 14.8 - - - +
333D ASN* 3.0 40.9 + - - +
334D GLU* 3.2 12.0 + - - -
336D VAL* 1.3 79.3 - - - +
338D PHE* 1.3 65.5 + - - +
342D ILE* 2.7 37.0 + - + -
343D VAL* 2.8 21.0 + - - +
352D PHE* 4.3 12.3 - - + -
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Residues in contact with PHE 338 (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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245D TRP* 3.8 22.2 - + - -
248D GLY* 3.7 23.6 - - - -
334D GLU* 2.8 36.9 + - + +
337D THR* 1.3 86.8 + - - +
339D GLY* 1.3 62.8 + - - +
340D MET 3.5 0.4 - - - -
341D PRO* 3.3 15.3 - - - +
343D VAL* 3.6 30.1 - - + -
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Residues in contact with GLY 339 (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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320D LEU* 4.1 14.1 - - - +
335D MET* 2.9 25.5 + - - -
338D PHE* 1.3 79.1 - - - +
340D MET* 1.3 67.3 + - - +
341D PRO* 3.1 2.6 - - - +
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Residues in contact with MET 340 (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* 4.3 15.5 - - - -
308D MET* 3.3 27.8 - - + +
316D GLN* 5.0 5.5 - - - +
317D LEU* 4.4 4.5 - - + +
320D LEU* 3.1 36.0 - - + +
336D VAL* 2.8 32.8 + - + +
339D GLY* 1.3 73.5 - - - +
341D PRO* 1.3 71.0 - - - +
342D ILE* 3.4 4.9 - - + +
348D LEU* 3.1 37.5 - - + -
419D LEU* 5.9 1.3 - - - -
422D TRP* 3.5 30.0 + - - +
426D LYS* 5.4 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