Contacts of the helix formed by residues 333 - 340 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B TRP* 4.8 2.6 - - - -
296B GLY 4.2 0.2 - - - +
297B GLY* 3.9 5.6 - - - -
298B SER* 3.1 30.7 + - - +
301B THR* 3.0 44.0 + - + -
324B SER* 6.5 0.2 - - - -
328B GLY* 5.6 0.2 - - - -
331B ASN 4.2 0.2 - - - -
332B ILE* 1.3 75.1 - - - +
334B GLU* 1.3 65.5 + - - +
335B MET* 3.0 5.4 - - - +
336B VAL* 2.9 16.4 + - + +
337B THR* 3.1 22.9 + - - +
2G NAG 2.6 37.9 + - - -
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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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175A THR* 4.0 38.5 + - + +
176A VAL* 4.0 3.3 - - - +
177A PRO* 3.9 3.7 - - - +
245B TRP* 3.5 18.1 - - + -
250B HIS* 3.7 4.0 - - - -
332B ILE* 3.8 10.6 - - + +
333B ASN* 1.3 78.6 + - - +
335B MET* 1.3 64.9 + - - +
337B THR* 3.8 7.0 - - - -
338B PHE* 3.1 47.0 + - + +
339B GLY 4.0 0.2 + - - -
2G NAG 2.8 43.8 + - - -
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Residues in contact with MET 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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175A THR* 5.2 17.3 + - + +
320B LEU* 3.6 20.0 - - + +
323B LEU* 4.5 18.8 - - + +
324B SER* 3.7 29.6 - - - -
327B PRO* 4.5 12.7 - - + +
333B ASN* 3.0 2.0 + - - +
334B GLU* 1.3 80.9 - - - +
336B VAL* 1.3 56.7 + - - +
338B PHE* 6.2 0.4 - - + -
339B GLY* 3.0 30.2 + - - +
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Residues in contact with VAL 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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301B THR* 4.1 17.5 - - + +
304B LEU* 4.2 11.0 - - + -
305B VAL* 3.7 20.2 - - + -
308B MET* 4.7 2.0 - - + -
320B LEU* 4.4 7.9 - - + -
324B SER* 3.4 27.8 - - - +
333B ASN* 2.9 10.4 + - + +
335B MET* 1.3 75.8 - - - +
337B THR* 1.3 67.3 + - - +
338B PHE 2.9 3.2 + - - -
340B MET* 3.0 42.9 + - + +
342B ILE* 3.4 23.6 - - + -
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Residues in contact with THR 337 (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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245B TRP* 3.8 14.9 - - + -
298B SER* 3.5 13.7 - - - +
333B ASN* 3.1 38.3 + - - +
334B GLU* 3.8 1.7 - - - -
336B VAL* 1.3 75.0 - - - +
338B PHE* 1.3 74.0 + - - +
341B PRO* 3.6 0.3 - - - +
342B ILE* 2.7 35.0 + - + -
343B VAL* 2.9 24.8 + - - +
352B PHE* 3.9 18.6 - - + -
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Residues in contact with PHE 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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245B TRP* 3.5 24.5 - + - -
248B GLY* 3.5 29.4 - - - -
334B GLU* 3.1 32.1 + - + +
335B MET* 6.2 0.9 - - + -
336B VAL 3.0 0.4 - - - -
337B THR* 1.3 91.4 + - - +
339B GLY* 1.3 62.3 + - - +
341B PRO* 3.5 12.6 - - - +
343B VAL* 3.7 25.6 - - + -
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Residues in contact with GLY 339 (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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320B LEU* 4.0 11.2 - - - +
335B MET* 3.0 27.0 + - - +
338B PHE* 1.3 77.5 - - - +
340B MET* 1.3 67.7 + - - +
341B PRO* 3.2 5.3 - - - +
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Residues in contact with MET 340 (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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304B LEU* 4.0 18.4 - - + -
308B MET* 3.5 31.0 - - - +
316B GLN* 4.3 11.6 - - - +
317B LEU* 4.1 11.5 - - + +
320B LEU* 3.4 18.9 - - + +
336B VAL* 3.0 31.1 + - + +
339B GLY* 1.3 73.4 - - - +
341B PRO* 1.3 75.2 - - + +
342B ILE* 3.8 3.6 - - + +
348B LEU* 3.3 40.2 - - + -
419B LEU* 5.8 2.0 - - + -
422B TRP* 3.5 27.6 + - + +
426B LYS* 4.5 0.9 + - - -
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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