Contacts of the helix formed by residues 333 - 338 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A TRP* 4.7 0.2 - - - -
296A GLY 3.9 5.4 - - - +
298A SER* 2.6 44.2 + - - +
301A THR* 3.1 37.2 + - + -
324A SER* 6.0 1.6 - - - -
327A PRO* 5.8 0.4 - - - -
328A GLY* 5.5 0.2 - - - -
332A ILE* 1.3 76.5 - - - +
334A GLU* 1.3 66.3 + - - +
335A MET* 3.2 4.5 - - - +
336A VAL* 2.9 15.3 + - + +
337A THR* 3.0 18.7 + - - +
2E NAG 2.7 33.9 + - - -
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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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245A TRP* 3.4 29.3 - - - -
250A HIS* 4.4 1.0 + - - -
332A ILE* 3.8 17.5 - - + +
333A ASN* 1.3 76.7 + - - +
335A MET* 1.3 65.2 + - - +
336A VAL 2.7 2.3 + - - -
337A THR* 3.1 3.9 + - - -
338A PHE* 3.0 41.3 + - + +
175B THR* 3.7 43.2 - - + +
176B VAL 4.3 0.2 - - - +
177B PRO* 3.8 12.0 - - - +
2E NAG 2.6 33.5 + - - -
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Residues in contact with MET 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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320A LEU* 3.6 21.9 - - + +
323A LEU* 3.8 37.2 - - + +
324A SER* 3.8 20.6 - - - +
327A PRO* 4.8 10.5 - - + -
333A ASN 3.2 1.7 - - - -
334A GLU* 1.3 78.7 - - + +
336A VAL* 1.3 56.8 + - - +
339A GLY* 2.9 27.5 - - - +
175B THR* 5.3 14.5 - - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR* 4.3 19.3 - - + +
304A LEU* 4.9 5.8 - - + -
305A VAL* 3.8 22.4 - - + -
308A MET* 4.9 2.9 - - + -
320A LEU* 4.8 11.4 - - + -
324A SER* 3.8 26.0 - - - +
333A ASN* 2.9 10.4 + - + +
334A GLU 2.7 4.4 + - - -
335A MET* 1.3 72.5 - - + +
337A THR* 1.3 71.1 + - - +
338A PHE 3.0 2.6 + - - -
339A GLY 3.3 6.9 + - - -
340A MET* 3.3 29.0 + - - +
342A ILE* 3.4 24.6 - - + +
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Residues in contact with THR 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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245A TRP* 3.9 14.1 - - + -
298A SER* 3.2 31.2 - - - +
301A THR* 4.9 1.3 - - - +
333A ASN* 3.0 27.2 + - - +
334A GLU* 3.1 22.9 + - - -
336A VAL* 1.3 73.1 - - - +
338A PHE* 1.3 62.8 + - - +
341A PRO* 3.7 0.2 - - - +
342A ILE* 3.0 19.1 + - + -
343A VAL* 2.8 40.9 + - - +
352A PHE* 4.2 11.7 - - + -
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Residues in contact with PHE 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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245A TRP* 4.5 16.2 - + - -
248A GLY* 3.3 27.8 - - - -
334A GLU* 3.0 23.4 + - + +
337A THR* 1.3 84.4 + - - +
339A GLY* 1.3 60.1 + - - +
340A MET 3.6 0.9 - - - -
341A PRO* 3.2 18.2 - - - +
343A VAL* 3.0 38.4 - - + -
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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