Contacts of the helix formed by residues 307 - 312 (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 GLY 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ALA 2.9 10.6 + - - -
304B LEU* 3.2 4.4 + - - -
305B VAL 3.2 0.2 - - - -
306B VAL* 1.3 75.9 - - - +
308B MET* 1.3 57.5 + - - +
310B LEU* 3.9 4.9 - - - -
311B PHE* 3.2 22.5 + - - +
312B ALA 3.8 1.6 + - - -
412B PHE* 3.7 20.2 - - - -
416B LEU* 4.5 2.5 - - - -
419B LEU* 3.2 28.0 - - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.2 21.3 + - + +
305B VAL* 3.8 23.6 - - + +
306B VAL 3.2 0.2 - - - -
307B GLY* 1.3 75.4 - - - +
309B LEU* 1.3 60.4 + - - +
310B LEU 2.9 10.0 + - - -
312B ALA* 2.9 32.5 + - + +
317B LEU* 4.1 28.9 - - + +
318B LYS* 4.4 6.2 - - - +
320B LEU* 3.8 13.5 - - + +
321B GLY* 3.2 32.5 - - - +
324B SER* 4.3 0.4 - - - +
336B VAL* 4.7 2.0 - - + -
340B MET* 3.5 29.6 - - - +
419B LEU* 4.4 9.4 - - + -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL 3.1 17.1 + - - +
306B VAL* 3.4 12.1 + - + +
308B MET* 1.3 76.7 - - - +
310B LEU* 1.3 71.5 + - + +
318B LYS* 5.7 4.3 - - - +
321B GLY* 3.8 24.2 - - - +
322B ARG* 4.9 5.8 - - + -
325B ILE* 4.1 23.8 - - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 2.9 34.9 + - + +
308B MET 2.9 0.4 - - - -
309B LEU* 1.3 94.1 - - + +
311B PHE* 1.3 89.8 + - + +
312B ALA 3.7 0.9 - - - -
412B PHE* 4.2 10.3 - - + -
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Residues in contact with PHE 311 (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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307B GLY* 3.2 14.0 + - - +
310B LEU* 1.3 108.9 - - + +
312B ALA* 1.3 59.9 + - - +
313B ARG* 3.2 8.9 + - - +
412B PHE* 4.2 13.0 - + - -
416B LEU* 4.1 31.9 - - + -
419B LEU* 5.2 4.1 - - + +
420B LYS* 4.4 27.3 - - + +
423B ASP* 4.2 4.7 - - - +
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Residues in contact with ALA 312 (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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307B GLY 3.8 1.4 + - - +
308B MET* 2.9 35.0 + - - +
310B LEU 3.7 1.0 - - - -
311B PHE* 1.3 74.4 - - - +
313B ARG* 1.3 64.6 + - - +
314B SER 3.8 3.5 - - - +
317B LEU* 4.0 5.8 - - + -
318B LYS* 3.8 31.7 - - - +
419B LEU* 4.8 2.5 - - + -
423B ASP* 3.1 19.3 - - - +
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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
------------------------------------------------------------
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