Contacts of the helix formed by residues 277 - 288 (chain A) in PDB entry 2QNJ
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 SER 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU* 2.7 35.1 + - - -
275A TYR 3.5 3.6 + - - -
276A MET* 1.3 73.4 - - - +
278A THR* 1.3 63.2 + - - +
279A ASP* 3.7 5.6 + - - -
280A CYS* 2.9 19.1 + - - +
281A GLU* 3.0 17.0 + - - +
306A TRP* 3.7 3.6 + - - -
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Residues in contact with THR 278 (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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276A MET 3.7 3.1 + - - +
277A SER* 1.3 73.1 - - - +
279A ASP* 1.3 60.8 + - - +
281A GLU* 3.4 18.7 + - - +
282A ASN* 3.0 37.9 + - - +
350B SER 4.0 10.7 + - - -
351B LYS* 3.5 19.6 + - - +
352B MET* 4.1 19.0 - - + +
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Residues in contact with ASP 279 (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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277A SER* 3.1 5.4 - - - +
278A THR* 1.3 77.0 + - - +
280A CYS* 1.3 65.4 + - - +
282A ASN* 3.0 16.6 + - - +
283A LEU* 2.9 23.2 + - - +
304A ASP* 4.9 1.7 - - - +
305A ARG* 3.2 46.6 + - - +
306A TRP* 3.9 24.4 + - + +
350B SER 4.6 4.0 - - - +
351B LYS* 3.3 22.6 + - - +
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Residues in contact with CYS 280 (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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152A GLU* 3.9 2.9 - - - +
243A LEU* 4.7 9.1 - - - +
247A VAL* 3.9 33.9 - - - -
276A MET* 3.8 22.2 - - + -
277A SER* 2.9 23.6 + - - +
279A ASP* 1.3 74.2 - - - +
281A GLU* 1.3 61.9 + - - +
283A LEU* 3.2 5.7 + - - +
284A LEU* 3.0 27.1 + - - +
306A TRP* 3.4 26.0 - - - +
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Residues in contact with GLU 281 (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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270A TYR* 4.9 0.9 + - - -
272A ILE* 3.8 43.4 - - + +
276A MET* 4.2 13.9 - - - +
277A SER 3.0 12.5 + - - +
278A THR* 3.6 23.0 - - - +
279A ASP 3.2 0.2 - - - -
280A CYS* 1.3 75.9 - - - +
282A ASN* 1.3 65.8 + - - +
284A LEU* 3.3 9.6 + - - +
285A LYS* 3.2 19.8 + - - +
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Residues in contact with ASN 282 (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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278A THR* 3.0 32.1 + - - +
279A ASP* 3.0 17.8 + - - +
281A GLU* 1.3 77.4 - - - +
283A LEU* 1.3 67.0 + - - +
285A LYS* 3.1 17.8 + - - +
286A ARG* 3.5 14.4 + - - +
304A ASP* 5.4 1.1 - - - +
305A ARG* 5.9 0.4 - - - +
350B SER* 4.5 8.1 + - - -
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Residues in contact with LEU 283 (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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159A PHE* 4.1 7.9 - - + -
243A LEU* 3.4 27.6 - - + -
279A ASP 2.9 12.5 + - - +
280A CYS* 3.6 10.1 - - - +
282A ASN* 1.3 76.8 - - - +
284A LEU* 1.3 62.6 + - - +
286A ARG* 3.0 21.5 + - + +
287A PHE* 3.4 26.5 - - + -
301A ILE* 3.9 15.3 - - + -
304A ASP* 3.6 39.4 + - + +
306A TRP* 4.0 23.3 - - + -
307A ILE* 4.2 6.3 - - + -
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Residues in contact with LEU 284 (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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240A GLY* 3.3 27.6 - - - +
243A LEU* 3.8 22.4 - - + -
244A TYR* 4.0 21.3 - - + +
247A VAL* 5.1 0.4 - - + -
270A TYR* 3.8 22.6 + - + +
272A ILE* 4.8 0.7 - - + -
276A MET* 3.8 35.9 - - + -
280A CYS* 3.0 18.2 + - - +
281A GLU* 3.5 9.2 - - - +
282A ASN 3.2 0.2 - - - -
283A LEU* 1.3 75.3 - - - +
285A LYS* 1.3 62.8 + - - +
287A PHE* 3.1 6.8 + - - -
288A LEU* 3.0 36.2 + - + +
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Residues in contact with LYS 285 (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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270A TYR* 4.1 8.7 - - - +
281A GLU* 3.2 10.5 + - + +
282A ASN* 3.1 14.4 + - - +
283A LEU 3.1 1.0 - - - -
284A LEU* 1.3 78.1 - - - +
286A ARG* 1.3 55.7 - - - +
287A PHE 3.5 0.2 - - - -
288A LEU 4.4 4.7 - - - +
289A VAL* 3.1 22.4 - - - +
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Residues in contact with ARG 286 (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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282A ASN 3.8 11.9 - - - +
283A LEU* 3.0 15.2 + - + +
285A LYS* 1.3 80.0 - - - +
287A PHE* 1.3 60.1 + - - +
289A VAL* 3.7 7.4 - - - +
296A GLY* 3.1 36.0 + - - -
300A GLN* 3.7 37.4 + - - +
301A ILE* 3.9 27.0 - - + +
303A LYS* 4.7 1.0 - - - +
304A ASP* 3.3 39.6 + - - +
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Residues in contact with PHE 287 (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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159A PHE* 3.9 22.2 - + - -
163A VAL* 4.7 3.4 - - + -
236A VAL* 3.0 33.4 - - + +
237A TRP* 3.8 7.1 - - - -
239A LEU* 3.9 15.3 - - + -
240A GLY* 3.3 28.7 - - - +
243A LEU* 4.5 2.9 - - + -
283A LEU* 3.4 43.5 - - + -
284A LEU* 3.1 7.8 + - - +
286A ARG* 1.3 78.0 - - - +
288A LEU* 1.3 58.9 + - - +
289A VAL 2.9 11.7 + - - -
295A ARG* 3.0 21.3 - - - -
298A LEU* 4.1 13.0 - - + -
301A ILE* 3.5 32.1 - - + -
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Residues in contact with LEU 288 (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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237A TRP* 3.5 53.1 - - + +
240A GLY* 3.6 20.4 - - - +
241A VAL* 3.8 7.2 - - + +
244A TYR* 5.3 0.4 - - + -
252A PRO* 4.7 7.0 - - + -
253A PHE* 4.3 11.4 - - + -
268A GLY* 4.9 4.6 - - - +
270A TYR* 3.7 48.0 + - + +
284A LEU* 3.0 27.2 + - + +
285A LYS* 4.4 5.1 - - - +
287A PHE* 1.3 74.0 - - - +
289A VAL* 1.3 62.2 + - - +
290A LEU* 4.0 2.6 + - - +
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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