Contacts of the helix formed by residues 287 - 299 (chain A) in PDB entry 3QN3
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 ASP 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A PHE* 4.4 11.9 - - + -
251A TYR* 2.6 28.3 + - - +
260A SER* 2.5 30.5 + - - -
283A LEU* 4.0 3.8 - - + +
284A ALA* 3.1 14.8 + - + +
286A ASN* 1.3 76.2 + - - +
288A PHE* 1.3 62.6 + - - +
289A GLU* 4.1 3.6 + - - +
290A GLY* 3.0 20.0 + - - -
291A TRP* 3.1 22.7 + - - -
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Residues in contact with PHE 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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46A LYS* 5.9 1.1 - - - -
285A GLU 3.4 20.9 - - - -
286A ASN* 3.1 30.9 + - + -
287A ASP* 1.3 72.9 - - - +
289A GLU* 1.3 63.7 - - + +
291A TRP* 3.1 5.5 + - - +
292A ILE* 3.1 27.3 + - + +
309A LEU* 4.7 8.5 - - + -
325A MET* 3.3 35.1 - - + +
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Residues in contact with GLU 289 (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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287A ASP* 3.4 3.7 + - - +
288A PHE* 1.3 78.4 - - + +
290A GLY* 1.3 61.8 + - - +
292A ILE* 3.2 23.0 + - - +
293A LYS* 3.1 45.3 + - + +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 4.1 11.6 - - - -
264A ILE* 3.8 1.1 - - - +
283A LEU* 3.0 23.5 - - - +
287A ASP* 3.0 24.1 + - - -
289A GLU* 1.3 75.5 - - - +
291A TRP* 1.3 57.0 + - - +
293A LYS* 3.3 10.2 + - - +
294A LEU 2.8 25.6 + - - -
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Residues in contact with TRP 291 (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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279A ILE 5.5 0.7 - - - -
281A ASP* 3.7 22.9 - - - -
282A GLY 4.1 5.2 - - - -
283A LEU* 3.1 35.0 + - + +
284A ALA 2.9 24.4 + - - -
287A ASP 3.1 25.7 + - - -
288A PHE* 3.1 8.0 + - - +
290A GLY* 1.3 72.7 - - - +
292A ILE* 1.3 58.4 + - - +
294A LEU* 3.7 18.7 - - + +
295A THR* 2.6 39.9 + - - -
304A LEU* 4.4 9.0 - - + -
305A VAL 3.7 21.8 - - - -
309A LEU* 3.6 35.3 - - + +
325A MET* 3.9 17.7 - - + -
326A ALA* 3.7 33.2 - - + -
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Residues in contact with ILE 292 (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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288A PHE* 3.1 16.1 + - + +
289A GLU* 3.2 26.9 + - - +
291A TRP* 1.3 77.3 - - - +
293A LYS* 1.3 64.5 + - + +
295A THR* 3.7 2.1 - - - -
296A GLU* 3.0 42.8 + - + +
323A LYS* 3.5 32.8 - - + +
324A LYS* 4.1 11.5 - - + +
325A MET* 4.0 16.6 - - + -
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Residues in contact with LYS 293 (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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260A SER* 4.8 3.4 - - - -
261A GLU* 2.3 44.6 + - - +
264A ILE* 3.8 14.8 - - + +
289A GLU* 3.1 41.6 + - + +
290A GLY* 3.7 10.7 - - - +
292A ILE* 1.3 76.3 - - + +
294A LEU* 1.3 59.4 - - - +
296A GLU* 3.3 16.3 + - - +
297A LYS* 2.8 31.4 + - - +
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Residues in contact with LEU 294 (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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264A ILE* 3.4 28.8 - - + +
267A TYR* 4.0 18.2 - - + -
279A ILE* 5.9 0.4 - - + -
282A GLY* 4.5 13.9 - - - -
283A LEU* 3.8 23.1 - - + -
290A GLY 2.8 20.9 + - - +
291A TRP* 3.7 24.9 - - + +
293A LYS* 1.3 72.0 - - - +
295A THR* 1.3 58.6 + - - +
297A LYS* 3.2 3.0 + - - -
298A LEU* 2.9 43.5 + - + -
304A LEU* 3.9 25.7 - - + +
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Residues in contact with THR 295 (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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291A TRP* 2.6 25.1 + - - -
292A ILE 3.7 0.7 - - - -
294A LEU* 1.3 77.0 - - - +
296A GLU* 1.3 57.9 + - - +
299A GLY* 2.7 34.7 + - - -
300A ASN* 5.4 1.7 + - - -
304A LEU* 3.7 13.2 - - + +
324A LYS* 3.4 23.2 + - + +
326A ALA* 2.8 43.8 + - - +
327A ASN* 5.3 2.5 - - + -
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Residues in contact with GLU 296 (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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292A ILE* 3.0 39.1 + - + +
293A LYS* 3.5 14.6 - - - +
295A THR* 1.3 78.6 - - - +
297A LYS* 1.3 62.2 + - - +
299A GLY 4.4 1.0 + - - -
300A ASN* 5.2 6.8 + - - +
324A LYS* 6.0 4.5 - - + +
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Residues in contact with LYS 297 (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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264A ILE* 3.7 28.3 - - + -
265A GLU* 3.2 26.5 + - - +
268A VAL* 3.7 23.0 - - + +
293A LYS 2.8 20.8 + - - +
294A LEU 3.7 2.9 - - - +
296A GLU* 1.3 78.4 - - + +
298A LEU* 1.3 63.3 + - + +
301A LYS* 5.7 0.7 - - - +
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Residues in contact with LEU 298 (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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264A ILE 4.7 0.4 - - - +
267A TYR* 3.8 31.6 - - + +
268A VAL* 4.0 33.9 - - + +
271A CYS* 4.6 6.3 - - + -
279A ILE* 5.0 0.4 - - + -
294A LEU* 2.9 25.7 + - + +
297A LYS* 1.3 81.0 - - + +
299A GLY* 1.3 56.7 + - - +
300A ASN 3.0 4.7 - - - -
301A LYS* 2.8 54.3 + - + +
302A ILE* 3.0 36.0 + - + +
304A LEU* 4.3 6.1 - - + -
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Residues in contact with GLY 299 (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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295A THR* 2.7 33.9 + - - -
296A GLU 4.4 0.4 + - - -
297A LYS 3.8 0.6 - - - -
298A LEU* 1.3 69.5 - - - +
300A ASN* 1.3 61.0 + - - +
301A LYS 3.5 0.2 - - - -
302A ILE 3.7 3.1 - - - +
304A LEU* 3.8 10.4 - - - +
327A ASN* 2.9 31.4 + - - +
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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