Contacts of the helix formed by residues 279 - 292 (chain N) in PDB entry 3Q84
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 279 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246M LYS* 4.8 1.6 - - - +
79N SER* 2.8 12.2 + - - +
80N LEU* 5.0 2.9 - - - -
277N GLY 3.8 4.2 + - - +
278N ALA* 1.3 76.2 - - - +
280N ALA* 1.3 70.7 + - - +
281N GLN* 3.1 23.0 + - - +
282N GLU* 4.1 23.2 + - + +
283N ASP* 3.5 22.3 + - - +
285N ARG* 4.4 7.6 + - - -
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Residues in contact with ALA 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M GLU* 4.2 22.9 - - + -
242M LEU* 3.9 27.4 - - + +
243M VAL* 4.3 16.2 - - + +
246M LYS* 5.9 2.8 - - - +
80N LEU* 5.0 2.5 - - - +
278N ALA 4.4 0.2 - - - -
279N ASP* 1.3 73.4 + - - +
281N GLN* 1.3 67.2 + - + +
283N ASP* 3.1 7.1 + - - +
284N LEU* 3.1 25.2 + - - +
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Residues in contact with GLN 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M GLU* 3.5 23.4 + - - +
279N ASP* 3.1 13.7 + - - +
280N ALA* 1.3 76.5 - - + +
282N GLU* 1.3 53.7 + - - +
284N LEU* 3.1 16.7 + - - +
285N ARG* 2.7 54.6 + - + +
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Residues in contact with GLU 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N SER* 3.6 17.7 + - - -
82N ARG* 5.0 6.5 + - - -
277N GLY 5.7 0.2 - - - +
279N ASP* 3.7 19.6 + - + +
280N ALA 3.3 0.6 - - - -
281N GLN* 1.3 77.9 - - - +
283N ASP* 1.3 71.9 + - - +
285N ARG* 3.7 31.1 - - - +
286N TRP* 2.8 29.6 + - + +
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Residues in contact with ASP 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M LEU* 4.1 13.5 - - + +
77N TYR* 3.9 22.8 - - + +
78N GLY* 3.9 9.4 - - - -
79N SER* 3.0 38.0 + - - -
80N LEU* 3.3 21.0 + - - +
279N ASP 3.5 10.0 + - - +
280N ALA 3.1 8.9 + - - +
282N GLU* 1.3 86.0 - - - +
284N LEU* 1.3 59.3 + - - +
286N TRP* 3.2 9.2 + - - +
287N PHE* 2.9 28.1 + - - +
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Residues in contact with LEU 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ARG* 4.2 1.3 - - - +
235M GLN* 3.5 46.5 - - + +
238M GLU* 3.9 27.8 - - + -
239M GLU* 3.5 33.7 - - + +
242M LEU* 4.3 9.2 - - + -
77N TYR* 4.8 2.2 - - - +
280N ALA 3.1 13.8 + - - +
281N GLN* 3.2 21.3 - - - +
283N ASP* 1.3 72.3 - - - +
285N ARG* 1.3 60.3 + - - +
287N PHE* 3.0 4.7 + - + +
288N ARG* 2.8 26.3 + - - +
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Residues in contact with ARG 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279N ASP* 4.4 6.5 + - - -
281N GLN* 2.7 30.3 + - + +
282N GLU* 3.7 44.4 - - - +
284N LEU* 1.3 70.9 - - - +
286N TRP* 1.3 63.7 + - - +
288N ARG* 3.3 12.4 + - - +
289N SER* 3.2 23.7 + - - -
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Residues in contact with TRP 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N TYR* 3.3 44.4 - + + -
78N GLY* 5.4 5.4 - - - -
282N GLU* 2.8 19.4 + - + +
283N ASP* 3.4 7.0 - - - +
284N LEU 3.1 0.2 - - - -
285N ARG* 1.3 77.0 - - - +
287N PHE* 1.3 72.2 + + - +
289N SER* 3.4 6.4 + - - -
290N THR* 3.1 58.9 + - + +
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Residues in contact with PHE 287 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ARG* 4.1 19.5 - - + -
28M THR* 3.7 22.0 - - - -
31M ARG* 3.5 48.0 - - + -
231M PHE* 4.3 7.0 - + - -
235M GLN* 3.9 11.0 - - - +
77N TYR* 4.3 20.0 - + + +
283N ASP 2.9 13.3 + - - +
284N LEU* 3.0 7.2 + - - +
286N TRP* 1.3 83.5 - + - +
288N ARG* 1.3 67.1 + - - +
290N THR* 4.4 1.1 - - - -
291N SER* 2.9 52.8 + - - -
292N GLY 3.1 4.7 + - - -
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Residues in contact with ARG 288 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M TRP* 6.0 0.2 - - - -
228M GLU* 2.7 43.0 + - - -
231M PHE* 3.9 29.0 - - + -
235M GLN* 4.4 2.7 - - - +
284N LEU 2.8 12.2 + - - +
285N ARG* 3.5 16.4 - - - +
287N PHE* 1.3 75.3 - - - +
289N SER* 1.3 58.6 + - - +
292N GLY* 3.0 33.0 + - - +
293N PRO* 3.8 15.9 + - + +
294N GLY* 3.2 24.3 + - - +
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Residues in contact with SER 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285N ARG 3.2 13.4 + - - -
286N TRP* 3.8 6.9 + - - -
288N ARG* 1.3 79.7 - - - +
290N THR* 1.3 67.2 + - - +
294N GLY* 4.1 19.0 - - - +
295N MSE 3.7 15.9 - - - +
296N PRO* 5.5 1.2 - - - +
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Residues in contact with THR 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ARG* 4.8 2.1 + - - -
286N TRP* 3.1 59.7 + - + +
287N PHE* 4.3 1.2 + - - -
289N SER* 1.3 87.8 - - - +
291N SER* 1.3 67.4 + - - +
295N MSE 3.7 17.9 - - - +
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Residues in contact with SER 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.8 11.1 - - - +
24M ASN 4.6 0.2 - - - +
27M ARG* 2.6 51.4 + - - +
28M THR* 4.4 5.4 + - - -
287N PHE* 2.9 45.1 + - - -
290N THR* 1.3 81.7 + - - +
292N GLY* 1.3 55.7 + - - +
295N MSE 3.7 4.3 - - - -
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Residues in contact with GLY 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.4 16.3 - - - +
28M THR* 5.1 0.2 - - - -
231M PHE* 4.1 9.2 - - - -
287N PHE 3.1 4.3 + - - -
288N ARG 3.0 11.6 + - - -
290N THR 3.9 0.4 - - - -
291N SER* 1.3 78.6 - - - +
293N PRO* 1.4 68.8 - - - +
294N GLY 2.9 11.6 + - - -
295N MSE 3.0 18.2 + - - +
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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