Contacts of the helix formed by residues 276 - 287 (chain A) in PDB entry 3DAE
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 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLU* 2.5 42.7 + - - -
274A PHE 3.5 4.0 + - - -
275A LEU* 1.3 74.4 - - - +
277A PRO* 1.3 67.9 - - - +
278A GLY 3.7 1.6 + - - -
279A ALA* 3.2 16.7 + - - +
280A ALA* 2.8 31.9 + - - +
305A TRP* 3.6 2.8 + - - -
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Residues in contact with PRO 277 (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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275A LEU 3.7 1.3 - - - +
276A SER* 1.3 89.6 - - - +
278A GLY* 1.3 57.6 - - - +
280A ALA* 4.0 5.6 - - + +
281A GLY* 2.9 24.9 + - - -
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Residues in contact with GLY 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 SER* 3.1 2.2 + - - -
277A PRO* 1.3 83.7 - - - +
279A ALA* 1.3 56.5 + - - +
281A GLY* 4.0 0.9 - - - -
282A LEU* 3.2 26.0 + - - +
303A ASP* 4.4 2.3 - - - +
305A TRP* 3.6 32.8 - - - +
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Residues in contact with ALA 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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151A GLU* 4.0 3.1 - - - +
242A LEU* 5.7 0.7 - - + -
246A LEU* 3.7 29.8 - - + -
275A LEU* 4.9 3.1 - - + -
276A SER* 3.2 22.7 + - - +
278A GLY* 1.3 74.8 - - - +
280A ALA* 1.3 69.4 + - - +
282A LEU* 3.2 2.9 + - - +
283A ILE* 2.9 29.2 + - + +
305A TRP* 3.6 19.6 - - + +
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Residues in contact with ALA 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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271A LEU* 3.9 23.0 - - + +
272A PRO 5.5 0.7 - - - +
275A LEU* 4.1 24.6 - - + +
276A SER 2.8 22.6 + - - +
277A PRO* 4.0 5.8 - - + +
279A ALA* 1.3 72.2 - - - +
281A GLY* 1.3 64.3 + - - +
283A ILE* 3.3 1.7 + - - +
284A LYS* 2.9 25.1 + - - +
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Residues in contact with GLY 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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277A PRO 2.9 20.5 + - - -
278A GLY* 4.0 1.8 - - - -
280A ALA* 1.3 76.9 - - - +
282A LEU* 1.3 57.4 + - - +
284A LYS* 3.5 6.8 + - - +
285A ARG* 3.4 35.2 + - - +
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Residues in contact with LEU 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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158A PHE* 3.8 21.8 - - + -
242A LEU* 4.2 1.8 - - + -
278A GLY 3.2 16.7 + - - +
279A ALA* 3.2 6.9 + - - +
281A GLY* 1.3 72.8 - - - +
283A ILE* 1.3 66.3 + - - +
285A ARG* 3.4 14.5 + - - +
286A MET* 3.0 45.3 + - + +
295A ILE* 4.5 6.7 - - + -
300A ILE* 4.4 17.9 - - + -
303A ASP* 3.3 35.4 + - + +
305A TRP* 4.0 20.4 - - + -
306A PHE* 4.4 6.7 - - + -
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Residues in contact with ILE 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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239A GLY 4.3 6.1 - - - +
242A LEU* 3.8 27.6 - - + -
243A TYR* 3.8 32.1 - - + +
246A LEU* 4.3 11.0 - - + -
247A CYS* 5.5 0.2 - - - -
269A TYR* 4.5 0.4 - - + -
271A LEU* 4.0 13.9 - - + -
275A LEU* 4.3 22.2 - - + -
279A ALA 2.9 21.0 + - - +
280A ALA 3.8 2.5 - - - +
282A LEU* 1.3 74.5 - - - +
284A LYS* 1.3 66.4 + - - +
286A MET* 2.9 20.4 + - - +
287A LEU* 3.2 34.9 + - + +
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Residues in contact with LYS 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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269A TYR* 3.3 21.7 + - - +
271A LEU* 3.9 23.4 - - + +
280A ALA 2.9 18.4 + - - +
281A GLY* 3.7 9.9 - - - +
282A LEU 3.3 0.4 - - - -
283A ILE* 1.3 77.2 - - - +
285A ARG* 1.3 62.0 + - + +
286A MET 3.5 0.3 + - - -
287A LEU 3.8 2.1 + - - +
288A ILE* 3.3 22.9 - - + +
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Residues in contact with ARG 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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281A GLY 3.4 19.6 + - - +
282A LEU* 3.4 12.1 + - - +
283A ILE 3.1 0.8 - - - -
284A LYS* 1.3 81.9 - - + +
286A MET* 1.3 57.7 + - - +
287A LEU 3.5 0.2 - - - -
288A ILE* 3.7 15.2 - - - +
293A ASN 5.7 2.0 - - - +
294A ARG* 3.8 0.7 - - - +
295A ILE* 3.1 63.3 + - + +
299A GLU* 5.5 1.4 + - - +
303A ASP* 2.9 30.7 + - - +
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Residues in contact with MET 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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158A PHE* 3.8 17.7 - - - -
235A VAL* 4.0 13.4 - - + +
236A TRP* 3.7 12.3 - - - -
238A CYS* 4.5 1.1 - - - -
239A GLY* 3.8 28.0 - - - -
242A LEU* 3.4 29.6 - - + -
282A LEU* 3.0 38.1 - - + +
283A ILE* 2.9 10.8 + - - +
285A ARG* 1.3 78.4 - - - +
287A LEU* 1.3 59.5 + - - +
288A ILE 3.3 6.6 + - - -
294A ARG* 3.5 19.4 - - - -
295A ILE* 3.5 20.0 - - + -
300A ILE* 4.0 15.5 - - + -
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Residues in contact with LEU 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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236A TRP* 3.3 54.6 - - + +
239A GLY 4.1 5.2 - - - +
240A VAL* 3.9 17.5 - - + +
243A TYR* 5.0 0.2 - - + -
251A PRO* 4.6 15.3 - - + -
252A PHE* 4.7 2.0 - - + -
267A GLY* 5.1 3.8 - - - -
269A TYR* 3.6 52.1 + - + +
283A ILE* 3.2 27.3 + - + +
284A LYS 3.8 1.6 + - - +
286A MET* 1.3 79.9 - - + +
288A ILE* 1.3 68.8 + - - +
289A VAL 4.0 1.0 + - - -
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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