Contacts of the helix formed by residues 276 - 282 (chain D) in PDB entry 3EDC
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 THR 276 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D HIS* 3.9 18.2 - - + +
75D ALA* 3.7 33.9 - - + +
78D GLN* 3.3 17.3 - - - +
247D ASP* 3.2 24.3 + - - +
248D GLN* 5.0 3.0 + - + +
274D ASP* 3.4 11.8 + - + +
275D ASP* 1.3 84.2 - - - +
277D GLU* 1.3 67.3 + - - +
278D ASP* 3.3 2.4 - - - +
279D SER* 3.1 18.1 + - - -
282D TYR* 5.0 1.7 + - - -
293D PHE* 3.8 11.4 - - + -
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA* 5.6 6.3 - - + +
74C HIS* 6.1 2.7 - - + -
221C SER* 5.7 9.2 - - - -
222C ALA* 5.4 1.8 - - + +
223C MET* 6.0 4.2 - - + +
248C GLN* 5.8 2.2 - - - +
74D HIS* 5.7 0.4 - - - +
78D GLN* 2.9 30.6 + - + +
275D ASP* 4.5 1.2 - - - +
276D THR* 1.3 73.4 - - - +
278D ASP* 1.3 67.2 + - - +
279D SER 3.2 1.4 + - - -
280D SER* 3.8 14.0 + - - -
281D CYS* 5.7 0.2 - - - -
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Residues in contact with ASP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 2.6 32.4 + - - -
222C ALA* 3.8 19.3 + - - +
248C GLN* 3.1 22.5 + - - +
251C LEU* 3.8 21.5 - - + +
278C ASP* 4.2 8.3 - - - +
282C TYR* 4.9 2.4 + - - -
74D HIS* 4.3 5.4 + - + -
276D THR* 3.3 1.4 - - - +
277D GLU* 1.3 79.6 - - - +
279D SER* 1.3 54.2 + - - +
280D SER 3.2 0.9 - - - -
281D CYS* 2.8 31.0 + - - +
282D TYR* 3.4 19.7 + - + +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ASP* 2.6 43.6 + - - +
275D ASP* 4.0 9.0 - - - -
276D THR* 3.1 16.3 + - - -
277D GLU 3.2 0.2 + - - -
278D ASP* 1.3 77.6 - - - +
280D SER* 1.3 61.2 + - - +
281D CYS 3.0 1.1 + - - -
282D TYR* 3.2 22.1 + - - +
286D LEU* 3.1 35.4 + - - +
288D THR* 4.9 0.2 - - - -
326D ARG* 4.1 4.7 - - - -
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Residues in contact with SER 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLN* 3.2 15.3 + - - +
235B GLU* 3.3 34.4 + - - +
223C MET* 5.3 2.1 - - - +
255C ARG* 2.8 27.2 + - - -
275D ASP* 5.4 0.2 - - - -
276D THR 4.8 0.4 + - - -
277D GLU 3.8 12.4 + - - -
279D SER* 1.3 78.5 - - - +
281D CYS* 1.3 57.8 + - - +
282D TYR 3.5 0.4 - - - -
285D PRO* 3.3 14.2 - - - +
326D ARG* 3.8 22.1 - - - +
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Residues in contact with CYS 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLN* 3.7 23.8 - - - -
222C ALA* 3.6 43.5 - - + -
223C MET* 3.7 4.3 - - - -
226C PHE* 4.0 12.8 - - - -
251C LEU* 3.6 17.0 - - + +
252C GLY* 4.2 8.1 - - - -
255C ARG* 3.6 20.2 - - - +
277D GLU 5.7 0.2 - - - -
278D ASP 2.8 12.0 + - - +
280D SER* 1.3 81.9 + - - +
282D TYR* 1.3 65.0 + - - +
283D ILE* 4.5 0.7 - - - +
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU* 3.9 17.7 - - + -
255C ARG* 3.6 5.0 - - - -
278C ASP* 4.9 4.4 + - - -
282C TYR* 5.6 0.7 - + - -
74D HIS* 5.3 2.1 - - - -
247D ASP* 3.3 32.4 + - - +
248D GLN* 4.1 8.7 + - - +
251D LEU* 3.7 37.3 - - + +
254D MET* 4.0 16.4 - - + -
276D THR* 5.0 1.7 + - - -
278D ASP* 3.5 29.4 - - + +
279D SER* 3.2 23.2 + - - +
281D CYS* 1.3 84.2 - - - +
283D ILE* 1.3 59.8 + - - +
284D PRO 3.3 11.7 - - - +
285D PRO* 2.9 22.0 - - - +
286D LEU* 3.7 30.7 - - + +
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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