Contacts of the helix formed by residues 287 - 295 (chain P) in PDB entry 5D4D
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 287 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814M GLU* 3.2 22.9 - - + +
284P ARG* 5.4 0.4 - - - +
285P GLU 5.1 2.2 - - - +
286P PRO* 1.3 78.2 - - - +
288P TYR* 1.3 66.4 + - - +
289P GLU* 3.2 24.9 + - - +
290P GLU* 3.0 37.4 + - - +
291P ILE* 3.3 13.6 + - - +
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Residues in contact with TYR 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808M ARG* 6.4 1.1 - - + -
814M GLU* 3.4 30.3 + - + -
815M LEU 3.4 10.7 + - - -
816M LYS 3.8 0.2 - - - -
817M PRO* 3.2 35.8 - - + +
286P PRO 5.5 0.9 - - - -
287P THR* 1.3 76.9 - - - +
289P GLU* 1.3 60.7 + - - +
291P ILE* 3.7 1.9 + - + -
292P ALA* 2.9 26.3 + - - +
301P ALA* 3.8 27.4 - - + +
304P VAL* 3.6 27.0 - - + +
305P GLU* 3.3 45.8 - - + -
308P LEU* 4.2 19.1 - - + -
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Residues in contact with GLU 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809M GLY* 5.9 3.3 - - - -
814M GLU* 5.3 0.2 - - - +
287P THR* 3.1 19.1 + - - +
288P TYR* 1.3 81.3 + - - +
290P GLU* 1.3 59.9 + - + +
292P ALA* 3.1 6.8 + - + +
293P GLU* 2.9 42.5 + - + +
301P ALA* 3.3 26.4 - - + +
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Residues in contact with GLU 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278P LEU* 3.6 11.7 - - + +
282P LEU* 3.1 29.1 - - - +
284P ARG* 2.7 33.1 + - - -
286P PRO* 3.7 13.5 - - + -
287P THR* 3.0 37.2 + - - +
289P GLU* 1.3 75.7 - - + +
291P ILE* 1.3 58.2 + - - +
293P GLU* 3.5 10.3 + - - +
294P ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 291 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271P LEU* 4.5 13.2 - - + +
274P THR* 4.7 8.1 - - + -
275P ALA* 3.6 26.2 - - + -
278P LEU* 3.7 19.5 - - + -
286P PRO* 4.1 10.1 - - + +
287P THR 3.3 14.1 + - - +
288P TYR* 3.7 8.5 - - + +
290P GLU* 1.3 78.1 - - - +
292P ALA* 1.3 52.0 + - - +
294P ALA* 3.0 2.3 + - - -
295P MET* 2.6 49.3 + - + +
304P VAL* 3.6 34.3 - - + -
308P LEU* 4.7 11.9 - - + -
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Residues in contact with ALA 292 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288P TYR 2.9 20.2 + - - +
289P GLU* 3.1 9.6 + - + +
291P ILE* 1.3 77.6 - - - +
293P GLU* 1.3 58.5 + - + +
295P MET* 3.5 9.1 + - - +
296P GLY 3.1 21.5 - - - +
299P TRP 3.5 5.4 - - - +
300P ASP* 3.3 36.1 - - - +
301P ALA 3.7 1.8 - - - +
304P VAL* 4.0 7.0 - - - -
2001P MG 3.1 6.2 - - - -
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Residues in contact with GLU 293 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289P GLU* 2.9 27.2 + - + +
290P GLU* 3.8 7.9 - - - +
292P ALA* 1.3 75.7 - - + +
294P ALA* 1.3 59.1 + - - +
295P MET 3.1 1.1 - - - -
296P GLY* 3.0 20.4 + - - -
2001P MG 4.3 5.2 - - - -
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Residues in contact with ALA 294 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274P THR* 3.9 17.9 + - + +
278P LEU* 3.7 28.7 - - + -
290P GLU 2.9 19.0 + - - +
291P ILE 3.0 2.9 + - - +
293P GLU* 1.3 75.9 - - - +
295P MET* 1.3 61.1 + - - +
296P GLY 3.3 0.4 - - - -
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Residues in contact with MET 295 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P THR* 5.8 0.4 - - - +
270P LYS* 4.4 32.8 + - + -
271P LEU* 3.7 29.6 - - + -
274P THR* 3.1 38.8 - - + +
291P ILE* 2.6 33.1 + - + +
292P ALA 3.6 0.9 - - - +
293P GLU 3.1 0.6 - - - -
294P ALA* 1.3 75.6 - - - +
296P GLY* 1.3 59.2 + - - +
297P PRO* 4.2 2.3 - - - +
299P TRP* 3.5 55.2 - - + -
304P VAL* 4.6 0.4 - - + -
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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