Contacts of the helix formed by residues 269 - 277 (chain P) in PDB entry 5IYB
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 ARG 269 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240M VAL 5.9 0.6 + - - -
243M ASP* 5.4 1.4 + - - +
268P ILE* 1.3 72.5 - - - +
270P LEU* 1.3 63.0 + - - +
271P GLU* 3.1 38.3 + - - +
272P GLY* 3.9 17.9 - - - +
273P LEU* 3.6 18.5 + - - +
335P PHE* 3.0 38.0 + - + +
337P LYS* 3.6 35.4 - - - +
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Residues in contact with LEU 270 (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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247M GLY* 6.1 1.1 - - - -
268P ILE* 3.6 37.2 + - + +
269P ARG* 1.3 74.4 - - - +
271P GLU* 1.3 66.9 + - - +
272P GLY 3.2 1.8 - - - -
273P LEU* 3.3 9.0 + - + +
274P VAL* 2.9 32.2 + - - +
283P TYR* 3.8 39.0 - - + +
289P PRO 5.2 2.7 - - - +
291P LEU* 4.0 25.0 - - + +
304P ILE* 4.4 14.8 - - + +
305P PHE* 5.1 0.2 - - - -
306P VAL* 4.2 27.8 - - + +
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Residues in contact with GLU 271 (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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208M LEU* 3.6 21.8 - - + +
269P ARG* 3.1 36.1 + - - -
270P LEU* 1.3 89.6 + - - +
272P GLY* 1.3 57.1 + - - +
274P VAL* 3.1 24.1 - - - +
275P LEU* 3.1 14.6 + - - +
283P TYR* 5.6 1.2 - - + -
337P LYS* 4.6 6.5 + - - -
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Residues in contact with GLY 272 (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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269P ARG* 3.9 14.1 - - - +
270P LEU 3.2 0.4 - - - -
271P GLU* 1.3 84.8 + - - +
273P LEU* 1.3 54.9 + - - +
274P VAL 3.2 0.2 - - - -
275P LEU* 3.0 12.6 + - - +
276P THR* 2.7 42.8 + - - +
335P PHE* 4.6 5.6 - - - -
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Residues in contact with LEU 273 (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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268P ILE* 5.5 0.4 - - + -
269P ARG 3.6 18.9 + - - +
270P LEU* 3.3 17.2 + - + +
272P GLY* 1.3 73.7 - - - +
274P VAL* 1.3 58.5 + - - +
276P THR* 3.3 6.3 + - - -
277P HIS* 2.9 46.4 + - + +
281P SER* 4.0 13.9 - - - +
291P LEU* 4.4 15.7 - - + -
293P TYR* 4.5 10.3 - - + -
304P ILE* 5.3 5.6 - - + -
328P ILE* 5.5 6.3 - - + -
331P ILE* 4.7 4.3 - - + -
332P LEU* 3.9 28.3 - - + -
335P PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 274 (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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208M LEU* 4.0 22.9 - - + -
270P LEU 2.9 16.1 + - - +
271P GLU* 3.1 26.5 - - - +
273P LEU* 1.3 74.2 - - - +
275P LEU* 1.3 64.6 + - - +
278P GLN* 3.1 27.0 + - + +
281P SER* 3.9 30.5 - - - +
282P SER* 5.2 0.4 - - - -
283P TYR* 4.1 28.0 - - + +
291P LEU* 4.4 1.3 - - + +
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Residues in contact with LEU 275 (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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271P GLU 3.1 16.2 + - - +
272P GLY* 3.0 14.5 + - - +
274P VAL* 1.3 80.6 - - + +
276P THR* 1.3 67.3 + - + +
277P HIS 3.5 0.2 + - - -
278P GLN* 3.8 18.2 + - - +
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Residues in contact with THR 276 (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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272P GLY* 2.7 26.4 + - - +
273P LEU* 3.3 10.6 + - - -
275P LEU* 1.3 82.0 - - + +
277P HIS* 1.3 80.2 + - - +
278P GLN 3.6 0.8 + - - -
335P PHE* 3.9 16.2 - - + -
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Residues in contact with HIS 277 (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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273P LEU* 2.9 27.0 + - + +
274P VAL 3.6 3.8 - - - -
276P THR* 1.3 103.2 + - - +
278P GLN* 1.3 63.1 + - - +
279P GLN* 3.1 4.3 - - - -
280P PHE* 3.0 10.2 + + + -
281P SER* 3.0 29.0 + - - +
293P TYR* 3.9 25.3 + + + +
328P ILE* 5.9 0.4 - - + -
331P ILE* 3.8 44.8 - - + +
335P PHE* 4.9 1.3 - + - -
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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