Contacts of the helix formed by residues 272 - 282 (chain D) in PDB entry 2P5G
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 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D LEU 4.9 1.1 - - - -
214D THR* 4.5 3.1 - - - +
215D GLY 2.9 14.7 - - - +
217D ASN* 3.0 17.4 + - - -
218D VAL* 2.8 12.4 + - - -
219D GLU* 2.8 45.1 + - + +
220D SER* 5.0 0.7 + - - -
270D VAL* 4.1 4.3 - - + +
271D LEU* 1.3 77.2 - - - +
273D TYR* 1.3 73.5 + - - +
274D ILE* 3.3 12.5 + - - +
275D ASP* 3.4 22.8 + - - +
276D LEU* 3.2 23.0 + - - +
359D PHE* 4.3 3.3 - - - -
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Residues in contact with TYR 273 (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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112D ASN* 6.0 0.4 - - - -
214D THR* 3.4 25.2 + - + +
215D GLY 4.0 7.0 + - - +
216D TRP* 4.2 17.9 - + + -
271D LEU 4.6 0.2 - - - -
272D ASP* 1.3 76.3 + - - +
274D ILE* 1.3 56.0 + - - +
275D ASP 3.2 0.7 - - - -
276D LEU* 3.2 6.7 + - + -
277D TYR* 2.8 38.4 + - + +
331D VAL* 3.8 28.7 - - + -
334D ILE* 3.4 25.6 + - + +
335D ASP* 3.1 49.6 + - + -
338D ARG* 4.8 1.7 - - + +
340D PHE* 3.3 25.9 + - + +
341D ILE* 4.1 14.8 - - + -
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Residues in contact with ILE 274 (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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216D TRP* 4.2 28.6 - - + +
217D ASN* 3.9 24.9 - - + +
220D SER* 5.8 0.9 - - - +
272D ASP* 3.3 23.8 + - - +
273D TYR* 1.3 78.1 - - - +
275D ASP* 1.3 73.4 + - - +
277D TYR* 3.4 8.2 - - - +
278D LYS* 3.4 19.6 + - - +
288D TYR* 3.7 38.9 - - + +
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Residues in contact with ASP 275 (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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219D GLU* 3.5 13.5 - - - +
272D ASP* 3.4 26.1 + - - +
273D TYR 3.2 0.2 - - - -
274D ILE* 1.3 84.0 - - - +
276D LEU* 1.3 61.2 + - - +
277D TYR 3.2 1.8 - - - -
278D LYS* 3.6 5.4 + - - +
279D LYS* 3.2 30.7 + - - +
359D PHE* 3.7 25.0 - - + -
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Residues in contact with LEU 276 (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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271D LEU* 4.0 18.2 - - + -
272D ASP 3.2 15.7 + - - +
273D TYR* 3.2 16.1 + - + +
275D ASP* 1.3 75.4 - - - +
277D TYR* 1.3 62.2 + - - +
279D LYS* 3.9 4.0 + - - +
280D PHE* 3.5 22.5 + - - +
340D PHE* 4.3 25.9 - - + +
341D ILE* 5.8 0.7 - - + +
359D PHE* 4.1 6.2 - - - -
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Residues in contact with TYR 277 (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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216D TRP* 4.5 15.3 - - + -
273D TYR* 2.8 23.8 + - + +
274D ILE* 3.4 11.4 - - - +
275D ASP 3.2 0.2 - - - -
276D LEU* 1.3 78.7 - - - +
278D LYS* 1.3 62.7 + - - +
281D SER* 3.3 33.9 + - - +
288D TYR* 5.3 10.3 - - + -
293D ILE* 5.5 5.6 - - + -
340D PHE* 6.1 0.2 - - - -
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Residues in contact with LYS 278 (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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274D ILE 3.4 12.4 + - - +
275D ASP* 3.6 6.0 + - - +
276D LEU 3.5 0.2 - - - -
277D TYR* 1.3 79.0 - - - +
279D LYS* 1.3 58.4 + - + +
280D PHE 3.1 6.2 + - - -
282D PHE* 3.5 21.7 + - - +
288D TYR* 4.9 19.5 - - + +
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Residues in contact with LYS 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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275D ASP 3.2 18.2 + - - +
276D LEU* 4.1 3.1 - - - +
277D TYR 3.4 0.6 - - - -
278D LYS* 1.3 74.2 - - + +
280D PHE* 1.3 60.3 + - - +
359D PHE* 4.7 16.8 - - + -
561D LEU* 4.4 17.5 - - - +
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Residues in contact with PHE 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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276D LEU 3.5 15.5 - - - +
277D TYR* 3.8 0.9 + - - +
278D LYS 3.1 2.2 + - - -
279D LYS* 1.3 81.9 - - - +
281D SER* 1.3 68.4 + - - +
282D PHE* 3.4 5.3 - - - +
338D ARG 5.6 5.6 - - - +
340D PHE* 5.8 7.4 - - + -
343D LEU* 6.6 0.7 - - + -
561D LEU* 5.4 11.9 - - + +
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D TYR* 3.3 19.6 + - - +
278D LYS* 5.5 0.2 - - - -
280D PHE* 1.3 77.6 - - - +
282D PHE* 1.3 65.8 + - - +
283D THR* 3.1 30.2 + - - -
297D GLU* 4.5 12.6 + - - -
338D ARG* 5.2 8.5 - - - +
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Residues in contact with PHE 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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278D LYS* 3.5 17.4 + - - +
280D PHE 3.4 6.1 - - - +
281D SER* 1.3 79.9 - - - +
283D THR* 1.3 60.1 + - - +
284D ASN 3.9 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