Contacts of the helix formed by residues 282 - 292 (chain A) in PDB entry 2R5A
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 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A PHE* 4.6 0.9 - - - -
278A MET* 4.2 23.6 - - - +
279A ASN* 2.9 35.0 + - - -
281A SER* 1.3 78.4 + - - +
283A TRP* 1.3 58.1 + - - +
284A PRO* 3.7 0.9 - - - -
285A GLY* 3.7 3.3 + - - -
286A TYR* 3.0 28.1 + - - +
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Residues in contact with TRP 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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224A ILE* 5.2 8.5 - - + -
240A ASP* 4.9 2.2 - - + -
270A LEU* 3.4 22.2 + - + -
271A GLN* 3.3 25.4 - - - -
272A PRO* 3.5 44.5 - - + +
273A PRO* 4.1 11.4 - - + -
276A PHE* 3.9 18.3 - + + -
279A ASN 4.0 1.2 + - - -
280A ALA 3.0 19.7 + - - +
282A SER* 1.3 75.1 - - - +
284A PRO* 1.4 76.8 - - + +
286A TYR* 3.0 27.4 + + - +
287A LEU* 2.9 56.3 + - + +
290A ILE* 4.9 5.8 - - + -
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Residues in contact with PRO 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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280A ALA 4.0 3.6 - - - +
281A SER* 3.8 15.0 - - - +
283A TRP* 1.4 103.3 - - + +
285A GLY* 1.3 61.1 + - - +
287A LEU* 3.4 13.6 + - + +
288A CYS* 3.5 18.0 + - - -
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Residues in contact with GLY 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 SER 5.5 0.2 + - - -
282A SER 3.7 4.8 + - - -
283A TRP 3.3 0.4 - - - -
284A PRO* 1.3 77.4 - - - +
286A TYR* 1.3 64.3 + - - +
288A CYS* 3.5 9.7 + - - +
289A LYS* 3.2 26.8 + - - +
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Residues in contact with TYR 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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240A ASP* 4.3 2.1 - - - +
241A GLY* 3.1 39.5 + - - -
276A PHE* 3.9 13.2 - + + -
277A CYS* 4.9 3.3 - - - -
278A MET* 3.9 35.0 - - + -
282A SER 3.0 20.2 + - - +
283A TRP* 3.0 28.1 + + - +
285A GLY* 1.3 74.6 - - - +
287A LEU* 1.3 63.6 + - - +
289A LYS* 3.2 9.8 + - + +
290A ILE* 3.1 52.1 + - + +
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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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224A ILE* 3.7 24.9 - - + -
270A LEU* 4.1 23.1 - - + +
283A TRP* 2.9 35.6 + - + +
284A PRO* 3.6 11.4 - - + +
285A GLY 3.4 0.2 - - - -
286A TYR* 1.3 75.6 - - - +
288A CYS* 1.3 60.0 + - - +
290A ILE* 3.3 14.8 - - + +
291A LEU* 3.0 52.1 + - + +
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Residues in contact with CYS 288 (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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284A PRO 3.5 14.5 + - - -
285A GLY* 3.6 10.3 - - - +
286A TYR 3.3 0.2 - - - -
287A LEU* 1.3 82.1 - - - +
289A LYS* 1.3 60.8 + - + +
291A LEU* 3.5 4.3 + - - +
292A ASN* 3.1 25.7 + - - +
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLY 3.2 13.6 + - - +
286A TYR* 3.2 14.2 + - + +
288A CYS* 1.3 79.5 - - + +
290A ILE* 1.3 65.8 + - + +
292A ASN* 3.5 21.3 + - - +
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Residues in contact with ILE 290 (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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210A LYS* 3.4 11.3 - - - +
224A ILE* 3.9 26.5 - - + -
240A ASP* 3.7 35.9 - - + +
283A TRP* 4.9 3.8 - - + -
286A TYR* 3.1 48.9 + - + +
287A LEU* 3.3 21.8 - - + +
289A LYS* 1.3 78.1 - - + +
291A LEU* 1.3 63.5 + - + +
292A ASN 3.5 2.1 + - - +
294A ALA* 3.4 16.6 - - - +
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Residues in contact with LEU 291 (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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210A LYS* 4.6 10.1 - - + -
224A ILE* 4.0 17.0 - - + -
260A ILE* 3.9 42.0 - - + -
270A LEU* 5.0 3.8 - - + -
287A LEU* 3.0 44.6 + - + +
288A CYS* 3.9 4.7 - - - +
290A ILE* 1.3 78.2 - - + +
292A ASN* 1.3 62.8 + - - +
293A ASN 3.1 4.0 + - - -
294A ALA* 3.4 13.6 + - + +
296A VAL* 5.5 2.4 - - + +
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Residues in contact with ASN 292 (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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288A CYS 3.1 17.8 + - - +
289A LYS* 3.5 16.0 - - - +
290A ILE 3.3 3.3 - - - +
291A LEU* 1.3 72.3 - - - +
293A ASN* 1.3 77.7 + - - +
294A ALA* 3.2 2.3 + - - -
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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