Contacts of the strand formed by residues 272 - 282 (chain A) in PDB entry 5D3Y
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 LEU 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LEU* 4.2 6.7 - - + +
253A LEU* 4.3 15.3 - - + -
271A GLN* 1.3 91.7 + - - +
273A LEU* 1.3 61.2 + - - +
274A LEU* 3.7 17.7 - - - +
275A GLN* 3.7 34.3 - - + +
292A PHE* 3.9 12.1 - - + -
293A LEU 3.6 13.9 - - - +
294A PHE* 3.5 35.7 - - + -
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Residues in contact with LEU 273 (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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271A GLN* 3.6 32.5 - - + +
272A LEU* 1.3 74.3 - - - +
274A LEU* 1.3 62.9 + - + +
293A LEU* 2.7 25.8 + - + +
294A PHE 3.7 4.7 - - - +
295A ASP* 3.6 25.1 - - + +
386A ALA* 5.1 6.2 - - + +
390A GLU* 3.7 31.6 - - + +
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Residues in contact with LEU 274 (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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272A LEU* 3.6 6.0 - - - +
273A LEU* 1.3 82.2 - - - +
275A GLN* 1.3 74.2 + - - +
292A PHE* 3.5 1.7 - - - -
293A LEU* 2.8 37.1 + - + +
379A GLU* 5.7 0.7 - - - +
382A LYS* 3.7 34.8 - - + +
383A TRP* 3.3 62.3 - - + +
386A ALA* 3.9 19.5 - - + -
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Residues in contact with GLN 275 (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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253A LEU* 5.8 0.3 - - - +
272A LEU* 3.7 23.0 - - + +
274A LEU* 1.3 87.3 - - - +
276A GLY* 1.3 59.4 + - - +
291A PHE 3.2 11.0 - - - +
292A PHE* 3.4 28.7 - - + -
325A TYR* 4.5 7.8 + - - -
379A GLU* 4.9 2.6 - - - +
383A TRP* 3.9 5.6 - - - -
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Residues in contact with GLY 276 (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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275A GLN* 1.3 77.5 - - - +
277A THR* 1.3 62.5 + - - -
278A LEU* 4.9 0.4 - - - -
290A ALA* 3.6 3.6 - - - +
291A PHE* 2.8 33.2 + - - +
379A GLU* 4.5 7.2 - - - -
383A TRP* 3.6 15.5 - - - -
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Residues in contact with THR 277 (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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276A GLY* 1.3 72.6 - - - -
278A LEU* 1.3 68.5 + - - +
288A GLU* 2.4 40.5 + - - +
289A ARG 3.4 9.9 + - - -
290A ALA* 4.3 5.2 - - - +
303A ARG* 4.5 10.9 + - - +
374A ALA* 5.2 2.1 - - - -
375A LYS* 5.4 2.8 + - - +
379A GLU* 5.1 5.3 + - - +
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Residues in contact with LEU 278 (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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277A THR* 1.3 82.8 + - - +
279A LEU* 1.3 66.3 + - - +
280A LYS 3.8 0.3 + - - -
288A GLU* 3.5 6.7 - - - +
289A ARG* 2.9 31.4 + - - +
291A PHE* 3.6 37.5 - - + -
359A TRP* 3.7 40.8 - - + -
372A CYS* 4.0 7.9 - - + -
373A MET 3.6 6.7 - - - +
374A ALA* 3.7 22.9 - - + -
379A GLU* 4.9 1.8 - - + -
383A TRP* 3.8 27.6 - - + +
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Residues in contact with LEU 279 (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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278A LEU* 1.3 74.4 - - - +
280A LYS* 1.3 59.0 + - - +
286A ILE* 4.2 18.8 - - + -
287A GLN 3.7 0.9 - - - -
288A GLU* 4.1 29.8 - - + +
353A TYR* 4.9 9.2 - - + +
371A VAL 3.6 0.2 - - - +
372A CYS* 3.3 5.0 - - - -
373A MET* 2.8 67.3 + - + +
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Residues in contact with LYS 280 (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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279A LEU* 1.3 75.2 - - - +
281A ILE* 1.3 64.6 + - - +
282A SER* 3.5 7.6 + - - -
285A ASN 3.4 3.5 - - - +
286A ILE* 3.4 1.4 - - - -
287A GLN* 2.8 46.5 + - - +
289A ARG* 4.1 8.5 - - + -
291A PHE* 4.1 18.2 - - + -
300A TYR* 3.6 18.6 - - - -
370A PHE* 3.5 47.1 - - + -
371A VAL 3.2 3.1 - - - +
372A CYS* 5.4 0.2 - - - -
501A 4IP 2.7 58.4 + - - -
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Residues in contact with ILE 281 (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 LYS* 1.3 71.0 - - - +
282A SER* 1.3 61.0 + - - +
284A GLY* 4.9 9.2 - - - +
285A ASN 3.2 10.1 - - - +
286A ILE* 3.9 17.5 - - + -
349A HIS 3.7 18.9 - - - +
350A SER* 3.7 37.2 - - - +
351A ASN* 4.6 1.8 - - + +
353A TYR* 4.0 14.6 - - + -
355A VAL* 4.5 0.4 - - + -
370A PHE* 3.2 5.4 - - - +
371A VAL* 2.8 51.4 + - + +
373A MET* 3.6 34.1 - - + -
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Residues in contact with SER 282 (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 LYS* 3.5 14.5 + - - -
281A ILE* 1.3 75.8 - - - +
283A ALA* 1.3 69.5 + - - +
284A GLY 3.1 1.8 - - - -
285A ASN* 2.9 27.4 + - - +
287A GLN* 5.5 0.9 + - - -
349A HIS 5.6 1.1 - - - -
368A LYS* 2.7 27.1 + - - +
369A TRP 5.1 1.3 - - - -
370A PHE* 3.8 11.1 - - - +
501A 4IP 2.5 35.1 + - - -
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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