Contacts of the strand formed by residues 271 - 278 (chain C) in PDB entry 5MG3
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 271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C SER* 3.8 14.1 - - - +
248C SER* 3.5 16.7 + - - -
249C LYS* 3.9 6.0 - - - +
270C GLY* 1.4 70.3 - - - -
272C ASN* 1.3 72.1 + - - +
289C LYS 4.7 0.2 - - - +
291C GLN* 3.3 46.2 + - - +
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Residues in contact with ASN 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ILE 3.6 1.7 - - - +
247C SER* 3.5 5.6 - - - -
248C SER 2.7 40.5 + - - +
250C GLY* 3.1 36.0 + - - +
266C PRO* 4.0 19.2 + - - +
268C ASN* 4.4 9.9 + - - +
269C ASP 5.0 0.2 - - - +
270C GLY 3.9 7.3 + - - +
271C THR* 1.3 78.7 + - - +
273C ASN* 1.4 60.0 + - - +
274C PHE* 3.8 19.9 - - + -
288C TYR* 4.9 2.5 - - + -
289C LYS 3.9 6.1 - - - +
290C SER* 2.7 29.5 + - - +
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Residues in contact with ASN 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ASN* 3.9 13.1 + - - +
246C ILE 3.6 11.2 + - - -
247C SER* 3.8 13.6 + - - +
272C ASN* 1.4 69.8 - - - +
274C PHE* 1.3 69.2 + - - +
275C TYR* 4.6 4.2 - - - +
288C TYR* 3.1 4.3 - - - -
289C LYS* 2.7 75.4 + - + +
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Residues in contact with PHE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C TYR* 5.0 7.6 - + + -
224C SER 4.2 15.7 - - - -
225C THR* 4.4 13.0 - - + -
244C LEU* 3.1 36.4 - - + +
246C ILE* 2.8 38.1 + - + +
248C SER* 4.9 3.8 - - - -
250C GLY 3.9 18.8 - - - -
251C GLY 4.4 0.7 - - - -
252C TRP* 4.1 14.1 - - - -
253C VAL* 3.9 20.6 - - + -
266C PRO* 5.0 4.5 - - + -
272C ASN* 3.8 19.5 - - + -
273C ASN* 1.3 89.9 + - - +
275C TYR* 1.3 63.5 + - - +
287C GLY 3.5 7.0 - - - +
288C TYR* 3.6 24.9 - + + -
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 4.4 7.0 - - + +
193C PHE* 3.3 21.5 - + - -
194C GLY 4.3 0.2 - - - -
195C GLN* 2.8 40.0 + - + +
243C ASN 3.9 5.8 - - - +
244C LEU* 3.6 13.2 - - - +
273C ASN* 4.6 4.7 - - - +
274C PHE* 1.3 79.0 - - - +
276C THR* 1.4 71.5 + - - +
277C ALA* 4.6 10.8 - - + -
286C ILE* 3.4 8.1 - - - +
287C GLY* 2.9 44.7 + - - +
288C TYR* 3.5 29.8 - - - -
289C LYS* 4.8 6.5 - - + -
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Residues in contact with THR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 2.9 30.6 + - + +
241C ASN* 5.6 0.2 - - - -
242C GLU* 3.3 26.5 - - + +
243C ASN* 2.7 28.0 + - - +
244C LEU* 3.6 21.5 - - + +
275C TYR* 1.4 80.4 - - - +
277C ALA* 1.3 62.2 + - - +
285C ALA 2.6 20.9 + - - -
286C ILE* 3.8 15.2 - - - +
55Y GLN* 5.3 0.7 + - - -
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Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 5.2 0.2 + - - -
241C ASN* 4.2 5.3 + - - -
242C GLU 4.3 5.6 + - - -
243C ASN* 4.9 5.6 - - - -
275C TYR* 4.6 13.5 - - + -
276C THR* 1.3 76.8 + - - +
278C ASN* 1.4 75.2 + - - +
279C LEU* 4.3 13.2 - - + -
284C ALA* 3.6 0.3 - - - -
285C ALA* 2.9 35.9 + - + +
55Y GLN* 5.0 10.3 - - - +
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Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ILE* 3.5 26.5 - - - +
239C ALA 5.3 0.8 - - - -
240C ASP* 3.9 14.6 + - - +
241C ASN* 2.9 33.0 + - - +
243C ASN* 5.4 2.4 + - - -
277C ALA* 1.4 76.1 - - - +
279C LEU* 1.3 68.5 - - - +
280C GLY 3.4 12.5 + - - +
281C ASN* 6.2 0.4 - - - +
282C GLY 5.3 4.4 - - - +
283C ILE 3.5 8.3 - - - +
284C ALA* 3.9 7.4 - - - -
55Y GLN* 5.6 2.6 + - - +
298Y THR* 4.1 14.9 + - - +
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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