Contacts of the strand formed by residues 283 - 290 (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 ILE 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ILE* 4.0 28.0 - - + -
197C LYS* 4.3 8.5 - - + +
198C GLN 3.7 10.5 - - - +
199C SER* 3.9 15.0 - - - +
238C ILE* 6.1 0.2 - - - -
278C ASN* 3.5 6.0 - - - -
279C LEU* 2.8 55.8 + - + +
280C GLY* 2.8 22.6 + - - +
281C ASN 4.5 3.6 - - - +
282C GLY* 1.4 76.1 - - - +
284C ALA* 1.3 69.2 + - - +
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Residues in contact with ALA 284 (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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197C LYS* 3.6 0.3 - - - -
198C GLN 2.9 30.2 + - - +
200C ILE 5.9 0.4 - - - +
233C TYR* 4.5 3.6 - - - +
235C PHE* 3.7 34.1 - - + -
238C ILE* 4.1 16.6 - - + -
241C ASN* 4.3 6.5 - - - +
255C MET* 3.8 3.9 - - + +
277C ALA 3.6 5.8 - - - -
278C ASN* 3.9 6.7 - - - +
282C GLY 4.2 0.8 - - - -
283C ILE* 1.3 76.1 - - - +
285C ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 285 (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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195C GLN* 4.2 9.2 - - + +
196C LEU 3.2 12.6 - - - +
197C LYS* 3.9 2.7 - - + -
233C TYR* 4.2 0.7 + - - -
255C MET* 3.6 4.7 - - - -
275C TYR* 5.5 0.9 - - + -
276C THR* 2.6 29.4 + - - -
277C ALA* 2.9 23.4 + - + +
279C LEU* 3.4 35.9 - - + -
284C ALA* 1.3 77.5 - - - +
286C ILE* 1.3 55.0 + - - +
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Residues in contact with ILE 286 (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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195C GLN* 3.6 1.8 - - - -
196C LEU* 2.8 42.2 + - + +
221C ALA* 4.2 12.6 - - + -
222C ALA 3.5 27.4 - - - +
223C TYR* 4.4 16.2 - - + -
233C TYR* 5.0 2.2 - - + -
244C LEU* 4.8 2.0 - - + -
253C VAL* 4.1 13.7 - - + -
254C ALA 3.6 23.3 - - - +
255C MET* 3.8 21.3 - - + -
275C TYR* 3.4 18.6 - - - +
276C THR* 3.8 13.9 - - - +
285C ALA* 1.3 75.1 - - - +
287C GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 287 (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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194C GLY 3.1 15.5 - - - -
195C GLN* 4.3 0.2 - - - -
253C VAL* 3.8 14.7 - - - +
274C PHE* 3.5 9.7 - - - +
275C TYR* 2.9 42.5 + - - +
286C ILE* 1.3 75.0 - - - +
288C TYR* 1.3 61.2 - - - -
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Residues in contact with TYR 288 (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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178C TYR* 3.6 6.4 + - - -
192C SER* 3.0 38.3 + - - -
193C PHE* 3.5 20.1 + - - -
194C GLY* 3.0 42.9 + - - +
253C VAL* 4.8 2.9 - - + -
264C TRP* 3.8 29.8 - + + -
266C PRO* 3.8 21.2 - - + +
268C ASN* 4.1 0.6 + - - -
272C ASN* 4.9 1.8 - - + -
273C ASN 3.1 8.3 - - - -
274C PHE* 3.6 24.7 - - + -
275C TYR* 3.5 6.9 - - - -
287C GLY* 1.3 73.8 - - - -
289C LYS* 1.3 62.2 + - - +
290C SER* 3.6 21.5 - - - -
305C SER* 3.3 24.9 + - - -
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Residues in contact with LYS 289 (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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115C THR* 4.2 18.6 - - + -
191C SER* 3.9 11.9 - - - +
192C SER 3.4 5.6 - - - +
193C PHE* 5.1 2.0 - - + -
271C THR 4.7 0.3 - - - +
272C ASN* 4.7 0.4 - - - -
273C ASN* 2.7 65.8 + - + +
275C TYR* 5.6 6.5 - - + -
288C TYR* 1.3 76.9 - - - +
290C SER* 1.4 64.3 + - - +
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Residues in contact with SER 290 (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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191C SER* 2.7 23.3 + - - -
192C SER* 2.7 22.0 + - - -
266C PRO* 4.3 0.5 - - - +
268C ASN* 2.9 36.8 + - - +
269C ASP 5.4 1.1 - - - -
271C THR 4.3 0.9 - - - -
272C ASN* 2.7 27.3 + - - -
288C TYR* 3.6 9.8 - - - -
289C LYS* 1.4 74.3 - - - +
291C GLN* 1.4 66.6 + - - +
292C PRO* 3.3 3.6 - - - +
293C VAL* 6.5 0.7 - - - -
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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