Contacts of the strand formed by residues 224 - 231 (chain C) in PDB entry 3MY0
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 GLU 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C LEU* 3.5 5.4 - - - -
221C TRP* 3.0 39.9 + - + +
222C HIS 3.1 5.5 + - - +
223C GLY* 1.3 77.5 - - - +
225C SER* 1.3 67.6 + - - +
226C VAL* 5.0 4.9 - - + -
278C HIS* 5.8 3.6 - - - -
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Residues in contact with SER 225 (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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218C ARG* 4.4 14.5 + - - -
219C GLY 3.4 7.8 + - - -
220C LEU* 4.7 7.9 - - - +
223C GLY 5.3 0.5 + - - -
224C GLU* 1.3 80.0 - - - +
226C VAL* 1.3 65.7 + - - +
278C HIS* 5.0 1.2 - - - -
279C TYR* 3.7 36.4 + - - +
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Residues in contact with VAL 226 (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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202C VAL* 4.0 23.1 - - + -
218C ARG* 3.6 3.5 - - - -
219C GLY* 2.7 53.9 + - - +
220C LEU 4.5 0.2 - - - +
221C TRP* 4.4 22.0 - - + -
224C GLU* 4.7 5.8 - - + +
225C SER* 1.3 79.3 - - - +
227C ALA* 1.3 58.2 + - - +
228C VAL* 4.3 2.9 - - + -
260C ILE* 3.6 25.6 - - + -
276C ILE* 4.0 16.4 - - + -
277C THR 3.5 9.6 - - - +
278C HIS* 5.5 0.2 - - - -
279C TYR* 3.5 8.6 - - - +
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Residues in contact with ALA 227 (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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216C VAL* 4.5 13.0 - - + -
217C TRP 3.5 6.7 - - - +
226C VAL* 1.3 73.2 - - - +
228C VAL* 1.3 59.7 + - - +
229C LYS 4.0 1.1 - - - +
257C LEU* 6.0 0.4 - - + -
275C LEU 3.7 0.7 - - - +
276C ILE* 3.2 7.1 - - - +
277C THR* 2.9 49.4 + - - +
278C HIS 3.5 8.7 - - - +
279C TYR* 3.7 16.8 - - + +
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Residues in contact with VAL 228 (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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202C VAL* 3.9 20.6 - - + -
204C LEU* 3.7 31.0 - - + -
215C GLU 3.8 0.3 - - - +
216C VAL* 3.6 2.4 - - - -
217C TRP* 2.9 37.4 + - - +
219C GLY* 4.8 1.1 - - - -
226C VAL* 4.3 7.9 - - + +
227C ALA* 1.3 75.9 - - - +
229C LYS* 1.3 60.2 - - - +
230C ILE* 3.6 13.4 + - + +
274C TRP* 3.7 36.1 - - + -
275C LEU 3.5 3.4 - - - +
276C ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 229 (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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213C TYR* 3.7 36.6 - - + +
215C GLU 3.4 11.2 - - - +
216C VAL* 3.9 18.1 - - + +
227C ALA* 4.0 1.8 - - + +
228C VAL* 1.3 71.0 - - - +
230C ILE* 1.3 64.6 + - - +
231C PHE* 3.6 46.6 - - + -
235C ASP* 5.0 1.8 + - - -
238C SER* 5.9 0.4 - - - -
242C GLU* 4.5 2.8 + - - -
274C TRP* 3.5 3.6 - - - -
275C LEU* 2.8 47.3 + - + +
277C THR* 6.4 0.2 - - + -
348C ASP* 4.4 23.8 + - - +
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Residues in contact with ILE 230 (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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204C LEU* 4.2 15.5 - - + -
214C GLY* 3.4 1.2 - - - -
215C GLU* 2.8 47.0 + - + +
217C TRP* 3.6 31.0 - - + +
228C VAL* 4.2 9.2 - - + +
229C LYS* 1.3 73.8 - - - +
231C PHE* 1.3 66.8 + - - +
268C ASN* 6.2 1.3 - - + -
272C GLN* 3.9 39.9 - - + +
273C LEU 3.6 3.1 - - - -
274C TRP* 3.6 22.2 - - + +
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Residues in contact with PHE 231 (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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213C TYR 3.6 7.4 - - - -
214C GLY* 4.2 0.2 - - - -
229C LYS* 3.6 48.5 - - + -
230C ILE* 1.3 81.2 - - - +
232C SER* 1.3 68.2 + - - +
235C ASP* 3.7 27.6 - - - +
236C GLU* 5.2 1.1 - - - +
238C SER* 3.9 10.8 - - - -
239C TRP* 3.5 42.4 - + + -
242C GLU* 3.7 18.4 - - - -
272C GLN* 5.3 1.7 - - - +
273C LEU* 3.1 31.6 + - + +
275C LEU* 3.7 24.2 - - + -
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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