Contacts of the strand formed by residues 224 - 229 (chain C) in PDB entry 2YVC
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 GLY 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 VAL* 3.8 2.8 - - - -
221C ASP* 3.0 31.6 + - - +
223C LEU* 1.3 82.2 - - - +
225C LEU* 1.3 66.6 + - - +
226C ASN* 4.7 0.9 - - - -
240C PHE 3.6 7.6 - - - -
242C TRP* 3.2 28.6 - - - +
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Residues in contact with LEU 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 LEU* 3.8 27.8 - - + -
219C GLY 3.3 3.4 - - - -
220C VAL* 4.4 6.5 - - + -
224C GLY* 1.3 78.4 - - - +
226C ASN* 1.3 69.5 + - - +
240C PHE* 2.9 48.8 + - + +
242C TRP* 3.6 18.4 - - + -
245C ILE* 4.4 5.4 - - + -
248C ILE* 4.7 6.1 - - + -
255C PHE* 4.8 4.0 - - + -
257C ILE* 3.8 33.0 - - + -
284C CYS* 3.6 32.1 - - - -
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Residues in contact with ASN 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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217C TRP 3.7 0.3 - - - +
218C LEU* 3.4 6.6 - - - +
219C GLY 2.7 40.5 + - - +
221C ASP* 2.8 31.7 + - - -
224C GLY 4.7 0.2 - - - -
225C LEU* 1.3 82.2 + - - +
227C ILE* 1.3 64.3 + - - +
228C TYR* 4.1 18.7 + - + +
236C PRO* 3.8 21.3 - - + +
238C ILE 3.5 4.8 - - - +
239C GLY* 3.3 22.3 - - - -
240C PHE* 4.1 1.5 + - - -
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Residues in contact with ILE 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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208C ILE* 4.3 7.6 - - + -
216C LEU* 4.4 15.7 - - + -
217C TRP 3.5 5.8 - - - +
218C LEU* 4.0 26.7 - - + -
226C ASN* 1.3 76.9 - - - +
228C TYR* 1.3 57.0 + - - +
236C PRO* 3.5 1.7 - - - +
237C LYS* 2.6 43.0 + - + -
238C ILE* 2.8 48.6 + - + +
240C PHE* 4.9 9.1 - - + -
267C PHE* 3.6 36.1 - - + -
269C PHE* 4.5 3.8 - - + -
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Residues in contact with TYR 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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199C GLU 4.8 5.9 + - - -
203C VAL* 4.1 13.7 - - - +
205C TYR* 3.5 29.1 + + - -
216C LEU* 3.3 14.1 - - - +
217C TRP* 2.8 46.6 + - + +
219C GLY* 3.7 23.3 - - - -
221C ASP* 5.1 1.6 + - - -
226C ASN* 4.1 17.7 + - + +
227C ILE* 1.3 74.0 - - - +
229C GLU* 1.3 61.6 + - - +
232C ASP 3.7 9.6 - - - +
233C LYS* 3.2 27.0 + - - -
234C LEU 4.2 2.0 + - - -
235C THR 3.3 17.7 - - - -
236C PRO* 3.4 30.6 - - + +
237C LYS* 4.3 3.8 - - - +
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Residues in contact with GLU 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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216C LEU* 3.8 13.5 - - + -
217C TRP* 4.2 0.9 - - - -
227C ILE 4.4 0.2 + - - -
228C TYR* 1.3 74.3 - - - +
230C HIS* 1.3 54.2 + - - +
231C ASP* 2.7 39.1 + - - +
232C ASP* 2.8 28.5 + - + +
235C THR 4.8 2.3 + - - +
237C LYS* 3.3 42.5 + - + +
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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