Contacts of the strand formed by residues 224 - 232 (chain C) in PDB entry 2VGB
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 224 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 4.4 20.0 - - + -
218C TYR* 3.1 12.9 - - - -
219C ILE* 2.8 70.0 + - + +
220C ASP* 4.6 8.1 - - + +
223C LEU* 1.3 81.7 - - + +
225C SER* 1.3 65.6 + - - +
226C LEU* 4.3 5.8 - - + -
242C ASN 3.8 6.1 - - - +
243C GLY* 3.6 4.0 - - - +
244C GLY* 3.5 46.2 - - - +
245C VAL 4.3 5.2 - - - +
246C LEU* 5.1 7.9 - - + -
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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
----------------------------------------------------------
216C ARG* 3.9 11.1 - - - -
217C ILE 3.5 3.8 - - - -
218C TYR* 4.4 11.0 - - - +
222C GLY 5.6 0.2 - - - -
223C LEU 5.4 0.4 - - - -
224C ILE* 1.3 81.0 - - - +
226C LEU* 1.3 57.7 + - - +
240C VAL 3.7 0.7 - - - -
241C GLU* 2.5 61.4 + - - -
242C ASN* 3.0 39.3 + - - +
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Residues in contact with LEU 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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177C LEU* 4.4 7.4 - - + -
183C VAL* 4.1 20.6 - - + -
185C VAL* 4.2 14.8 - - + -
200C VAL* 5.0 0.4 - - + -
215C GLY 3.7 0.4 - - - +
216C ARG* 3.2 7.1 - - - +
217C ILE* 2.6 53.6 + - + +
219C ILE* 3.4 31.9 - - + -
224C ILE* 4.5 2.5 - - + -
225C SER* 1.3 75.4 + - - +
227C VAL* 1.3 62.6 + - - +
228C VAL 4.3 0.4 - - - -
238C THR* 4.0 20.2 - - + +
239C GLN 3.7 1.6 - - - -
240C VAL* 3.7 38.8 - - + -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C GLY* 3.8 25.6 - - - +
215C GLY 3.4 9.0 - - - +
216C ARG* 3.4 30.1 - - + +
226C LEU* 1.3 78.5 - - - +
228C VAL* 1.3 67.6 + - - +
229C GLN* 3.3 4.2 + - - +
238C THR* 4.2 2.0 - - - -
239C GLN* 3.0 38.9 + - + +
241C GLU* 3.5 23.3 - - + +
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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
----------------------------------------------------------
211C VAL* 3.5 24.7 - - + +
212C PRO 3.5 20.0 - - - +
213C VAL* 3.6 9.4 - - + +
214C GLY* 2.6 31.0 + - - -
215C GLY 2.8 20.5 + - - +
217C ILE* 3.8 17.9 - - + -
227C VAL* 1.3 72.0 - - - +
229C GLN* 1.3 60.3 + - - +
230C LYS 4.0 20.0 - - - +
231C ILE* 4.6 1.3 - - + +
236C LEU* 4.2 19.1 - - + -
237C VAL 3.8 5.4 - - - +
238C THR* 4.2 7.6 - - + -
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Residues in contact with GLN 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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182C GLN* 3.4 28.9 + - - +
213C VAL* 3.3 24.1 - - - +
227C VAL 4.0 8.7 - - - +
228C VAL* 1.3 74.8 - - - +
230C LYS* 1.3 76.2 + - + +
237C VAL* 2.8 24.8 + - + +
238C THR 4.2 1.1 - - - -
239C GLN* 3.4 33.7 + - - +
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Residues in contact with LYS 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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213C VAL* 4.6 4.1 - - + +
228C VAL* 4.0 5.8 - - - +
229C GLN* 1.3 90.8 + - + +
231C ILE* 1.3 67.2 + - - +
236C LEU* 3.6 1.7 - - - -
237C VAL* 2.6 59.2 + - + +
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Residues in contact with ILE 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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208C VAL* 3.9 23.1 - - + +
211C VAL 5.0 4.9 - - - +
212C PRO* 6.4 0.4 - - + -
213C VAL* 4.3 17.1 - - + +
228C VAL* 5.4 0.7 - - + -
230C LYS* 1.3 84.1 - - - +
232C GLY* 1.3 86.5 + - - +
235C GLY 4.4 2.7 - - - +
236C LEU* 3.9 22.7 - - + -
237C VAL* 5.4 1.9 - - - +
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Residues in contact with GLY 232 (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 VAL* 5.7 1.7 - - - +
231C ILE* 1.3 94.5 - - - +
233C PRO* 1.4 75.3 - - - +
234C GLU* 3.4 2.5 - - - -
235C GLY 3.3 17.6 + - - +
237C VAL* 5.9 2.2 - - - -
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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