Contacts of the strand formed by residues 220 - 227 (chain C) in PDB entry 1DVM
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 TYR 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212C GLU* 2.9 34.1 - - - +
213C PHE 3.2 6.3 - - - -
214C THR* 3.5 26.9 - - + +
218C GLY 3.9 13.9 - - - -
219C HIS* 1.3 75.2 - - - +
221C TYR* 1.3 59.7 + - - +
240C PRO* 3.9 4.0 - - - +
241C TYR* 3.2 26.9 + - + +
242C GLU* 3.7 15.0 + - - +
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Residues in contact with TYR 221 (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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212C GLU* 3.4 4.3 - - - +
213C PHE* 2.8 49.1 + - + +
214C THR 3.7 22.4 + - - -
215C THR* 3.9 7.6 - - - -
219C HIS 3.9 10.8 - - - -
220C TYR* 1.3 73.9 - - - +
222C ASP* 1.3 67.3 + - - +
223C ILE* 3.5 29.1 + - + -
238C ALA* 4.8 0.2 - - + -
239C ALA 3.6 13.5 - - - +
240C PRO* 3.7 9.9 - - + -
241C TYR 4.1 1.3 - - - +
250C LEU* 3.7 25.6 - - + -
253C ILE* 3.7 27.0 - - + +
258C LEU* 4.0 6.6 - - - +
262C TRP* 3.3 33.4 + + - -
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Residues in contact with ASP 222 (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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210C TYR* 3.0 32.5 + - + +
211C THR 4.0 2.2 - - - -
212C GLU* 3.0 24.9 - - - +
221C TYR* 1.3 75.2 - - - +
223C ILE* 1.3 62.9 + - - +
224C LEU 4.3 0.2 - - - -
237C ILE 3.4 1.4 - - - +
238C ALA* 3.1 24.9 - - - +
239C ALA 2.9 15.8 + - - +
240C PRO 5.0 0.2 - - - -
241C TYR* 3.8 29.9 - - - +
352C ILE* 6.5 0.9 - - + -
354C ILE* 6.5 0.4 - - + -
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Residues in contact with ILE 223 (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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210C TYR* 3.3 7.2 - - - -
211C THR* 3.0 45.0 + - + +
213C PHE* 3.5 33.2 - - + +
221C TYR* 3.5 32.5 - - + -
222C ASP* 1.3 78.9 - - - +
224C LEU* 1.3 63.4 + - - +
236C PHE* 4.1 11.7 - - + -
237C ILE 3.3 7.0 - - - +
238C ALA* 4.2 4.3 - - + -
262C TRP* 3.5 39.0 - - + +
266C MET* 3.3 15.8 - - + +
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Residues in contact with LEU 224 (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 PHE* 3.8 25.6 - - + -
209C ASN 3.0 19.7 - - - +
210C TYR* 3.3 28.5 - - + -
222C ASP 5.8 0.2 - - - -
223C ILE* 1.3 73.6 - - - +
225C GLU* 1.3 59.8 + - - +
226C LEU* 3.7 26.7 - - + -
235C MET 3.6 0.5 - - - +
236C PHE* 3.0 8.7 - - - +
237C ILE* 2.8 42.6 + - + +
266C MET* 3.9 3.6 - - - -
273C LEU* 3.8 25.8 - - + -
352C ILE* 3.9 18.2 - - + -
354C ILE* 6.4 0.7 - - + -
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Residues in contact with GLU 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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208C PHE* 4.3 10.7 - - - -
209C ASN* 3.1 49.6 + - + +
224C LEU* 1.3 73.8 - - - +
226C LEU* 1.3 69.3 + - - +
227C PRO* 3.5 18.9 - - + +
231C ASP* 5.6 0.7 - - - +
234C SER* 2.8 35.7 + - - +
235C MET 3.4 1.6 - - - -
236C PHE* 3.6 18.7 - - + -
263C LYS* 3.4 31.7 + - - -
266C MET* 3.7 10.1 - - - +
365C ASN* 4.2 3.3 + - - -
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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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175C TRP* 3.2 34.8 - - + -
176C LYS* 4.3 3.8 - - - +
179C PHE* 4.6 5.2 - - + -
208C PHE* 4.3 7.6 - - + -
224C LEU* 3.7 12.6 - - + -
225C GLU* 1.3 85.2 - - - +
227C PRO* 1.3 69.2 - - - +
228C TYR* 3.8 0.3 - - - -
234C SER* 3.6 3.3 - - - -
235C MET* 2.6 30.5 + - + +
237C ILE* 3.3 32.1 - - + -
273C LEU* 3.6 26.7 - - + -
275C LEU* 3.5 25.8 - - + -
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Residues in contact with PRO 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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175C TRP* 3.1 16.5 - - - -
176C LYS* 3.1 49.5 + - + +
208C PHE* 6.0 0.9 - - + -
209C ASN* 6.2 1.6 - - + -
225C GLU* 3.5 19.1 - - + +
226C LEU* 1.3 88.5 - - - +
228C TYR* 1.3 59.0 + - - +
231C ASP* 3.3 25.4 - - - +
233C LEU 3.8 2.7 - - - +
234C SER* 3.8 13.7 - - - +
268C ARG* 5.0 13.9 - - - +
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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