Contacts of the helix formed by residues 253 - 268 (chain V) in PDB entry 4ADV
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 SER 253 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152V PRO* 4.0 13.9 - - - -
157V TYR* 3.4 2.5 - - - -
251V ASN 3.7 3.0 + - - -
252V ILE* 1.3 75.1 - - - +
254V VAL* 1.3 65.0 + - - +
255V ALA* 3.5 9.7 + - - +
256V GLN* 2.8 40.3 + - - +
257V TYR* 3.1 22.2 + - - -
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Residues in contact with VAL 254 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V PRO* 5.0 1.4 - - + +
157V TYR* 3.2 16.7 + - + +
162V VAL* 4.0 35.4 - - + +
165V GLN* 3.5 30.5 - - + +
166V TYR* 4.3 12.1 - - - +
202V HIS* 4.4 12.8 - - + +
253V SER* 1.3 71.1 - - - +
255V ALA* 1.3 64.0 + - - +
257V TYR* 3.1 9.5 + - - +
258V CYS* 3.0 35.2 + - - -
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Residues in contact with ALA 255 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202V HIS* 3.4 41.7 - - + +
253V SER* 3.3 9.9 + - - +
254V VAL* 1.3 76.7 - - - +
256V GLN* 1.3 57.9 + - + +
258V CYS* 3.2 4.7 + - - +
259V GLN* 2.9 27.9 + - - +
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Residues in contact with GLN 256 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241V MET 5.5 0.6 + - - +
242V GLY 3.9 13.3 + - - -
243V ILE* 3.9 30.0 - - + +
247V MET* 4.3 7.5 - - - +
251V ASN 4.3 2.4 - - - +
252V ILE* 3.6 23.4 - - + +
253V SER* 2.8 40.7 + - - +
255V ALA* 1.3 70.9 - - + +
257V TYR* 1.3 60.9 + - - +
259V GLN* 3.2 17.8 + - - +
260V MET* 2.9 34.5 + - - +
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Residues in contact with TYR 257 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162V VAL* 3.8 20.4 - - + -
210V LEU* 3.7 22.0 - - + +
213V ILE* 3.9 19.0 - - + +
214V THR* 3.9 13.7 - - + -
217V ALA* 3.5 19.0 - - + +
218V PHE* 3.4 23.7 - + - -
225V ILE* 4.9 0.3 - - - +
229V LEU* 4.9 1.6 - - + -
249V ALA* 2.6 36.8 + - - +
252V ILE* 3.4 29.6 - - + +
253V SER 3.1 23.4 + - - -
254V VAL 3.5 7.2 - - - +
256V GLN* 1.3 76.1 - - - +
258V CYS* 1.3 58.0 + - - +
260V MET* 3.3 25.4 + - + +
261V ALA* 3.0 22.5 + - - +
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Residues in contact with CYS 258 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166V TYR* 3.7 15.5 - - - -
202V HIS* 3.6 36.6 - - + +
203V PRO 4.9 0.7 - - - +
204V VAL* 3.6 22.6 - - + +
210V LEU* 4.2 11.4 - - - -
254V VAL* 3.0 25.6 + - - +
255V ALA 3.6 7.9 - - - +
256V GLN 3.2 0.2 - - - -
257V TYR* 1.3 74.3 - - - +
259V GLN* 1.3 64.1 + - - +
261V ALA* 3.2 2.2 + - - +
262V ASN* 3.0 32.6 + - - +
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Residues in contact with GLN 259 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241V MET* 3.4 50.6 + - - +
243V ILE* 4.6 1.8 - - - +
255V ALA 2.9 14.1 + - - +
256V GLN* 3.2 24.4 + - - +
258V CYS* 1.3 78.2 - - - +
260V MET* 1.3 54.7 + - - +
262V ASN* 3.6 6.9 + - - +
263V TYR* 3.0 28.6 + - - +
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Residues in contact with MET 260 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213V ILE* 3.5 6.7 - - + -
225V ILE* 5.3 0.9 - - + -
229V LEU* 3.7 24.7 - - + -
233V PHE* 3.3 29.8 - - + -
238V LEU* 4.2 9.6 - - - -
241V MET* 3.6 20.6 - - + -
243V ILE* 3.8 14.8 - - + -
252V ILE* 3.6 20.6 - - + -
256V GLN 2.9 19.0 + - - +
257V TYR* 3.5 38.1 - - + +
258V CYS 3.2 0.2 - - - -
259V GLN* 1.3 73.4 - - - +
261V ALA* 1.3 61.0 + - - +
263V TYR* 4.4 2.2 - - - -
264V LEU* 3.0 23.4 + - - +
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Residues in contact with ALA 261 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204V VAL* 3.9 20.0 - - + -
209V VAL* 3.7 10.8 - - + +
210V LEU* 3.9 32.5 - - + +
213V ILE* 3.4 10.5 - - + +
257V TYR 3.0 13.2 + - - +
258V CYS 3.2 8.2 + - - +
260V MET* 1.3 75.3 - - - +
262V ASN* 1.3 58.7 + - - +
264V LEU 3.5 0.7 + - - -
265V ALA* 3.1 28.1 + - - +
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Residues in contact with ASN 262 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PRO 2.9 24.0 + - - -
204V VAL* 3.4 2.2 - - - -
205V LYS* 2.8 34.5 + - - +
258V CYS* 3.0 22.7 + - - +
259V GLN* 3.9 6.3 - - - +
261V ALA* 1.3 74.3 - - - +
263V TYR* 1.3 54.7 + - - +
265V ALA* 3.1 5.1 + - - +
266V GLU* 2.7 57.0 + - - +
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Residues in contact with TYR 263 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232V LEU 6.0 0.4 - - - -
233V PHE* 4.1 11.4 - + + -
237V VAL* 3.5 41.0 - - + +
241V MET* 4.0 24.5 - - + -
259V GLN* 3.0 18.3 + - + +
260V MET* 3.8 4.5 - - - +
261V ALA 3.4 0.2 - - - -
262V ASN* 1.3 76.3 - - - +
264V LEU* 1.3 62.0 + - + +
266V GLU* 3.2 4.6 + - - +
267V ASN* 2.9 75.3 + - + +
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Residues in contact with LEU 264 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209V VAL* 3.9 23.1 - - + -
212V ARG* 5.2 9.6 - - - +
213V ILE* 4.1 10.1 - - + -
232V LEU* 3.9 44.9 - - + +
233V PHE* 4.0 21.3 - - + -
260V MET 3.0 16.0 + - - +
261V ALA 3.8 3.8 - - - +
263V TYR* 1.3 83.3 - - + +
265V ALA* 1.3 56.5 + - - +
267V ASN* 5.0 0.4 - - - -
268V ALA* 3.0 48.1 + - + +
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Residues in contact with ALA 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205V LYS* 3.8 26.7 - - + -
206V ASP* 5.2 10.1 - - + +
209V VAL* 5.0 7.8 - - + +
261V ALA 3.1 16.9 + - - +
262V ASN 3.1 4.2 + - - +
264V LEU* 1.3 74.6 - - - +
266V GLU* 1.3 59.7 + - + +
267V ASN 3.1 6.0 + - - -
268V ALA* 4.1 11.4 + - - +
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Residues in contact with GLU 266 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205V LYS* 5.2 4.7 - - - +
262V ASN* 2.7 46.7 + - - +
263V TYR* 4.0 4.2 + - - +
265V ALA* 1.3 71.6 - - + +
267V ASN* 1.3 69.5 + - - +
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Residues in contact with ASN 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263V TYR* 2.9 67.7 + - + +
264V LEU* 5.0 0.7 - - - -
266V GLU* 1.3 92.4 + - - +
268V ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264V LEU* 3.0 37.7 + - + +
265V ALA* 4.1 10.1 + - - +
266V GLU 4.0 0.2 - - - -
267V ASN* 1.3 81.2 - - - +
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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