Contacts of the helix formed by residues 228 - 241 (chain D) in PDB entry 5VQ9
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 LEU 228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ILE 4.9 3.3 - - - +
227D LYS* 1.3 89.7 - - + +
229D VAL* 1.3 64.9 + - + +
231D LYS* 3.4 36.5 + - + +
232D MET* 3.2 21.5 + - - +
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LYS 3.2 3.7 - - - +
228D LEU* 1.3 81.4 - - + +
230D THR* 1.3 58.9 + - + +
232D MET* 3.1 12.5 + - + +
233D PHE* 2.9 55.3 + - + -
276D VAL* 4.1 26.2 - - + +
279D ALA* 4.8 7.4 - - + +
280D VAL* 3.8 23.6 - - + +
283D GLN* 4.3 9.4 - - + -
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Residues in contact with THR 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LYS* 2.4 45.8 + - - +
229D VAL* 1.3 75.3 - - + +
231D LYS* 1.3 67.3 + - - +
232D MET 3.0 0.2 + - - -
233D PHE* 3.2 1.1 + - - +
234D GLN* 2.9 28.7 + - - +
283D GLN* 4.4 21.5 - - + +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE 5.5 2.2 - - - +
227D LYS* 3.0 57.8 + - - +
228D LEU* 3.5 28.5 - - + +
229D VAL 3.4 0.2 - - - -
230D THR* 1.3 84.0 + - - +
232D MET* 1.3 58.7 + - - +
234D GLN* 4.3 4.8 - - - +
235D LYS* 3.2 40.3 + - - +
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Residues in contact with MET 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 6.4 1.3 - - + -
120D ILE 4.1 14.8 - - - +
121D ALA 4.1 13.2 - - - +
122D ALA* 4.0 26.7 - - + -
212D ILE* 3.6 36.6 - - + -
228D LEU 3.2 11.3 + - - +
229D VAL* 3.1 16.7 + - + +
230D THR 3.0 0.6 - - - -
231D LYS* 1.3 78.1 - - - +
233D PHE* 1.3 86.1 + - + +
235D LYS* 3.6 10.0 + - + +
236D ILE* 3.2 29.9 + - + +
280D VAL* 5.7 2.9 - - + -
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ILE* 4.2 15.7 - - + -
229D VAL* 2.9 37.8 + - + +
230D THR 4.1 1.6 - - - +
232D MET* 1.3 93.6 - - + +
234D GLN* 1.3 59.1 + - - +
236D ILE* 3.6 18.2 - - + +
237D GLN* 2.8 29.3 + - - +
249D VAL* 5.2 2.0 - - + -
251D ILE* 6.2 0.2 - - + -
280D VAL* 4.3 15.5 - - + -
283D GLN* 3.4 55.4 - - + +
284D ILE* 4.1 11.4 - - + -
287D ILE* 4.0 33.9 - - + +
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D THR 2.9 17.5 + - - +
231D LYS* 4.3 5.6 - - - +
233D PHE* 1.3 75.7 - - - +
235D LYS* 1.3 59.6 + - + +
237D GLN* 3.4 19.4 + - - +
238D ASP* 2.9 38.5 + - - +
241D ASP* 5.5 2.0 + - - -
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Residues in contact with LYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 4.0 22.4 - - + +
120D ILE* 3.6 33.7 + - - +
231D LYS* 3.2 28.7 + - - +
232D MET* 3.6 8.5 + - + +
233D PHE 3.4 0.2 - - - -
234D GLN* 1.3 74.9 - - + +
236D ILE* 1.3 66.3 + - + +
238D ASP* 2.9 19.4 + - - +
239D LEU* 3.0 20.2 + - + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ILE* 4.1 31.2 - - + -
212D ILE* 4.6 10.1 - - + -
232D MET* 3.2 29.5 + - + +
233D PHE* 3.6 30.1 - - + +
235D LYS* 1.3 76.4 - - + +
237D GLN* 1.3 62.9 + - - +
239D LEU* 3.1 12.5 + - + +
240D ILE* 2.9 41.7 + - + +
247D VAL* 4.7 5.8 - - + -
249D VAL* 4.4 18.8 - - + -
287D ILE* 4.5 7.6 - - + -
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Residues in contact with GLN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D PHE 2.8 21.2 + - - +
234D GLN* 3.5 23.8 - - - +
236D ILE* 1.3 72.8 - - - +
238D ASP* 1.3 57.7 + - - +
240D ILE* 3.1 11.0 + - - +
241D ASP* 2.9 58.3 + - - +
286D GLN 5.2 0.5 - - - +
287D ILE* 3.8 18.7 - - + +
290D HIS* 3.6 34.8 + - - -
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLN* 2.9 25.3 + - - +
235D LYS* 2.9 16.5 + - - +
237D GLN* 1.3 77.1 - - - +
239D LEU* 1.3 59.1 + - + +
241D ASP* 3.6 23.6 + - - +
242D ASP* 4.1 3.8 + - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D HIS* 3.9 19.7 - - + +
206D TYR* 4.9 1.3 + - - +
208D GLN* 3.1 35.3 + - + +
210D ILE* 3.5 31.6 - - + -
235D LYS* 3.0 16.8 + - + +
236D ILE* 3.1 10.1 + - + +
238D ASP* 1.3 74.0 - - + +
240D ILE* 1.3 64.3 + - - +
241D ASP 3.1 2.8 + - - -
242D ASP* 3.3 22.6 + - - +
245D ALA* 4.7 3.6 - - - +
247D VAL* 4.0 10.7 - - + +
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Residues in contact with ILE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 2.9 34.7 + - + +
237D GLN* 3.1 17.2 + - - +
239D LEU* 1.3 77.3 - - - +
241D ASP* 1.3 62.3 + - - +
242D ASP 3.2 0.3 + - - -
243D LYS* 3.1 10.1 + - - +
247D VAL* 3.6 29.6 - - + -
249D VAL* 5.3 0.2 - - + -
287D ILE* 3.8 23.8 - - + -
290D HIS* 3.8 16.6 - - + -
292D ASN* 3.1 23.7 + - - +
293D VAL* 3.6 33.7 - - + -
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Residues in contact with ASP 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLN* 5.5 2.1 + - - -
237D GLN* 2.9 41.3 + - - +
238D ASP* 3.7 20.5 - - - +
239D LEU 3.1 0.8 - - - -
240D ILE* 1.3 77.2 - - - +
242D ASP* 1.3 58.6 + - - +
243D LYS* 3.3 18.3 + - - +
290D HIS* 5.1 2.4 - - - -
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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