Contacts of the helix formed by residues 225 - 239 (chain F) in PDB entry 3SDI
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 LYS 225 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223F PHE* 3.6 28.8 + - + +
224F VAL* 1.3 81.0 - - - +
226F GLY* 1.3 67.2 + - - +
227F ASP 3.2 2.9 + - - -
228F LEU* 3.4 14.3 + - - +
229F LEU* 3.6 8.4 + - - -
70M PRO 5.1 8.3 + - - -
73M ASP* 5.9 4.2 + - - -
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Residues in contact with GLY 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F LYS* 1.3 70.8 - - - +
227F ASP* 1.3 59.7 - - - -
229F LEU* 3.3 8.1 + - - +
230F GLN* 3.0 30.2 + - - +
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Residues in contact with ASP 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F LYS 3.2 2.6 + - - -
226F GLY* 1.3 72.6 - - - -
228F LEU* 1.3 58.7 + - - +
230F GLN* 3.4 5.2 + - - +
231F GLU* 2.9 32.6 + - - +
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Residues in contact with LEU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ARG* 3.7 37.7 - - + +
190F VAL* 4.8 11.6 - - + +
191F LYS* 6.5 1.1 - - + -
214F TRP* 3.6 38.1 - - + +
224F VAL* 4.0 17.2 - - + +
225F LYS 3.4 9.5 + - - +
226F GLY 3.3 0.6 - - - -
227F ASP* 1.3 77.0 - - - +
229F LEU* 1.3 63.8 + - - +
231F GLU* 4.1 15.8 - - - +
232F ALA* 3.2 23.4 + - - +
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Residues in contact with LEU 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLN* 4.2 21.5 - - - +
210F LEU* 4.5 22.0 - - + +
211F GLU* 5.4 0.2 - - - -
212F ILE* 4.0 28.5 - - + +
224F VAL* 3.7 33.0 - - + +
225F LYS* 3.6 15.0 + - - -
226F GLY 3.3 10.2 + - - +
228F LEU* 1.3 78.7 - - - +
230F GLN* 1.3 57.8 + - - +
232F ALA* 3.3 4.8 + - - +
233F ILE* 2.9 44.7 + - + +
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Residues in contact with GLN 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F GLY 3.0 18.1 + - - +
227F ASP* 3.8 5.4 - - - +
228F LEU 3.4 0.2 - - - -
229F LEU* 1.3 77.2 - - - +
231F GLU* 1.3 55.8 + - - +
233F ILE* 3.1 26.2 + - - +
234F ASP* 2.8 64.5 + - - +
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Residues in contact with GLU 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ARG* 5.0 7.6 + - - -
191F LYS* 3.1 34.1 + - + +
227F ASP 2.9 19.4 + - - +
228F LEU* 4.1 19.4 - - - +
230F GLN* 1.3 76.0 - - - +
232F ALA* 1.3 57.3 + - - +
234F ASP* 3.8 9.7 - - - +
235F PHE* 3.2 25.3 + - - +
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Residues in contact with ALA 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F VAL* 4.2 21.1 - - + -
191F LYS* 4.2 14.0 - - + +
194F ALA* 3.3 27.9 - - + +
212F ILE* 4.5 6.3 - - + -
228F LEU* 3.2 19.0 + - + +
229F LEU* 3.6 4.9 - - - +
230F GLN 3.2 0.2 - - - -
231F GLU* 1.3 74.1 - - - +
233F ILE* 1.3 64.8 + - - +
235F PHE* 3.4 7.6 + - - +
236F ALA 3.1 16.3 + - - -
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Residues in contact with ILE 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ALA* 4.8 0.4 - - - -
198F TYR* 3.7 23.3 - - - +
210F LEU* 3.8 27.4 - - + +
229F LEU* 2.9 37.1 + - + +
230F GLN* 3.4 29.6 - - - +
232F ALA* 1.3 73.3 - - - +
234F ASP* 1.3 56.7 + - - +
236F ALA* 2.9 8.8 + - - +
237F GLN* 2.8 41.9 + - + +
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Residues in contact with ASP 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F GLN* 2.8 48.1 + - - +
231F GLU* 3.8 8.8 - - - +
233F ILE* 1.3 73.5 - - - +
235F PHE* 1.3 57.7 + - - +
237F GLN* 3.8 8.4 - - - +
238F LYS* 2.9 32.0 + - - +
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Residues in contact with PHE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F GLU* 5.3 6.1 - - - -
191F LYS* 3.6 53.6 - - + -
192F GLN* 3.4 29.8 - - - -
195F LYS* 4.4 5.6 - - + -
231F GLU 3.2 15.0 + - - +
232F ALA* 3.4 11.9 - - - +
233F ILE 3.1 0.4 - - - -
234F ASP* 1.3 76.9 - - - +
236F ALA* 1.3 60.2 + - - +
238F LYS* 3.5 26.8 + - - +
239F GLU* 2.9 59.0 + - + +
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Residues in contact with ALA 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ALA 3.5 21.1 - - - +
195F LYS* 3.8 12.6 - - - +
198F TYR* 3.4 37.1 - - + +
199F LEU* 5.6 0.7 - - - +
232F ALA 3.1 6.6 + - - +
233F ILE 2.9 6.8 + - - +
235F PHE* 1.3 78.1 - - - +
237F GLN* 1.3 66.7 + - - +
239F GLU* 3.6 2.3 + - - +
240F ILE* 3.2 27.0 + - - +
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Residues in contact with GLN 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F TYR* 3.9 24.0 - - + +
233F ILE* 2.8 29.8 + - + +
234F ASP* 3.8 9.6 - - - +
236F ALA* 1.3 75.7 - - - +
238F LYS* 1.3 61.4 + - - +
240F ILE* 3.1 34.3 + - - +
241F ASN* 3.4 10.1 + - - +
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Residues in contact with LYS 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F ASP 2.9 17.4 + - - +
235F PHE* 4.0 24.3 - - - +
237F GLN* 1.3 75.8 - - - +
239F GLU* 1.3 91.9 + - - +
240F ILE 3.3 1.0 + - - -
241F ASN* 3.5 22.7 + - - +
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Residues in contact with GLU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F GLN* 4.9 0.5 + - - -
195F LYS* 3.5 32.4 - - + +
199F LEU* 4.9 7.7 - - - +
235F PHE* 2.9 39.2 + - + +
236F ALA 3.9 3.1 - - - +
237F GLN 3.3 0.2 - - - -
238F LYS* 1.3 97.3 + - - +
240F ILE* 1.3 60.5 + - - +
241F ASN* 3.4 2.6 - - - -
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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