Contacts of the helix formed by residues 223 - 230 (chain D) in PDB entry 6D6U
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 223 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PRO* 4.6 21.5 - - + +
148D MET* 3.5 43.7 - - + -
221D ARG 3.9 1.9 + - - +
222D LYS* 1.3 71.7 - - - +
224D GLY* 1.3 69.2 + - - +
225D TYR 3.2 3.1 - - - -
226D PHE* 3.1 11.2 + - + +
227D VAL* 3.0 35.4 + - + +
231D TYR* 5.0 4.3 - - + -
341D TRP* 4.3 12.1 - - + -
345D LEU* 4.6 7.0 - - + -
407D Y01 3.9 24.2 - - + +
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Residues in contact with GLY 224 (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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278C VAL* 3.9 11.1 - - - +
222D LYS* 3.6 5.3 - - - +
223D ILE* 1.3 82.9 - - - +
225D TYR* 1.3 61.5 + - - +
227D VAL* 3.5 11.7 + - - +
228D ILE* 3.6 14.4 + - - +
406D Y01 4.0 19.5 + - - -
407D Y01 5.8 1.6 - - - -
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Residues in contact with TYR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ARG* 4.1 7.9 + - - +
275C ILE 4.2 11.1 + - - -
276C PRO* 3.1 29.8 - - + +
277C TYR* 3.8 27.8 - - - -
278C VAL* 3.9 12.8 - - + +
279C LYS* 5.2 3.1 + - - -
282C ASP* 3.8 20.0 + - - -
222D LYS* 4.9 4.1 + - - +
223D ILE 3.2 0.6 - - - -
224D GLY* 1.3 76.8 - - - +
226D PHE* 1.3 92.0 + + + +
227D VAL 3.2 0.3 + - - -
228D ILE* 3.3 10.7 + - + +
229D GLN* 2.9 58.9 + - + +
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Residues in contact with PHE 226 (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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276C PRO* 5.3 8.3 - - + -
146D PHE* 3.8 19.5 - + - -
147D PRO* 3.3 35.9 - - + -
221D ARG* 4.2 18.6 - - - -
222D LYS 4.7 10.3 - - - -
223D ILE* 3.1 9.2 + - + +
225D TYR* 1.3 104.3 - + + +
227D VAL* 1.3 66.1 + - - +
229D GLN* 3.6 11.0 - - + -
230D THR* 3.1 21.2 + - - +
231D TYR* 3.4 25.0 - - + -
276D SER* 5.4 9.2 - - - -
286D MET* 6.0 3.4 - - - -
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Residues in contact with VAL 227 (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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223D ILE* 3.0 33.2 + - + +
224D GLY* 3.7 9.2 - - - +
225D TYR 3.1 0.4 - - - -
226D PHE* 1.3 78.8 - - - +
228D ILE* 1.3 60.5 + - - +
229D GLN 3.4 0.2 + - - -
231D TYR* 4.5 7.9 - - + -
232D LEU* 3.2 35.0 + - + +
341D TRP* 5.1 3.6 - - + -
406D Y01 3.8 24.5 - - + -
407D Y01 3.3 57.2 - - + -
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Residues in contact with ILE 228 (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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269C ARG* 4.0 14.6 + - - +
278C VAL* 3.9 35.2 - - + -
282C ASP* 4.1 25.1 - - + +
283C MET* 4.2 13.7 - - - -
286C MET* 4.9 19.0 - - + +
224D GLY 3.6 6.9 + - - +
225D TYR* 3.4 16.4 - - + +
227D VAL* 1.3 74.9 - - + +
229D GLN* 1.3 60.7 + - - +
232D LEU* 4.7 7.9 - - + -
233D PRO* 4.4 8.7 - - - +
406D Y01 3.2 43.5 - - + -
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Residues in contact with GLN 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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269C ARG* 2.6 54.4 + - - +
225D TYR* 2.9 43.7 + - + +
226D PHE* 3.7 13.9 - - + -
227D VAL 3.2 0.4 - - - -
228D ILE* 1.3 79.9 - - - +
230D THR* 1.3 71.9 + - - +
233D PRO* 3.3 16.8 - - - +
269D LEU* 4.4 7.2 - - - +
272D SER* 4.7 12.3 + - - -
273D ALA* 5.9 2.7 - - + +
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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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226D PHE* 3.1 7.8 + - - +
229D GLN* 1.3 90.3 + - - +
231D TYR* 1.3 75.5 + - + +
232D LEU 3.3 2.0 - - - -
233D PRO* 3.2 6.5 - - - +
234D CYS* 3.1 22.7 + - + +
269D LEU* 4.0 14.0 - - + +
270D SER* 6.3 0.2 - - - -
273D ALA* 3.3 34.2 - - + +
286D MET* 4.6 20.1 - - + -
289D PHE* 6.0 1.6 - - + -
290D ILE* 4.6 12.6 - - + -
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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