Contacts of the helix formed by residues 226 - 234 (chain F) in PDB entry 3HU1
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 HIS 226 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431E ASP 3.8 9.0 + - - -
432E LEU* 3.8 15.8 + - + -
434E ASP 3.1 27.9 + - - -
435E GLU 3.5 17.9 + - - -
436E THR* 4.3 0.8 - - - -
437E ILE* 3.7 33.5 + - + +
222F LEU* 2.9 36.6 + - + +
225F ARG* 1.3 94.7 + - + +
227F PRO* 1.4 64.9 - - - +
228F ALA* 3.1 5.8 + - + +
229F LEU* 3.2 31.0 + - + +
230F PHE* 3.8 3.6 - - - -
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Residues in contact with PRO 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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223F PRO* 3.5 17.6 - - + +
224F LEU 3.7 11.2 - - - +
225F ARG 3.5 9.9 - - - +
226F HIS* 1.4 85.2 - - - +
228F ALA* 1.4 64.5 + - + +
229F LEU 3.2 0.7 + - - -
230F PHE* 3.2 7.6 + - + +
231F LYS* 3.0 25.2 + - + +
237F PRO* 6.4 1.1 - - + -
340F HIS* 4.2 28.3 - - + +
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Residues in contact with ALA 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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442E MET* 4.7 17.0 - - + -
226F HIS* 3.1 4.4 - - + +
227F PRO* 1.4 82.8 - - + +
229F LEU* 1.4 52.5 + - - +
231F LYS* 3.8 5.2 - - - +
232F ALA* 2.8 38.3 + - - +
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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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423E ILE* 4.0 23.1 - - + -
430E ILE* 4.5 20.6 - - + -
437E ILE* 4.7 19.5 - - + -
442E MET* 4.6 12.2 - - - -
445E LEU* 3.7 28.9 - - + +
222F LEU* 3.9 38.4 - - + -
226F HIS* 3.2 18.1 + - + +
227F PRO 3.2 0.6 + - - -
228F ALA* 1.4 77.9 - - - +
230F PHE* 1.3 62.5 + - + +
232F ALA* 3.4 4.3 + - - +
233F ILE* 3.1 30.9 + - - +
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Residues in contact with PHE 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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420E LEU* 4.9 15.9 - - + -
423E ILE* 4.4 16.4 - - + -
218F GLU 4.1 12.1 - - - -
222F LEU* 3.9 23.8 - - + -
223F PRO* 3.6 43.1 - - + -
226F HIS 3.8 12.6 - - - -
227F PRO* 3.2 6.0 + - + +
229F LEU* 1.3 80.2 - - + +
231F LYS* 1.3 65.0 + - - +
233F ILE* 3.3 6.4 - - - +
234F GLY 3.2 5.0 + - - -
235F VAL* 3.0 60.2 + - + +
237F PRO* 4.4 22.9 - - + -
238F PRO* 5.0 6.3 - - + -
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Residues in contact with LYS 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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191E ARG* 6.1 2.2 - - - +
192E GLU* 6.0 1.6 - - - +
195E GLU* 5.2 14.1 + - - +
227F PRO 3.0 18.6 + - - +
228F ALA* 3.9 5.8 - - - +
230F PHE* 1.3 79.1 - - - +
232F ALA* 1.4 60.4 + - - +
234F GLY* 3.5 10.4 + - - -
235F VAL 4.1 3.1 + - - +
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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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387E ASN 4.8 0.5 - - - +
389E LYS* 4.3 16.5 - - - +
442E MET* 4.1 28.5 - - + +
445E LEU* 5.7 2.2 - - + -
228F ALA 2.8 22.2 + - - +
229F LEU 3.8 4.5 - - - +
230F PHE 3.3 0.2 - - - -
231F LYS* 1.4 72.9 - - - +
233F ILE* 1.3 62.7 + - - +
234F GLY* 3.5 0.7 + - - -
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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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387E ASN 3.4 1.5 - - - +
388E MET* 3.2 25.4 - - + +
389E LYS* 3.4 10.3 + - + +
419E ALA* 4.0 25.4 - - + +
422E ALA* 4.5 3.1 - - + -
423E ILE* 4.4 13.5 - - + -
445E LEU* 4.2 43.7 - - + +
447E VAL* 4.0 25.4 - - + -
229F LEU 3.1 15.9 + - - +
230F PHE* 3.3 19.1 - - - +
232F ALA* 1.3 76.8 - - - +
234F GLY* 1.3 58.0 + - - +
235F VAL* 3.9 17.5 - - + -
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Residues in contact with GLY 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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384E HIS 4.8 4.7 - - - +
387E ASN* 3.4 28.3 + - - +
388E MET* 3.6 13.9 - - - +
230F PHE 3.2 3.6 + - - -
231F LYS 3.5 8.5 + - - -
232F ALA 3.3 3.2 - - - -
233F ILE* 1.3 77.9 - - - +
235F VAL* 1.3 63.5 + - - +
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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