Contacts of the helix formed by residues 226 - 234 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B ASP 3.5 17.3 + - - -
432B LEU* 3.7 14.3 + - + -
434B ASP 3.1 26.3 + - - -
435B GLU 3.9 13.7 + - - -
437B ILE* 3.5 35.4 + - + +
222C LEU* 2.9 36.8 + - + +
223C PRO 4.3 0.2 - - - -
225C ARG* 1.3 93.6 + - + +
227C PRO* 1.4 65.2 - - - +
228C ALA* 3.1 6.4 + - + +
229C LEU* 3.1 30.9 + - + +
230C PHE* 4.0 3.1 - - - -
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Residues in contact with PRO 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PRO 3.3 19.9 - - - +
224C LEU 3.8 7.2 - - - +
225C ARG 3.6 8.3 - - - +
226C HIS* 1.4 86.3 - - - +
228C ALA* 1.3 63.3 + - + +
230C PHE* 3.2 10.9 + - + +
231C LYS* 3.0 23.2 + - - +
237C PRO* 6.5 0.4 - - + -
340C HIS* 4.2 28.0 - - + +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ILE* 6.4 0.4 - - + -
442B MET* 4.6 18.6 - - + -
226C HIS* 3.1 4.4 + - + +
227C PRO* 1.3 81.3 - - + +
229C LEU* 1.3 52.8 + - - +
231C LYS* 3.4 6.1 + - - +
232C ALA* 2.7 39.2 + - + +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B ILE* 3.9 29.2 - - + -
430B ILE* 4.2 23.6 - - + -
437B ILE* 4.7 15.3 - - + -
442B MET* 4.6 11.1 - - - -
445B LEU* 3.7 28.2 - - + +
222C LEU* 3.9 32.3 - - + -
226C HIS* 3.1 21.8 + - + +
228C ALA* 1.3 76.9 - - - +
230C PHE* 1.3 62.0 + - + +
232C ALA* 3.7 4.9 - - - +
233C ILE* 2.9 32.4 + - - +
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Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B SER 6.2 0.2 - - - -
420B LEU* 4.8 17.9 - - + -
423B ILE* 4.6 14.1 - - + -
218C GLU 4.0 11.4 - - - -
222C LEU* 3.9 21.8 - - + -
223C PRO* 3.5 48.9 - - + -
226C HIS 4.0 9.6 - - - -
227C PRO* 3.2 7.5 + - + +
229C LEU* 1.3 79.5 - - + +
231C LYS* 1.3 64.8 - - - +
233C ILE* 3.4 5.8 - - - +
234C GLY 3.1 5.5 + - - -
235C VAL* 2.9 59.7 + - + +
237C PRO* 4.4 23.6 - - + -
238C PRO* 5.0 6.3 - - + -
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLU* 5.8 7.3 - - - +
227C PRO 3.0 17.5 + - - +
228C ALA* 3.8 6.7 - - - +
230C PHE* 1.3 77.2 - - - +
232C ALA* 1.3 62.6 + - - +
234C GLY* 3.4 12.5 + - - -
235C VAL 4.6 2.5 - - - +
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ASN 4.7 0.5 - - - +
389B LYS* 4.2 17.5 - - - +
442B MET* 4.1 29.4 - - + +
445B LEU* 5.4 3.6 - - + -
228C ALA* 2.7 22.2 + - + +
229C LEU* 3.7 4.5 - - - +
231C LYS* 1.3 73.5 - - - +
233C ILE* 1.3 64.4 + - - +
234C GLY* 3.4 0.7 + - - -
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ASN 3.5 1.4 - - - +
388B MET* 3.2 25.2 - - + +
389B LYS* 3.4 11.2 + - - +
419B ALA* 3.7 28.3 - - + +
422B ALA* 4.4 4.5 - - + -
423B ILE* 4.4 11.4 - - + -
445B LEU* 4.3 39.2 - - + +
447B VAL* 3.9 27.6 - - + -
229C LEU 2.9 17.8 + - - +
230C PHE* 3.4 15.5 - - - +
232C ALA* 1.3 75.2 - - - +
234C GLY* 1.3 58.6 + - - +
235C VAL* 3.8 18.8 - - + -
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Residues in contact with GLY 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B HIS 4.8 4.3 - - - +
387B ASN* 3.6 27.0 + - - +
388B MET* 3.6 14.2 - - - +
230C PHE 3.1 3.4 + - - -
231C LYS 3.8 10.3 - - - -
232C ALA 3.2 3.0 - - - -
233C ILE* 1.3 78.7 - - - +
235C VAL* 1.3 63.0 + - - +
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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