Contacts of the helix formed by residues 226 - 236 (chain F) in PDB entry 5UH8
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 ASP 226 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224F SER* 3.4 2.8 - - - +
225F ALA* 1.3 78.1 - - - +
227F SER* 1.3 70.8 + - - +
228F VAL* 2.9 14.5 + - - +
229F ARG* 2.6 35.0 + - + +
230F ALA* 2.8 32.0 + - - +
8H G 2.8 28.5 + - - +
9H G 5.9 1.1 - - - -
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Residues in contact with SER 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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372D ARG* 2.8 30.2 + - - +
376D GLU* 3.1 39.6 + - - -
225F ALA 3.3 5.9 + - - -
226F ASP* 1.3 74.7 + - - +
228F VAL* 1.3 69.9 + - - +
230F ALA* 3.4 2.9 + - - -
231F TYR* 3.1 14.7 + - - +
318F LEU* 3.5 18.6 - - - +
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Residues in contact with VAL 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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226F ASP* 2.9 16.5 + - - +
227F SER* 1.3 80.2 + - - +
229F ARG* 1.3 62.5 + - - +
231F TYR* 3.2 5.8 + - + +
232F LEU* 3.1 25.7 + - + +
317F PHE* 4.0 32.3 - - + -
318F LEU* 4.0 30.3 - - + -
321F ILE* 5.6 1.6 - - + -
8H G 3.5 36.3 - - + +
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Residues in contact with ARG 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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282C ARG* 3.0 39.8 - - - +
283C PRO* 4.6 3.8 + - - +
285C GLU* 3.2 26.8 + - + -
224F SER* 3.5 32.3 + - - -
226F ASP* 2.6 29.6 + - + +
228F VAL* 1.3 73.1 - - - +
230F ALA* 1.3 63.5 + - - +
232F LEU* 3.1 9.5 + - + +
233F LYS* 3.0 23.1 + - + +
7H G 5.7 0.2 + - - -
8H G 2.8 29.6 + - - +
9H G 3.4 16.5 + - - +
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Residues in contact with ALA 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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372D ARG* 4.2 17.7 - - - +
223F ALA* 5.6 2.9 - - + -
224F SER* 4.4 15.3 - - - +
226F ASP 2.8 19.7 + - - +
227F SER* 3.6 4.9 - - - +
228F VAL 3.2 0.2 - - - -
229F ARG* 1.3 76.4 - - - +
231F TYR* 1.3 61.3 + - - +
233F LYS* 3.4 19.2 + - - +
234F GLN* 3.3 25.9 + - - +
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Residues in contact with TYR 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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365D ILE* 4.7 11.4 - - + -
366D ILE* 5.7 0.7 - - - -
369D ASN* 3.0 46.7 - - + +
372D ARG* 3.8 5.3 - - - +
227F SER 3.1 11.7 + - - +
228F VAL* 3.6 11.4 - - + +
229F ARG 3.2 0.2 - - - -
230F ALA* 1.3 77.5 - - - +
232F LEU* 1.3 67.7 + - + +
234F GLN* 3.2 14.1 + - + +
235F ILE* 3.1 45.3 + - + +
300F LEU* 3.4 20.8 - - + +
304F VAL* 3.8 4.3 - - + +
318F LEU* 4.7 4.5 - - + -
321F ILE* 3.5 38.8 - - + +
325F ASN* 3.0 28.5 + - - -
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Residues in contact with LEU 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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228F VAL* 3.1 18.5 + - + +
229F ARG* 3.1 10.4 + - + +
231F TYR* 1.3 80.6 - - + +
233F LYS* 1.3 61.4 + - - +
235F ILE* 3.3 13.5 + - + +
236F GLY 3.3 16.8 + - - -
304F VAL* 3.9 28.0 - - + -
317F PHE* 5.7 1.6 - - + -
321F ILE* 6.2 0.2 - - + -
7H G 4.0 45.0 - - - +
8H G 3.4 53.6 - - + +
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Residues in contact with LYS 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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284C GLY* 3.9 23.1 - - - +
132D ALA* 6.1 0.4 - - - +
220F GLU* 3.7 31.0 - - + +
221F LEU 5.3 0.9 - - - -
222F THR 4.1 11.2 - - - +
223F ALA* 3.6 25.4 - - - +
224F SER 5.0 1.8 - - - +
229F ARG* 3.0 13.5 + - + +
230F ALA* 3.6 23.0 + - - +
231F TYR 3.3 0.2 - - - -
232F LEU* 1.3 76.8 - - - +
234F GLN* 1.3 82.1 + - - +
236F GLY* 3.4 12.0 + - - -
237F LYS* 4.0 12.6 - - - +
7H G 4.1 15.6 + - - +
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Residues in contact with GLN 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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238D GLU* 3.6 11.1 + - - -
365D ILE* 3.5 35.1 - - + +
372D ARG* 5.6 3.6 - - - +
230F ALA 3.3 13.7 + - - +
231F TYR* 3.2 12.1 + - + +
232F LEU 3.2 0.6 - - - -
233F LYS* 1.3 93.5 + - - +
235F ILE* 1.3 65.3 + - - +
237F LYS* 2.9 59.5 + - - +
238F VAL* 4.6 3.3 + - - +
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Residues in contact with ILE 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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365D ILE* 5.8 2.0 - - + -
231F TYR* 3.1 55.4 - - + +
232F LEU* 3.3 16.5 + - + +
234F GLN* 1.3 71.4 - - + +
236F GLY* 1.3 58.0 + - - +
237F LYS 2.8 12.7 + - - -
238F VAL* 3.4 22.3 + - - +
297F GLU 4.7 3.8 - - - +
300F LEU* 3.6 42.4 - - + +
301F ARG* 3.6 18.8 + - + +
304F VAL* 3.6 18.4 - - + -
7H G 5.1 5.4 - - - +
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Residues in contact with GLY 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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232F LEU 3.3 7.5 + - - -
233F LYS 3.4 6.0 + - - -
234F GLN 3.3 1.4 - - - -
235F ILE* 1.3 76.7 - - - +
237F LYS* 1.3 61.5 + - - +
301F ARG* 3.7 19.2 + - - -
7H G 3.6 38.3 - - - +
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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