Contacts of the helix formed by residues 229 - 238 (chain F) in PDB entry 1LWU
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 GLY 229 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F TYR 3.5 11.2 - - - -
212F ARG 3.7 7.2 - - - -
213F GLU 4.0 0.9 - - - -
214F GLY* 3.8 8.7 - - - -
227F TRP* 3.0 6.8 + - - +
228F LEU* 1.3 80.8 - - - +
230F ASN* 1.3 69.3 + - - -
231F GLU 3.3 3.0 + - - -
232F LYS* 3.3 6.1 + - - +
233F ILE* 2.9 28.6 + - - +
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Residues in contact with ASN 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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208F TRP* 5.2 0.3 - - - -
211F TYR* 2.9 20.6 + - - +
212F ARG* 3.5 3.0 + - - -
227F TRP* 2.7 41.8 - - - +
229F GLY* 1.3 73.9 - - - +
231F GLU* 1.3 57.8 + - - +
233F ILE* 3.4 6.8 + - - +
234F HIS* 2.9 28.9 + - - +
265F LEU* 4.4 8.2 - - + +
272F TYR* 3.3 39.3 - - + -
310F PHE* 3.3 35.9 - - - -
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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
----------------------------------------------------------
176F LYS* 6.1 4.9 - - - -
212F ARG* 3.2 22.2 + - + +
213F GLU* 5.3 3.4 - - - +
230F ASN* 1.3 75.1 - - - +
232F LYS* 1.3 68.8 + - + +
234F HIS* 3.2 14.5 + - - +
235F LEU* 3.0 47.6 + - + +
267F PRO* 5.9 0.2 - - - +
268F GLU* 4.8 5.4 + - - +
272F TYR* 2.7 37.1 + - - +
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Residues in contact with LYS 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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226E VAL* 3.8 22.4 + - - +
179F PHE* 3.6 56.7 - - + +
180F LEU 4.5 3.0 + - - +
212F ARG 5.2 0.7 - - - +
213F GLU 3.5 14.5 + - - +
228F LEU* 3.2 45.6 + - + +
229F GLY* 3.3 6.7 + - - +
231F GLU* 1.3 78.0 - - + +
233F ILE* 1.3 56.5 + - - +
235F LEU* 2.9 15.3 + - + +
236F LEU* 2.7 36.9 + - - +
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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 ILE* 3.1 50.7 - - + -
227F TRP* 4.0 20.2 - - + -
228F LEU* 4.5 2.4 - - + +
229F GLY 2.9 36.1 + - - +
230F ASN* 3.6 7.4 - - - +
232F LYS* 1.3 75.3 - - - +
234F HIS* 1.3 49.9 + - - +
236F LEU* 3.8 6.2 - - - +
237F THR* 2.6 41.6 + - + +
263F PHE* 4.2 18.6 - - + -
265F LEU* 3.5 27.4 - - + -
333F TRP* 6.0 0.7 - - + -
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Residues in contact with HIS 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 ASN 2.9 13.8 + - - +
231F GLU* 3.3 26.5 - - - +
233F ILE* 1.3 73.8 - - - +
235F LEU* 1.3 62.8 + - + +
237F THR* 3.1 6.2 + - - -
238F GLY* 2.8 38.4 + - - -
265F LEU* 2.6 30.3 + - + +
267F PRO* 3.1 52.0 - - + +
272F TYR* 4.2 10.1 - - + -
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Residues in contact with LEU 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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172F PRO* 3.9 15.2 - - + +
173F LEU* 5.0 1.4 + - - +
174F LYS* 3.5 39.7 + - + +
175F ALA* 3.8 22.2 - - + +
176F LYS* 5.1 4.0 - - + +
179F PHE* 5.3 2.2 - - + -
231F GLU* 3.0 42.5 + - + +
232F LYS* 2.9 13.2 + - + +
234F HIS* 1.3 82.5 - - + +
236F LEU* 1.3 64.9 + - - +
238F GLY* 4.1 1.5 - - - -
239F GLN* 3.4 19.6 + - - +
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Residues in contact with LEU 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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152F LYS 3.8 6.1 - - - +
153F ASP* 3.7 16.2 - - + -
170F ILE* 4.3 11.9 - - + -
172F PRO* 3.9 14.1 - - + +
179F PHE* 5.1 1.3 - - + -
192F THR* 3.3 26.7 - - + +
194F ILE* 4.4 11.2 - - + -
228F LEU* 4.9 6.3 - - + -
232F LYS 2.7 18.8 + - - +
233F ILE* 3.8 5.2 - - - +
235F LEU* 1.3 73.5 - - - +
237F THR* 1.3 58.7 + - + +
239F GLN* 3.1 21.8 - - - +
242F TYR* 2.9 51.1 - - + +
384F LEU* 4.4 17.9 - - + -
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Residues in contact with THR 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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233F ILE 2.6 25.3 + - - +
234F HIS* 3.1 7.1 + - - -
236F LEU* 1.3 70.4 - - - +
238F GLY* 1.3 56.5 + - - +
239F GLN 3.0 5.6 + - - -
240F GLN 2.7 26.3 - - - +
242F TYR* 3.7 9.3 - - + -
263F PHE* 3.6 28.6 - - + +
264F LYS* 3.4 29.5 - - - +
265F LEU 3.5 8.0 + - - -
384F LEU* 3.3 31.6 - - + -
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Residues in contact with GLY 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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173F LEU* 6.1 0.2 - - - +
234F HIS* 2.8 26.8 + - - -
235F LEU* 4.1 2.7 - - - -
237F THR* 1.3 73.9 + - - +
239F GLN* 1.3 59.3 + - - +
240F GLN 3.5 1.7 - - - +
264F LYS* 5.2 12.3 - - - -
265F LEU 5.9 0.4 - - - -
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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