Contacts of the helix formed by residues 230 - 237 (chain F) in PDB entry 1LT9
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 ASN 230 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F TRP* 5.6 0.2 - - - -
211F TYR 2.9 19.0 + - - +
212F LYS* 3.5 1.3 + - - -
227F TRP* 2.9 37.2 - - - +
229F GLY* 1.3 70.7 - - - -
231F GLU* 1.3 56.9 + - - +
233F ILE* 3.7 8.2 - - - +
234F HIS* 2.7 30.8 + - - +
267F VAL* 4.2 3.4 - - + +
274F TYR* 3.3 39.0 - - + -
312F PHE* 3.1 36.8 - - - -
335F TRP* 5.1 3.7 - - - -
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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
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212F LYS* 3.3 27.5 + - + +
213F GLU* 5.5 4.5 - - - +
229F GLY 3.1 1.0 - - - -
230F ASN* 1.3 73.8 - - - +
232F LYS* 1.3 68.9 + - + +
234F HIS* 3.2 12.8 + - - +
235F LEU* 2.9 51.3 + - + +
270F GLU* 4.7 4.3 + - - +
274F TYR* 2.9 31.5 + - - +
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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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205E VAL* 3.5 24.7 + - - +
206E VAL* 4.7 1.4 - - - +
207E SER* 5.2 2.6 - - - +
178F PHE* 3.4 59.2 - - + +
179F LEU 5.4 1.7 + - - -
212F LYS 5.6 0.4 - - - +
213F GLU* 2.9 30.0 + - - +
228F LEU* 3.2 35.8 + - + +
229F GLY* 2.9 6.1 + - - +
231F GLU* 1.3 80.8 - - + +
233F ILE* 1.3 64.2 + - - +
235F LEU* 2.8 18.1 + - + +
236F ILE* 2.9 18.0 + - - +
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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 PHE* 3.4 56.8 - - + -
227F TRP* 3.7 23.6 - - + -
228F LEU* 4.5 3.1 - - + -
229F GLY 2.9 22.8 + - - +
230F ASN* 3.7 9.0 - - - +
232F LYS* 1.3 74.4 - - - +
234F HIS* 1.3 55.7 + - - +
236F ILE* 3.5 9.7 + - - +
237F SER* 2.6 34.0 + - - -
265F PHE* 4.1 10.8 - - + -
267F VAL* 3.8 23.3 - - + -
335F TRP* 5.4 2.7 - - + -
386F ILE* 5.0 2.9 - - + -
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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 2.7 22.1 + - - +
231F GLU* 3.3 23.8 - - - +
233F ILE* 1.3 74.0 - - - +
235F LEU* 1.3 65.7 + - + +
237F SER* 3.2 3.4 + - - -
238F THR* 2.6 56.6 + - + -
267F VAL* 2.5 33.2 + - + +
268F GLY 3.2 13.2 + - - +
269F PRO* 3.4 41.0 - - + +
274F TYR* 4.2 2.0 - - + -
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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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171F PRO* 4.0 17.5 - - + +
173F LYS* 4.0 27.1 - - + +
174F ALA* 4.0 20.9 - - + -
175F ASN 5.3 1.3 - - - +
178F PHE* 4.5 7.9 - - + -
231F GLU* 2.9 43.8 + - + +
232F LYS* 2.8 13.0 + - + +
234F HIS* 1.3 87.3 - - + +
236F ILE* 1.3 61.1 + - - +
237F SER 3.3 0.7 + - - -
238F THR* 3.5 9.5 + - - +
239F GLN* 3.5 19.2 + - - +
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Residues in contact with ILE 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 ASP* 4.3 8.7 - - + -
169F ILE* 3.9 19.7 - - + -
171F PRO* 4.1 19.3 - - + -
178F PHE* 4.0 9.9 - - + -
192F THR* 3.9 21.3 - - + +
194F PHE* 6.1 0.7 - - + -
228F LEU* 4.0 22.9 - - + -
232F LYS 2.9 17.0 + - - +
233F ILE* 4.1 3.8 - - - +
235F LEU* 1.3 75.8 - - - +
237F SER* 1.3 57.4 + - - +
239F GLN* 3.5 8.4 - - - +
244F TYR* 3.0 36.1 - - + +
386F ILE* 3.5 24.2 - - + -
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Residues in contact with SER 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 22.8 + - - -
234F HIS 3.2 6.1 + - - -
236F ILE* 1.3 75.4 - - - +
238F THR* 1.3 59.4 + - - +
239F GLN 3.5 2.9 + - - +
242F ILE 4.8 3.5 - - - +
244F TYR* 4.1 15.2 + - - +
265F PHE* 3.9 22.6 - - - +
266F LYS* 3.7 33.6 - - - +
267F VAL* 3.4 18.9 + - - +
386F ILE* 4.5 4.7 - - - -
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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