Contacts of the helix formed by residues 229 - 238 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211L TYR 3.5 11.0 - - - -
212L ARG 3.8 6.7 - - - -
213L GLU 4.0 1.1 - - - -
214L GLY* 3.8 9.0 - - - -
227L TRP* 3.0 6.8 + - - +
228L LEU* 1.3 81.3 - - - +
230L ASN* 1.3 68.6 + - - -
231L GLU 3.3 2.9 + - - -
232L LYS* 3.4 5.3 + - - +
233L ILE* 3.0 28.6 + - - +
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Residues in contact with ASN 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L TRP* 5.2 0.5 - - - -
211L TYR* 2.9 22.4 + - - +
212L ARG* 3.5 2.8 + - - -
227L TRP* 2.7 44.4 - - - +
229L GLY* 1.3 71.4 - - - -
231L GLU* 1.3 57.2 - - - +
233L ILE* 3.4 7.4 + - - +
234L HIS* 2.9 29.5 + - - +
265L LEU* 4.4 7.1 - - + +
272L TYR* 3.2 39.5 - - + -
310L PHE* 3.3 36.6 - - - -
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Residues in contact with GLU 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L LYS* 6.1 4.9 - - - -
212L ARG* 3.1 23.1 + - + +
213L GLU* 5.4 2.9 - - - +
230L ASN* 1.3 79.1 - - - +
232L LYS* 1.3 65.6 + - + +
234L HIS* 3.2 16.5 + - - +
235L LEU* 3.0 47.2 + - + +
267L PRO* 5.9 0.2 - - - +
268L GLU* 4.8 5.4 + - - +
272L TYR* 2.7 36.1 + - - +
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Residues in contact with LYS 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K VAL* 3.4 26.7 + - - +
179L PHE* 3.6 50.0 - - + +
180L LEU 4.6 2.8 + - - -
212L ARG 5.2 1.1 - - - +
213L GLU 3.5 14.3 + - - +
228L LEU* 3.2 49.8 + - + +
229L GLY* 3.4 6.5 + - - +
230L ASN 3.4 0.2 - - - -
231L GLU* 1.3 77.3 - - + +
233L ILE* 1.3 57.0 + - - +
235L LEU* 2.8 14.8 + - + +
236L LEU* 2.7 37.7 + - - +
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Residues in contact with ILE 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L ILE* 3.1 50.5 - - + +
227L TRP* 4.0 20.2 - - + -
228L LEU* 4.5 2.0 - - + +
229L GLY 3.0 36.1 + - - +
230L ASN* 3.6 6.7 - - - +
232L LYS* 1.3 74.8 - - - +
234L HIS* 1.3 50.8 + - - +
236L LEU* 4.2 6.5 - - - -
237L THR* 2.7 50.1 + - + +
263L PHE* 4.2 11.0 - - + -
265L LEU* 3.5 26.9 - - + -
333L TRP* 5.9 0.7 - - + -
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Residues in contact with HIS 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230L ASN 2.9 15.4 + - - +
231L GLU* 3.3 25.8 - - - +
232L LYS 3.0 0.2 - - - -
233L ILE* 1.3 76.1 - - - +
235L LEU* 1.3 62.4 + - + +
237L THR* 3.1 6.2 + - - -
238L GLY* 2.8 38.1 + - - -
265L LEU* 2.5 28.6 + - + +
266L THR* 4.1 0.9 - - - +
267L PRO* 3.1 52.3 - - + +
272L TYR* 4.2 9.6 - - + -
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Residues in contact with LEU 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L PRO* 3.9 15.3 - - + +
173L LEU* 5.0 1.4 + - - +
174L LYS* 3.4 41.1 + - + +
175L ALA* 3.7 23.1 - - + +
176L LYS* 5.1 3.8 - - + +
179L PHE* 5.3 2.5 - - + -
231L GLU* 3.0 41.8 + - + +
232L LYS* 2.8 13.4 + - + +
234L HIS* 1.3 82.2 - - + +
236L LEU* 1.3 64.8 + - - +
238L GLY* 3.6 1.4 + - - -
239L GLN* 3.4 19.6 + - - +
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Residues in contact with LEU 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L LYS 3.8 6.5 - - - +
153L ASP* 3.7 15.5 - - + -
170L ILE* 4.3 11.9 - - + -
172L PRO* 3.9 14.1 - - + +
179L PHE* 5.1 1.6 - - + -
192L THR* 3.3 26.9 - - + +
194L ILE* 4.4 10.8 - - + -
228L LEU* 4.9 6.5 - - + -
232L LYS 2.7 18.5 + - - +
233L ILE* 3.8 5.4 - - - +
235L LEU* 1.3 73.7 - - - +
237L THR* 1.3 57.9 + - - +
239L GLN* 3.1 23.3 - - - +
242L TYR* 3.0 46.3 - - + +
384L LEU* 4.4 17.9 - - + -
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Residues in contact with THR 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233L ILE* 2.7 25.8 + - + +
234L HIS* 3.1 7.1 + - - -
236L LEU* 1.3 70.6 - - - +
238L GLY* 1.3 56.7 + - - +
239L GLN 3.0 5.6 - - - -
240L GLN 2.7 26.7 - - - +
242L TYR* 3.7 8.5 - - + -
263L PHE* 3.6 28.7 - - + +
264L LYS* 3.4 30.2 - - - +
265L LEU 3.4 7.4 + - - -
384L LEU* 3.3 31.9 - - + -
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Residues in contact with GLY 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L LEU* 6.0 0.3 - - - +
234L HIS* 2.8 27.4 + - - -
235L LEU* 4.0 2.7 - - - -
237L THR* 1.3 72.6 + - - +
239L GLN* 1.3 59.2 + - - +
240L GLN 3.5 1.1 - - - -
264L LYS* 5.2 12.8 - - - -
265L LEU 5.9 0.7 - - - -
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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