Contacts of the helix formed by residues 229 - 238 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I TYR 3.5 10.8 - - - -
212I ARG 3.8 6.5 - - - -
213I GLU 4.0 0.9 - - - -
214I GLY* 3.7 9.9 - - - -
227I TRP* 3.0 6.6 + - - +
228I LEU* 1.3 80.9 - - - +
230I ASN* 1.3 69.6 + - - -
231I GLU 3.3 2.9 - - - -
232I LYS* 3.4 6.1 + - - +
233I ILE* 3.0 28.2 + - - +
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Residues in contact with ASN 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I TRP* 5.2 0.7 - - - -
211I TYR* 2.8 22.3 + - - +
212I ARG* 3.4 3.0 + - - -
227I TRP* 2.7 45.2 - - - +
229I GLY* 1.3 71.0 - - - -
231I GLU* 1.3 58.0 - - - +
233I ILE* 3.4 7.4 + - - +
234I HIS* 2.9 29.3 + - - +
265I LEU* 4.4 7.3 - - + +
272I TYR* 3.3 40.0 - - + -
310I PHE* 3.3 34.9 - - - -
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Residues in contact with GLU 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I LYS* 6.1 4.9 - - - -
212I ARG* 3.1 22.9 + - + +
213I GLU* 5.3 3.1 - - - +
230I ASN* 1.3 74.1 - - - +
232I LYS* 1.3 69.5 + - + +
234I HIS* 3.2 15.6 + - - +
235I LEU* 3.0 48.8 + - + +
268I GLU* 4.7 5.5 + - - +
272I TYR* 2.7 36.0 + - - +
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Residues in contact with LYS 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H VAL* 3.5 27.1 + - - +
179I PHE* 3.6 58.3 - - + +
180I LEU 4.6 2.6 + - - -
212I ARG 5.2 0.9 - - - +
213I GLU 3.5 14.5 + - - +
228I LEU* 3.2 42.9 + - + +
229I GLY* 3.4 6.0 + - - +
230I ASN 3.4 0.4 - - - -
231I GLU* 1.3 78.0 - - + +
233I ILE* 1.3 54.8 + - - +
235I LEU* 2.9 14.3 + - + +
236I LEU* 2.7 37.5 + - - +
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Residues in contact with ILE 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I ILE* 3.1 50.7 - - + +
227I TRP* 4.0 23.1 - - + -
228I LEU* 4.6 2.0 - - + -
229I GLY 3.0 33.1 + - - +
230I ASN* 3.6 7.0 - - - +
232I LYS* 1.3 75.3 - - - +
234I HIS* 1.3 52.2 + - - +
236I LEU* 4.2 6.5 - - - -
237I THR* 2.6 41.7 + - + +
263I PHE* 4.2 18.6 - - + -
265I LEU* 3.6 25.4 - - + -
333I TRP* 5.9 0.9 - - + -
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Residues in contact with HIS 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I ASN 2.9 14.5 + - - +
231I GLU* 3.3 25.4 - - - +
232I LYS 3.0 0.2 - - - -
233I ILE* 1.3 76.1 - - - +
235I LEU* 1.3 62.6 + - + +
237I THR* 3.1 5.9 + - - -
238I GLY* 2.8 38.7 + - - -
265I LEU* 2.6 27.8 + - + +
267I PRO* 3.1 53.1 - - + +
272I TYR* 4.1 10.8 - - + -
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I PRO* 3.9 15.0 - - + +
173I LEU* 5.0 1.6 + - - +
174I LYS* 3.5 40.2 + - + +
175I ALA* 3.8 22.2 - - + +
176I LYS* 5.1 3.8 - - + +
179I PHE* 5.3 2.7 - - + -
231I GLU* 3.0 41.4 + - + +
232I LYS* 2.9 13.2 + - + +
234I HIS* 1.3 82.8 - - + +
236I LEU* 1.3 63.5 + - - +
238I GLY* 4.0 1.3 - - - -
239I GLN* 3.4 20.1 + - - +
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Residues in contact with LEU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I LYS 3.9 6.5 - - - +
153I ASP* 3.7 16.2 - - + -
170I ILE* 4.3 12.1 - - + -
172I PRO* 3.9 14.5 - - + +
179I PHE* 5.1 1.6 - - + -
192I THR* 3.3 27.1 - - + +
194I ILE* 4.4 10.3 - - + -
228I LEU* 4.9 6.3 - - + -
232I LYS 2.7 18.9 + - - +
233I ILE* 3.8 5.4 - - - +
235I LEU* 1.3 74.6 - - - +
237I THR* 1.3 57.8 + - + +
239I GLN* 3.2 22.1 - - - +
242I TYR* 2.9 50.4 - - + +
384I LEU* 4.4 17.9 - - + -
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Residues in contact with THR 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I ILE* 2.6 25.5 + - + +
234I HIS* 3.1 7.1 + - - -
236I LEU* 1.3 70.6 - - - +
238I GLY* 1.3 54.8 + - - +
239I GLN 3.0 5.6 + - - -
240I GLN 2.6 28.4 - - - +
242I TYR* 3.7 8.9 - - + -
263I PHE* 3.6 28.7 - - + +
264I LYS* 3.4 29.8 - - - +
265I LEU 3.4 7.4 + - - -
384I LEU* 3.3 31.9 - - + -
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Residues in contact with GLY 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I LEU* 6.0 0.5 - - - +
234I HIS* 2.8 28.0 + - - -
235I LEU* 4.0 2.7 - - - -
236I LEU 3.5 0.2 - - - -
237I THR* 1.3 72.4 + - - +
239I GLN* 1.3 60.0 + - - +
240I GLN 3.5 0.9 - - - -
264I LYS* 5.3 11.4 - - - -
265I 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