Contacts of the helix formed by residues 229 - 238 (chain L) in PDB entry 2HPC
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 3.6 0.9 - - - -
212L LYS 3.7 4.9 - - - -
214L GLY* 3.6 18.8 - - - -
227L TRP* 2.7 16.9 + - - -
228L LEU* 1.3 78.5 - - - +
230L ASN* 1.3 57.1 + - - -
231L GLU 3.6 1.6 - - - -
232L LYS* 3.2 5.7 - - - +
233L ILE* 2.6 43.2 + - - +
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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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211L TYR* 3.0 13.0 + - - +
212L LYS* 3.5 2.2 + - - -
227L TRP* 2.6 48.5 - - - +
229L GLY* 1.3 66.3 - - - -
231L GLU* 1.3 57.8 + - - +
232L LYS 2.5 16.6 + - - -
233L ILE* 2.9 11.2 + - - +
234L HIS* 2.9 23.2 + - - +
267L VAL* 4.8 3.5 - - + +
274L TYR* 3.6 32.7 - - + +
312L PHE* 3.2 41.4 - - - -
335L TRP* 5.3 1.7 - - - -
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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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212L LYS* 3.3 47.5 + - + +
213L GLU* 5.0 3.8 - - - +
230L ASN* 1.3 77.6 - - - +
232L LYS* 1.3 59.6 + - - +
234L HIS* 3.6 15.7 - - - +
235L LEU* 3.6 25.5 - - + +
270L GLU* 4.2 7.8 + - - +
274L TYR* 2.7 33.4 + - - +
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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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205K VAL* 4.2 11.7 - - - +
206K VAL* 5.0 3.4 - - - +
207K SER* 5.1 5.1 - - - +
178L PHE* 3.2 56.2 - - + +
179L LEU 5.6 1.1 + - - +
212L LYS 4.3 2.1 + - - -
213L GLU* 3.3 26.9 + - - +
228L LEU* 3.3 33.9 + - + -
229L GLY* 3.2 10.7 + - - +
230L ASN 2.5 4.6 + - - -
231L GLU* 1.3 73.9 - - - +
233L ILE* 1.3 56.3 + - - +
234L HIS 2.7 15.7 + - - -
235L LEU* 2.8 22.6 + - + +
236L ILE* 3.2 10.6 + - - +
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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 PHE* 3.0 55.9 - - + -
227L TRP* 3.9 6.5 - - + -
228L LEU* 5.0 0.9 - - + -
229L GLY 2.6 40.0 + - - +
230L ASN* 2.9 23.3 + - - +
232L LYS* 1.3 71.5 - - + +
234L HIS* 1.3 66.8 + - - +
236L ILE* 3.3 12.3 + - + +
237L SER* 2.9 31.7 + - - +
265L PHE* 4.2 3.6 - - + -
267L VAL* 3.7 22.9 - - + -
335L TRP* 5.9 0.7 - - + -
386L ILE* 5.2 6.3 - - + -
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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 9.9 + - - +
231L GLU* 3.6 23.8 - - - +
232L LYS 2.7 4.0 + - - -
233L ILE* 1.3 79.5 - - - +
235L LEU* 1.3 72.5 + - + +
237L SER* 2.6 19.8 + - - -
238L THR* 2.9 30.7 + - + -
267L VAL* 2.5 33.1 + - - +
268L GLY* 3.1 11.8 - - - +
269L PRO* 3.0 49.3 - - + +
274L TYR* 4.5 1.6 - - + -
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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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171L PRO* 3.7 20.3 - - + +
173L LYS* 4.2 30.1 - - + +
174L ALA* 3.7 21.8 - - + -
175L ASN* 5.2 2.7 - - - +
178L PHE* 4.8 6.5 - - + -
231L GLU* 3.6 30.3 - - + +
232L LYS* 2.8 14.5 + - + +
234L HIS* 1.3 87.5 - - + +
236L ILE* 1.3 61.6 + - - +
238L THR* 3.8 5.7 - - - -
239L GLN* 3.3 26.3 + - - +
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Residues in contact with ILE 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 ASP* 4.5 9.6 - - + -
169L ILE* 3.9 11.4 - - + -
171L PRO* 3.8 18.8 - - + -
178L PHE* 3.8 27.6 - - + -
180L VAL* 5.0 0.9 - - + -
192L THR* 4.3 13.5 - - + +
194L PHE* 5.8 3.4 - - + -
228L LEU* 4.4 15.3 - - + -
232L LYS 3.2 7.0 + - - +
233L ILE* 3.9 10.3 - - + +
234L HIS 2.9 3.0 + - - -
235L LEU* 1.3 75.9 - - - +
237L SER* 1.3 52.3 + - - +
239L GLN* 3.1 8.5 - - - +
244L TYR* 2.7 47.9 - - + +
386L ILE* 3.1 28.3 - - + -
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Residues in contact with SER 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* 2.9 20.8 + - - +
234L HIS 2.6 10.3 + - - -
236L ILE* 1.3 73.9 - - - +
238L THR* 1.3 59.9 + - - +
239L GLN 3.7 1.3 + - - -
242L ILE* 4.9 4.7 - - - +
244L TYR* 3.5 21.5 - - - +
265L PHE* 3.4 31.4 - - - +
266L LYS* 3.6 35.9 - - - +
267L VAL 3.6 5.5 + - - -
386L ILE* 4.3 3.9 - - - +
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Residues in contact with THR 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 LYS* 3.4 18.4 + - - +
234L HIS* 2.9 31.9 + - + +
235L LEU* 3.8 5.2 + - - +
237L SER* 1.3 79.8 - - - +
239L GLN* 1.3 57.0 + - - +
240L SER 4.1 0.8 + - - -
266L LYS* 3.2 48.9 - - + +
267L VAL 4.0 15.9 - - - +
268L GLY* 5.8 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