Contacts of the helix formed by residues 207 - 214 (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 ASN 207 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205L LYS 3.9 0.6 + - - -
206L LYS* 1.3 71.3 - - - +
208L TRP* 1.3 58.8 + - - +
209L ILE* 2.8 25.7 + - - +
210L GLN* 2.5 42.3 + - - +
211L TYR* 3.0 33.6 + - - -
314L THR* 3.7 5.8 - - - -
315L TRP* 3.4 22.6 - - + +
316L ASP* 3.2 26.2 + - - +
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Residues in contact with TRP 208 (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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207L ASN* 1.3 77.3 - - - +
209L ILE* 1.3 79.1 + - + +
210L GLN 3.2 0.2 - - - -
211L TYR* 3.1 2.4 + - + +
212L LYS* 3.0 24.9 + - + +
270L GLU* 3.2 32.6 + - + -
273L LYS* 4.0 20.6 - - + -
274L TYR* 3.2 39.5 - + - -
312L PHE* 3.8 32.1 - + - -
314L THR* 3.2 28.5 + - + +
316L ASP* 3.3 14.2 + - - +
317L ASN* 3.5 42.1 + - + +
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Residues in contact with ILE 209 (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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216K ARG 3.9 23.3 - - - +
217K LYS* 4.1 14.4 - - - -
218K GLY* 4.6 1.1 - - - +
207L ASN* 2.8 15.7 + - - +
208L TRP* 1.3 86.7 - - + +
210L GLN* 1.3 59.5 + - + +
212L LYS* 3.4 5.8 + - + +
213L GLU* 3.1 46.8 + - + +
316L ASP* 5.6 2.0 - - - +
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Residues in contact with GLN 210 (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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217K LYS 4.4 6.7 - - - -
218K GLY* 4.0 24.1 + - - +
220K GLU* 3.4 29.5 + - - -
206L LYS* 2.8 37.2 - - + +
207L ASN* 2.5 46.7 + - - +
209L ILE* 1.3 79.4 - - + +
211L TYR* 1.3 60.7 + - - +
212L LYS 3.4 0.2 - - - -
214L GLY 3.2 15.9 + - - +
215L PHE* 3.0 27.0 - - + -
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Residues in contact with TYR 211 (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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204L PHE* 3.2 35.1 + - - -
206L LYS 3.5 8.3 - - - -
207L ASN 3.0 25.8 + - - +
208L TRP* 3.1 6.0 + - + +
210L GLN* 1.3 80.2 - - - +
212L LYS* 1.3 57.6 + - - +
215L PHE* 3.7 18.4 - + - -
227L TRP* 3.1 47.7 + + - -
229L GLY* 3.6 0.5 - - - -
230L ASN* 3.0 25.0 + - - +
312L PHE* 3.8 20.9 - + + -
314L THR* 3.6 11.9 - - + -
333L GLY* 3.3 15.0 - - - -
345L ASN* 3.0 47.1 + - - +
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Residues in contact with LYS 212 (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* 3.0 19.8 + - + +
209L ILE* 3.7 7.0 - - + +
211L TYR* 1.3 73.8 - - - +
213L GLU* 1.3 85.6 + - + +
214L GLY 3.1 4.7 + - - -
229L GLY* 3.7 2.6 - - - -
230L ASN* 3.5 8.8 + - - -
231L GLU* 3.3 55.9 + - + +
232L LYS* 4.3 3.3 + - - -
270L GLU* 3.1 38.2 + - - +
274L TYR* 3.6 16.8 - - + +
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Residues in contact with GLU 213 (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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206K VAL* 3.9 12.3 - - + -
207K SER 4.9 0.7 + - - -
217K LYS* 3.3 68.2 + - + +
209L ILE* 3.1 24.4 + - + +
212L LYS* 1.3 103.7 + - - +
214L GLY* 1.3 61.3 + - - +
231L GLU* 5.0 3.6 - - - +
232L LYS* 3.3 24.0 + - - +
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Residues in contact with GLY 214 (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* 4.1 5.2 - - - -
206K VAL* 3.4 13.9 - - - +
217K LYS 4.9 1.2 - - - +
210L GLN* 3.2 17.1 + - - +
211L TYR 4.3 0.4 - - - -
212L LYS 3.1 5.3 - - - -
213L GLU* 1.3 84.4 - - - +
215L PHE* 1.3 65.2 + - - +
227L TRP 3.2 14.6 - - - -
228L LEU 3.9 2.9 - - - -
229L GLY* 3.6 12.3 - - - -
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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