Contacts of the helix formed by residues 214 - 221 (chain D) in PDB entry 4PE5
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 CYS 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B GLY 4.4 7.6 - - - -
213B ASP 4.4 1.1 - - - -
214B CYS* 2.0 52.7 - - + -
217B GLN* 4.1 2.5 - - - +
211D ASP* 3.7 17.4 + - - -
212D GLY* 3.2 8.3 - - - -
213D ASP* 1.3 76.9 + - - +
215D LYS* 1.3 64.9 + - - +
216D ILE 3.3 2.7 - - - -
217D GLN* 3.5 21.6 + - + +
218D ASN* 3.1 24.7 + - - +
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Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLN* 5.7 1.1 - - - +
211D ASP* 3.5 3.0 + - - +
213D ASP* 3.2 28.5 + - - +
214D CYS* 1.3 75.7 - - - +
216D ILE* 1.3 71.1 + - + +
218D ASN* 3.0 8.6 + - - +
219D GLN* 3.0 34.0 + - - +
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Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 4.2 18.6 - - + +
206D ASP* 4.3 17.0 - - + +
207D MET* 3.6 30.5 - - + -
210D ASP 6.0 0.4 - - - +
211D ASP* 3.2 27.7 + - - +
215D LYS* 1.3 84.6 - - + +
217D GLN* 1.3 63.9 + - - +
219D GLN* 3.0 23.8 + - - +
220D LEU* 2.9 28.1 + - + +
239D TYR* 4.4 7.2 - - + -
240D ILE* 5.7 2.0 - - + -
243D VAL* 4.2 21.8 - - + -
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Residues in contact with GLN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASP* 3.0 29.1 + - - +
214B CYS* 3.9 10.3 - - - +
218B ASN* 3.9 19.2 - - - +
211D ASP* 4.1 3.7 + - - +
214D CYS* 3.5 19.2 + - + +
216D ILE* 1.3 79.8 - - - +
218D ASN* 1.3 62.7 + - - +
220D LEU* 3.3 3.1 + - - +
221D LYS* 2.8 29.8 + - + +
243D VAL* 3.8 21.1 - - + +
246D SER* 5.3 5.5 - - - +
247D VAL* 4.1 21.2 - - + +
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Residues in contact with ASN 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLN* 3.7 16.9 + - - +
218B ASN* 2.7 47.0 + - - +
221B LYS* 4.7 9.3 - - - +
214D CYS 3.1 12.5 + - - +
215D LYS* 3.0 11.2 + - - +
217D GLN* 1.3 79.9 + - - +
219D GLN* 1.3 63.5 + - + +
221D LYS* 3.3 9.1 - - - +
222D LYS* 3.1 20.3 + - - +
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 3.1 34.4 - - + +
204D LEU 3.3 26.8 + - - +
205D LEU* 3.6 23.1 - - + +
206D ASP 5.2 0.8 - - - +
215D LYS* 3.0 23.0 + - + +
216D ILE* 3.0 23.6 + - - +
218D ASN* 1.3 76.4 - - + +
220D LEU* 1.3 67.8 + - - +
221D LYS 2.9 1.1 - - - -
222D LYS* 2.8 20.0 + - - +
223D LEU 3.6 0.3 + - - -
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D VAL* 4.4 16.6 - - + -
203D LEU* 4.4 3.4 - - + -
205D LEU* 4.6 5.6 - - + -
216D ILE* 2.9 22.7 + - + +
217D GLN 3.9 4.0 - - - +
219D GLN* 1.3 75.7 - - - +
221D LYS* 1.3 58.4 + - - +
222D LYS 2.9 5.4 + - - -
223D LEU* 3.0 34.8 + - + +
240D ILE* 3.5 31.2 - - + +
243D VAL* 3.6 15.9 - - + -
244D ALA* 3.4 33.2 - - + +
247D VAL* 5.1 1.8 - - + -
249D LEU* 3.2 28.8 - - + +
256D TRP* 4.5 5.4 - - + -
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Residues in contact with LYS 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASN* 5.0 10.5 - - - +
217D GLN* 2.8 18.8 + - + +
218D ASN* 3.3 12.8 - - - +
219D GLN 2.9 0.4 - - - -
220D LEU* 1.3 77.0 - - - +
222D LYS* 1.3 57.3 + - - +
223D LEU 3.4 4.0 - - - +
224D GLN* 5.5 1.7 + - - +
247D VAL* 4.0 22.9 - - + +
249D LEU* 4.8 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