Contacts of the helix formed by residues 215 - 222 (chain P) in PDB entry 5A31
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 ASP 215 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213P ILE* 3.7 7.6 - - - +
214P THR* 1.3 106.3 + - - +
216P LYS* 1.3 66.4 + - - +
217P GLU* 3.2 31.2 - - + +
218P MET* 3.1 16.1 + - + +
219P LEU* 3.1 17.8 + - - +
241P LEU* 3.9 7.4 - - - -
397P ARG* 5.5 2.0 + - - -
427P GLN* 4.2 14.4 - - - +
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Residues in contact with LYS 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P ASP* 1.3 73.9 - - - +
217P GLU* 1.3 62.6 + - - +
219P LEU* 3.3 11.1 + - - +
220P LYS* 3.2 37.7 + - - +
238P TYR* 6.3 2.9 - - + -
241P LEU* 3.8 18.5 - - + +
242P GLN* 4.6 23.8 - - - +
243P LEU* 4.3 31.8 - - + +
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Residues in contact with GLU 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P ASP* 3.9 23.4 - - + +
216P LYS* 1.3 76.6 - - - +
218P MET* 1.3 68.0 + - + +
220P LYS* 3.1 12.5 + - - +
221P PHE* 3.0 43.2 + - + -
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Residues in contact with MET 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P VAL* 6.5 0.4 - - + -
189P ILE* 3.9 21.1 - - + -
212P LEU 4.2 2.2 - - - +
213P ILE* 3.8 17.0 - - + -
214P THR* 3.1 40.8 - - - +
215P ASP* 3.1 20.8 + - + +
217P GLU* 1.3 83.5 - - + +
219P LEU* 1.3 62.4 + - - +
221P PHE* 3.4 13.0 + - + +
222P LEU* 3.3 26.6 + - + +
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Residues in contact with LEU 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213P ILE* 4.1 21.2 - - + +
215P ASP 3.1 11.8 + - - +
216P LYS* 3.3 14.4 - - - +
217P GLU 3.2 0.2 - - - -
218P MET* 1.3 73.7 - - - +
220P LYS* 1.3 64.7 + - + +
222P LEU* 3.4 22.0 + - + +
224P LEU* 4.3 12.2 - - + +
233P PHE* 4.1 26.9 - - + -
234P LEU* 4.4 26.2 - - + -
237P ILE* 4.1 23.3 - - + -
238P TYR* 4.7 10.3 - - + +
241P LEU* 5.4 2.2 - - + -
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Residues in contact with LYS 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216P LYS* 3.2 22.3 + - - +
217P GLU* 3.1 13.5 + - - +
219P LEU* 1.3 78.0 - - + +
221P PHE* 1.3 62.8 + - + +
222P LEU 3.4 6.2 + - - +
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Residues in contact with PHE 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217P GLU* 3.0 44.0 + - + -
218P MET* 3.6 10.8 - - + +
219P LEU 3.3 0.2 - - - -
220P LYS* 1.3 79.0 - - + +
222P LEU* 1.3 63.3 + - + +
223P SER* 3.7 2.3 + - - -
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Residues in contact with LEU 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P ILE* 3.6 22.0 - - + -
190P ASP* 5.1 4.9 - - - +
193P VAL* 3.7 28.0 - - + -
209P LEU* 4.7 6.7 - - + -
213P ILE* 3.4 34.3 - - + -
218P MET* 3.3 17.1 + - + +
219P LEU* 3.4 20.9 - - + +
220P LYS 3.3 6.8 - - - +
221P PHE* 1.3 81.3 - - + +
223P SER* 1.3 59.3 + - - +
224P LEU* 4.0 13.7 + - + +
230P LYS* 5.5 1.4 + - - -
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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