Contacts of the helix formed by residues 215 - 221 (chain P) in PDB entry 2I2X
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 215 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M ARG* 5.4 5.7 - - - +
213P ALA 4.3 0.9 + - - +
214P VAL* 1.3 75.0 - - - +
216P GLN* 1.3 65.7 + - - +
217P ASP* 3.8 21.9 + - - +
218P PHE* 3.2 29.8 + - - +
219P VAL* 3.2 15.8 + - - +
227P TYR* 3.8 15.3 - - + +
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Residues in contact with GLN 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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64M ARG* 5.6 6.2 + - - +
215P ASN* 1.3 76.3 - - - +
217P ASP* 1.3 74.6 + - - +
219P VAL* 3.2 4.5 + - - +
220P SER* 2.8 28.8 + - - +
227P TYR* 3.6 24.4 - - + -
256P HIS* 3.4 40.0 - - + +
257P LYS* 3.0 33.2 + - - +
258P HIS* 3.1 36.9 + - + +
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Residues in contact with ASP 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ARG* 4.7 10.0 + - - -
64M ARG* 4.4 16.2 + - - -
215P ASN* 3.4 17.3 + - - +
216P GLN* 1.3 85.7 - - - +
218P PHE* 1.3 65.9 + - - +
220P SER* 3.3 15.6 + - - -
221P GLN* 3.5 11.3 + - - +
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Residues in contact with PHE 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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188P MET* 3.2 57.9 - - + -
189P TYR* 3.5 23.3 - + - -
191P PHE* 4.0 9.2 - + - -
213P ALA 5.7 0.2 - - - +
214P VAL* 4.0 19.7 - - + -
215P ASN* 3.2 28.4 + - - +
216P GLN 3.2 0.4 - - - -
217P ASP* 1.3 78.3 - - - +
219P VAL* 1.3 61.7 + - + +
221P GLN* 3.0 54.5 + - - +
222P PHE* 3.5 28.0 - + - -
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Residues in contact with VAL 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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209P CYS* 3.9 19.3 - - + -
214P VAL* 3.4 23.8 - - + -
215P ASN 3.4 14.6 - - - +
216P GLN 3.2 3.4 + - - +
218P PHE* 1.3 76.8 - - + +
220P SER* 1.3 65.0 + - - +
221P GLN 3.1 0.2 - - - -
222P PHE* 3.1 35.6 + - + +
225P GLY* 3.7 14.5 - - - +
226P VAL 3.6 7.0 - - - +
227P TYR* 3.3 41.7 - - + +
252P ARG* 3.7 1.2 + - - -
256P HIS* 4.6 2.0 - - + -
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Residues in contact with SER 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216P GLN* 2.8 21.9 + - - +
217P ASP* 3.7 9.9 - - - -
218P PHE 3.2 0.6 - - - -
219P VAL* 1.3 78.9 - - - +
221P GLN* 1.3 58.2 + - - +
222P PHE 3.1 2.6 + - - +
252P ARG* 3.3 32.5 + - - +
256P HIS* 2.9 29.5 + - - -
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Residues in contact with GLN 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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189P TYR* 3.9 14.3 + - - -
217P ASP 3.5 6.5 + - - +
218P PHE* 3.0 52.9 + - - +
219P VAL 3.1 1.2 - - - -
220P SER* 1.3 76.3 - - - +
222P PHE* 1.3 77.2 + - + +
223P ALA 4.2 0.3 + - - -
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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