Contacts of the helix formed by residues 219 - 228 (chain D) in PDB entry 2PI8
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 SER 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D HIS* 1.3 75.3 - - - +
220D GLU* 1.3 60.7 + - - +
221D ALA* 3.9 6.9 + - - +
222D GLU* 3.1 33.0 + - - +
223D VAL* 2.9 31.3 + - - +
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Residues in contact with GLU 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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118D TYR* 3.2 32.3 + - + +
153D LEU* 3.6 28.3 - - - +
219D SER* 1.3 73.5 - - - +
221D ALA* 1.3 58.6 + - - +
223D VAL* 3.2 9.6 + - - +
224D ARG* 2.8 36.4 + - + +
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Residues in contact with ALA 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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219D SER* 3.3 7.5 + - - +
220D GLU* 1.3 78.9 - - - +
222D GLU* 1.3 59.2 + - + +
224D ARG* 3.7 6.6 + - - +
225D GLU* 3.2 29.1 + - - +
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Residues in contact with GLU 222 (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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214D TRP* 3.4 18.4 - - + -
218D HIS* 3.5 31.6 - - + +
219D SER* 3.1 36.6 + - - +
221D ALA* 1.3 75.9 - - + +
223D VAL* 1.3 64.2 + - - +
225D GLU* 3.8 9.3 + - - +
226D LEU* 3.4 13.3 + - - +
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Residues in contact with VAL 223 (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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153D LEU* 5.3 4.3 - - + -
154D MSE 3.9 31.2 - - + +
214D TRP* 3.9 11.9 - - + -
215D GLY* 3.4 33.7 - - - +
218D HIS 3.9 3.1 - - - +
219D SER 2.9 22.0 + - - +
220D GLU* 3.2 11.6 + - - +
222D GLU* 1.3 75.0 - - - +
224D ARG* 1.3 65.6 + - - +
226D LEU* 3.1 4.3 + - - +
227D LEU* 2.9 40.5 + - + +
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Residues in contact with ARG 224 (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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134D ALA 4.6 0.4 + - - -
137D TYR* 3.5 50.5 + - + +
138D ALA* 3.7 10.9 - - - +
153D LEU* 4.1 22.4 - - + +
220D GLU* 2.8 22.7 + - - +
221D ALA* 4.0 6.1 - - - +
223D VAL* 1.3 76.5 - - - +
225D GLU* 1.3 63.2 + - - +
227D LEU* 3.3 3.1 + - - +
228D GLU* 3.0 52.1 + - - +
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Residues in contact with GLU 225 (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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194D VAL* 5.7 1.1 - - - +
198D ARG* 4.6 10.1 + - - -
214D TRP* 5.8 0.7 - - - -
221D ALA 3.2 17.4 + - - +
222D GLU* 3.9 10.3 - - - +
223D VAL 3.2 0.2 - - - -
224D ARG* 1.3 79.4 - - - +
226D LEU* 1.3 69.1 + - - +
228D GLU* 3.5 18.1 + - - +
229D GLN* 3.0 53.3 + - - +
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Residues in contact with LEU 226 (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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154D MSE 5.4 4.3 - - + -
191D ILE* 3.1 40.6 - - + +
194D VAL* 3.6 37.5 - - + -
195D LEU* 3.5 35.2 - - + -
211D ILE* 5.5 2.5 - - + -
214D TRP* 3.5 25.1 - - + -
222D GLU 3.4 11.0 + - - +
223D VAL 3.1 9.0 + - - +
225D GLU* 1.3 84.9 + - - +
227D LEU* 1.3 69.5 + - + +
229D GLN* 3.1 13.8 + - - +
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Residues in contact with LEU 227 (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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133D ARG* 3.2 19.5 - - - -
137D TYR* 4.1 8.7 - - + +
153D LEU* 3.8 42.0 - - + +
154D MSE 4.0 22.4 - - + -
157D PHE* 3.4 47.5 - - + -
191D ILE* 4.2 10.1 - - + -
211D ILE* 5.7 0.7 - - + -
223D VAL* 2.9 34.7 + - + +
224D ARG 3.9 4.3 - - - +
226D LEU* 1.3 79.3 - - + +
228D GLU* 1.3 59.7 - - - +
229D GLN 3.1 0.8 + - - -
230D ASN* 3.4 7.1 + - - +
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Residues in contact with GLU 228 (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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133D ARG* 4.3 6.7 - - - +
134D ALA* 3.7 39.5 + - + +
137D TYR* 3.5 20.7 - - + -
224D ARG* 3.0 51.2 + - - +
225D GLU* 3.7 16.5 - - - +
226D LEU 3.2 0.4 - - - -
227D LEU* 1.3 73.4 - - - +
229D GLN* 1.3 62.0 + - - +
230D ASN* 2.9 17.0 + - - +
231D PRO* 4.0 4.5 - - - +
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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