Contacts of the helix formed by residues 218 - 226 (chain D) in PDB entry 3E5X
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 218 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D ASN 4.1 13.8 + - - +
206D ILE* 3.3 12.0 + - + +
216D VAL* 3.8 3.4 - - - -
217D TYR* 1.3 82.2 - - - +
219D LEU* 1.3 56.6 + - - +
220D GLY* 3.7 4.9 + - - -
221D GLU* 3.3 34.5 + - + +
222D LEU* 3.0 25.8 + - - +
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Residues in contact with LEU 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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158D TYR* 3.9 28.5 - - + +
161D CYS* 3.7 27.1 - - + +
162D SER* 5.1 5.4 - - - +
172D TYR* 3.3 51.7 - - + +
216D VAL* 3.6 9.9 + - + +
217D TYR 4.0 0.8 - - - -
218D ASN* 1.3 74.1 - - - +
220D GLY* 1.3 63.8 + - - +
222D LEU* 3.3 7.3 + - + +
223D LYS* 3.0 22.2 + - + +
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Residues in contact with GLY 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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218D ASN* 3.3 6.0 + - - -
219D LEU* 1.3 79.1 - - - +
221D GLU* 1.3 57.8 + - - +
223D LYS* 3.5 9.2 - - - +
224D HIS* 2.9 29.9 + - - +
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Residues in contact with GLU 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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206D ILE* 3.6 26.5 - - + +
218D ASN* 3.3 34.4 + - + +
220D GLY* 1.3 73.2 - - - +
222D LEU* 1.3 55.5 + - - +
224D HIS* 3.5 22.3 - - - +
225D LEU* 2.8 55.1 + - + +
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Residues in contact with LEU 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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154D LEU* 3.9 37.7 - - + +
157D PHE* 3.9 17.9 - - + +
158D TYR* 3.7 30.5 - - - +
161D CYS* 4.8 0.2 - - + -
201D LEU* 4.3 10.3 - - + -
206D ILE* 3.8 13.4 - - + +
207D LEU* 4.1 12.1 - - + -
216D VAL* 4.3 15.5 - - + -
218D ASN 3.0 14.8 + - - +
219D LEU* 3.3 15.2 + - + +
221D GLU* 1.3 76.7 - - - +
223D LYS* 1.3 57.4 + - - +
225D LEU* 3.3 3.3 + - - +
226D SER* 2.8 29.5 + - - -
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Residues in contact with LYS 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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158D TYR* 3.0 51.7 + - + +
219D LEU 3.0 14.7 + - - +
220D GLY* 3.5 8.3 - - - +
222D LEU* 1.3 74.7 - - - +
224D HIS* 1.3 61.6 + - - +
226D SER* 2.8 22.9 + - - +
227D GLU* 3.2 39.5 + - + +
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Residues in contact with HIS 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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220D GLY 2.9 19.0 + - - +
221D GLU* 3.5 28.5 - - - +
223D LYS* 1.3 74.4 - - - +
225D LEU* 1.3 69.4 + - + +
227D GLU* 2.9 37.2 + - - +
228D GLN* 3.6 26.4 - - + +
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Residues in contact with LEU 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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151D ILE* 3.5 12.5 - - - +
154D LEU* 3.7 17.5 - - + +
201D LEU* 4.5 11.4 - - + -
204D GLU* 4.5 9.0 - - - +
206D ILE* 3.2 36.3 - - + -
221D GLU* 2.8 42.3 + - + +
222D LEU* 3.8 3.4 - - - +
224D HIS* 1.3 80.7 - - + +
226D SER* 1.3 62.8 + - - +
227D GLU 3.1 1.0 + - - -
228D GLN* 3.3 22.1 + - + +
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Residues in contact with SER 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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147D TYR* 5.5 2.8 - - - -
151D ILE* 3.6 22.7 - - - +
154D LEU* 3.7 38.3 - - - +
155D ARG* 3.9 18.5 + - - +
158D TYR* 4.2 10.0 - - - +
222D LEU 2.8 17.0 + - - -
223D LYS* 2.8 25.8 + - - +
225D LEU* 1.3 70.5 - - - +
227D GLU* 1.3 58.4 + - - +
228D GLN 3.5 1.1 - - - -
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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