Contacts of the helix formed by residues 210 - 218 (chain N) in PDB entry 5X6E
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 210 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198N VAL* 4.8 7.6 - - + +
208N VAL* 4.4 2.9 - - - +
209N GLN* 1.3 89.5 - - + +
211N LEU* 1.3 65.0 + - - +
212N ASP* 3.0 26.9 + - - +
213N TYR* 3.1 31.7 + - - +
214N LEU* 4.0 2.6 + - - +
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Residues in contact with LEU 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LEU* 5.8 2.5 - - + -
151N THR* 4.3 13.2 - - + -
152N TYR* 3.5 33.4 - - + +
162N ILE* 3.5 31.9 - - + -
208N VAL* 5.6 1.3 - - + -
209N GLN 5.1 0.2 - - - -
210N ASN* 1.3 75.3 - - - +
212N ASP* 1.3 57.0 + - - +
214N LEU* 2.8 19.7 + - + +
215N LYS* 2.5 47.0 + - + +
236N LEU* 3.3 33.2 - - + +
237N ASN 5.0 3.1 - - - +
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Residues in contact with ASP 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N ASN* 3.2 18.4 - - - +
211N LEU* 1.3 84.3 + - - +
213N TYR* 1.3 54.5 + - - +
215N LYS* 3.7 24.7 + - - +
216N ARG* 3.0 41.8 + - - +
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Residues in contact with TYR 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N LEU* 5.2 5.2 - - + +
144N CYS* 4.4 5.6 - - - -
193N LEU* 4.0 16.9 - - + +
196N GLU* 4.1 21.7 + - + +
198N VAL* 3.4 47.8 - - + -
210N ASN* 3.1 22.3 + - - +
211N LEU 3.0 0.2 + - - -
212N ASP* 1.3 78.0 - - - +
214N LEU* 1.3 64.6 + - - +
216N ARG* 3.5 20.3 + - - +
217N TYR* 3.5 53.0 + + - -
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Residues in contact with LEU 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N CYS* 3.7 38.9 - - + +
147N LEU* 4.1 17.7 - - + -
148N LEU* 3.6 32.6 - - + +
151N THR* 3.7 23.6 - - + +
193N LEU* 5.7 0.9 - - + -
198N VAL* 4.5 15.3 - - + -
208N VAL* 3.7 29.4 - - + -
210N ASN 4.9 1.1 - - - +
211N LEU* 2.8 12.8 + - + +
213N TYR* 1.3 75.9 - - - +
215N LYS* 1.3 64.0 + - - +
217N TYR* 3.2 3.5 + - - +
218N ALA* 3.0 21.5 + - - +
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Residues in contact with LYS 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LEU* 3.6 15.2 - - + +
152N TYR* 4.3 5.8 - - - +
211N LEU* 2.5 33.4 + - + +
212N ASP* 3.7 24.7 + - - +
214N LEU* 1.3 72.6 - - - +
216N ARG* 1.3 61.6 + - - +
217N TYR 3.3 0.9 + - - -
218N ALA 3.4 1.0 - - - -
219N PRO* 3.3 26.7 - - - +
222N ASP* 3.4 34.1 + - - +
233N TRP* 5.7 5.9 - - + -
237N ASN 5.3 9.2 + - - +
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Residues in contact with ARG 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M GLU* 5.7 5.8 - - - +
137N ASN* 5.0 2.9 + - - -
212N ASP* 3.0 25.2 + - - +
213N TYR* 3.8 22.2 - - - +
214N LEU 3.3 0.2 - - - -
215N LYS* 1.3 77.3 - - - +
217N TYR* 1.3 63.1 + - + +
219N PRO* 4.1 9.6 - - - +
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Residues in contact with TYR 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N ASP* 4.1 13.2 - - - +
136N ILE* 4.9 0.5 - - - +
137N ASN* 3.2 50.9 + - + +
140N LEU* 3.7 30.2 - - + +
141N GLY* 4.3 12.6 - - - -
144N CYS* 3.7 26.7 - - + -
213N TYR* 3.5 51.6 + + - +
214N LEU 3.2 1.2 + - - +
215N LYS 3.2 0.4 - - - -
216N ARG* 1.3 82.2 - - + +
218N ALA* 1.3 60.7 + - - +
219N PRO* 3.4 8.8 - - - +
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Residues in contact with ALA 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N ASP* 3.1 22.2 - - + +
141N GLY 4.9 0.7 - - - +
144N CYS 4.5 0.7 - - - +
145N GLY* 3.6 33.0 - - - +
148N LEU* 4.4 6.7 - - + +
214N LEU 3.0 13.2 + - - +
215N LYS 3.4 5.7 - - - +
217N TYR* 1.3 78.2 - - - +
219N PRO* 1.3 64.8 - - - +
221N LEU* 3.7 6.2 - - + +
222N ASP* 3.3 17.2 + - - +
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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