Contacts of the helix formed by residues 211 - 218 (chain F) 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 LEU 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F LEU* 4.9 4.0 - - + -
151F THR* 3.5 28.9 - - + -
152F TYR* 3.4 21.1 - - + +
208F VAL* 4.4 4.9 - - + +
210F ASN* 1.3 72.2 - - - +
212F ASP* 1.3 66.8 - - - +
213F TYR 2.8 6.0 + - - -
214F LEU* 3.1 30.0 + - + +
215F LYS* 3.1 17.5 + - + +
235F LYS* 3.0 34.5 - - + +
237F ASN* 3.9 17.5 - - - +
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Residues in contact with ASP 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F ASN* 2.5 47.6 + - - +
211F LEU* 1.3 76.0 - - - +
213F TYR* 1.3 79.4 + - - +
215F LYS* 3.1 27.7 - - - +
216F ARG* 3.4 11.1 + - - +
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Residues in contact with TYR 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 4.5 2.6 - - - +
144F CYS* 4.2 17.3 - - - -
194F LYS* 5.3 0.2 - - - -
196F GLU* 2.5 37.2 + - - +
197F LYS* 3.5 33.9 - - + -
198F VAL* 3.3 25.8 - - + -
211F LEU 2.8 1.8 + - - -
212F ASP* 1.3 89.5 + - - +
214F LEU* 1.3 74.7 + - + +
215F LYS 3.1 1.1 - - - -
216F ARG* 3.1 54.2 + - - +
217F TYR* 3.3 35.9 + + - +
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Residues in contact with LEU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F CYS* 3.7 39.3 - - + +
147F LEU* 4.3 15.5 - - + -
148F LEU* 3.3 34.5 - - + +
151F THR* 3.8 22.4 - - - +
198F VAL* 4.4 24.4 - - + +
199F ILE* 4.9 3.1 - - + -
208F VAL* 4.9 5.8 - - + -
211F LEU* 3.1 17.4 + - + +
213F TYR* 1.3 85.3 - - + +
215F LYS* 1.3 57.3 + - - +
217F TYR* 3.4 2.2 + - - +
218F ALA* 3.0 26.9 + - - +
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Residues in contact with LYS 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LEU* 3.6 7.8 - - + +
152F TYR* 3.6 9.5 + - - +
211F LEU* 3.1 26.5 - - + +
212F ASP* 3.1 15.3 - - - +
214F LEU* 1.3 77.5 - - - +
216F ARG* 1.3 60.9 + - - +
218F ALA 3.1 1.9 - - - -
219F PRO* 3.1 29.1 - - - +
222F ASP* 2.7 47.9 + - + +
223F GLU* 4.4 9.5 + - - +
233F TRP* 6.1 4.4 - - - -
235F LYS* 5.5 0.4 - - - +
237F ASN* 4.8 17.0 + - - -
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Residues in contact with ARG 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ASN* 4.9 1.7 - - - +
197F LYS* 5.5 1.6 - - - +
212F ASP 3.4 8.9 + - - +
213F TYR* 3.1 37.9 + - - +
215F LYS* 1.3 81.9 - - - +
217F TYR* 1.3 96.3 + - + +
218F ALA 3.2 1.1 + - - -
219F PRO* 3.5 12.7 - - - +
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Residues in contact with TYR 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASP* 3.8 13.3 - - - +
137F ASN* 3.7 31.3 - - + +
140F LEU* 3.5 36.4 - - + +
141F GLY* 4.2 9.3 - - - +
144F CYS* 3.5 38.8 - - + -
213F TYR* 3.3 26.1 + + - +
214F LEU 3.4 0.4 + - - +
216F ARG* 1.3 118.8 + - + +
218F ALA* 1.3 59.6 + - - +
219F PRO* 3.7 3.7 - - - +
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Residues in contact with ALA 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASP* 3.1 24.2 - - + +
145F GLY* 3.9 28.7 - - - +
148F LEU* 4.0 6.7 - - + +
214F LEU 3.0 13.8 + - - +
215F LYS 3.1 6.3 - - - +
217F TYR* 1.3 80.3 - - - +
219F PRO* 1.3 64.6 - - - +
221F LEU* 4.2 6.5 - - + -
222F ASP* 3.4 17.8 + - - +
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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