Contacts of the helix formed by residues 252 - 257 (chain B) in PDB entry 3LUE
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B ARG* 5.2 1.0 - - - +
227B MET* 3.3 31.7 - - + +
230B ALA* 4.0 23.4 - - + +
237B GLU* 4.7 2.8 + - - -
251B GLY* 1.4 69.8 - - - +
253B GLU* 1.3 84.9 + - - +
254B ARG 3.3 1.1 + - - -
255B PHE* 3.5 18.0 + - - -
256B ARG* 2.8 58.9 + - - +
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Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU* 4.6 4.4 - - + +
192B ILE* 3.9 23.4 - - + +
193B LEU* 3.9 20.7 - - + +
196B ARG* 3.2 41.4 + - - +
217B CYS* 4.4 0.6 - - - -
250B ILE* 3.6 13.8 - - + -
251B GLY 2.8 23.4 + - - -
252B ASN* 1.3 93.4 + - - +
254B ARG* 1.3 63.8 + - - +
256B ARG* 3.8 21.5 + - - +
257B CYS* 3.0 28.1 + - - +
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 2.8 44.7 + - + +
217B CYS* 3.0 37.6 - - - +
218B TYR* 3.1 43.4 + - + +
235B SER 4.7 0.2 + - - -
236B LEU* 3.2 35.9 + - - +
238B LYS* 3.7 36.3 - - - +
250B ILE* 3.7 24.7 - - + +
251B GLY 3.0 15.0 + - - +
253B GLU* 1.3 76.3 - - - +
255B PHE* 1.3 59.8 + - + +
258B PRO* 3.3 2.9 - - - +
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TYR* 3.0 24.3 - - + +
219B VAL* 5.0 0.7 - - - -
220B ALA* 4.2 14.4 - - + +
223B PHE* 3.2 36.8 - + - -
226B GLU* 3.5 48.2 - - + -
227B MET* 3.2 29.2 - - + -
229B THR 4.7 1.8 - - - -
230B ALA* 4.2 6.7 - - + -
236B LEU* 5.3 6.7 - - + -
251B GLY 4.9 2.7 - - - -
252B ASN* 3.5 24.2 + - + -
253B GLU 3.3 0.2 - - - -
254B ARG* 1.3 77.1 - - + +
256B ARG* 1.4 64.8 + - - +
257B CYS 3.2 2.7 + - - -
258B PRO* 3.3 9.5 - - - +
259B GLU* 3.2 18.7 + - - +
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 3.3 24.1 + - - +
192B ILE* 3.8 35.1 + - + +
195B GLU* 5.4 3.2 + - - +
223B PHE* 3.9 19.1 - - + -
227B MET* 3.9 21.5 - - - -
252B ASN* 2.8 57.8 + - - +
253B GLU* 3.8 22.5 + - - +
255B PHE* 1.4 74.9 - - - +
257B CYS* 1.3 66.5 + - - +
259B GLU* 3.8 9.3 - - - +
266B PHE* 3.9 7.0 - - + -
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Residues in contact with CYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.2 37.5 - - - +
188B TYR* 4.2 10.2 - - - -
189B LEU* 3.6 25.1 - - + -
192B ILE* 4.4 2.5 - - + -
213B LYS* 4.0 17.5 - - - -
217B CYS* 3.7 10.1 - - - -
253B GLU 3.0 16.9 + - - +
255B PHE 3.2 0.4 - - - -
256B ARG* 1.3 76.9 - - - +
258B PRO* 1.4 73.4 - - + +
259B GLU 2.9 1.9 + - - -
260B ALA* 3.0 17.7 + - - +
306B TYR* 5.0 0.2 - - - -
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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