Contacts of the helix formed by residues 252 - 257 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196E ARG* 5.2 1.0 - - - +
227E MET* 3.3 30.9 - - + +
230E ALA* 4.0 22.5 - - + +
237E GLU* 4.7 2.8 + - - -
251E GLY* 1.4 70.4 - - - +
253E GLU* 1.3 85.0 + - - +
254E ARG 3.3 0.6 + - - -
255E PHE* 3.5 17.3 + - - -
256E ARG* 2.8 58.4 + - - +
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Residues in contact with GLU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LEU* 4.6 4.4 - - + +
192E ILE* 3.9 25.5 - - + +
193E LEU* 3.9 20.9 - - + +
196E ARG* 3.2 41.1 + - - +
217E CYS* 5.0 0.4 - - - -
250E ILE* 3.6 14.8 - - + -
251E GLY 2.8 24.0 + - - -
252E ASN* 1.3 91.3 + - - +
254E ARG* 1.3 64.2 + - - +
256E ARG* 3.8 21.4 + - - +
257E CYS* 3.0 27.4 + - - +
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Residues in contact with ARG 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E LEU* 2.8 44.9 + - + +
217E CYS* 3.0 37.7 - - - +
218E TYR* 3.1 42.7 + - + +
235E SER 4.7 0.4 + - - -
236E LEU* 3.2 35.7 + - - +
238E LYS* 3.7 37.2 - - - +
250E ILE* 3.7 25.8 - - + -
251E GLY 3.0 13.7 + - - +
253E GLU* 1.3 76.1 - - - +
255E PHE* 1.3 59.7 + - + +
258E PRO* 3.3 3.3 - - - +
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Residues in contact with PHE 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E TYR* 3.0 24.1 - - + +
219E VAL* 5.0 0.7 - - - -
220E ALA* 4.2 14.6 - - + +
223E PHE* 3.2 36.8 - + - -
226E GLU* 3.5 47.3 - - + -
227E MET* 3.2 28.5 - - + -
229E THR 4.7 2.2 - - - -
230E ALA* 4.2 6.5 - - + -
236E LEU* 5.3 7.4 - - + -
251E GLY 4.9 2.7 - - - -
252E ASN* 3.5 24.2 + - + -
254E ARG* 1.3 78.2 - - + +
256E ARG* 1.4 65.0 + - - +
257E CYS 3.2 3.1 + - - -
258E PRO* 3.3 9.4 - - - +
259E GLU* 3.2 18.9 + - - +
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Residues in contact with ARG 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E TYR* 3.3 23.4 + - - +
192E ILE* 3.8 34.9 + - + +
195E GLU* 5.4 2.8 + - - +
223E PHE* 3.9 20.9 - - + -
227E MET* 3.9 22.0 - - - -
252E ASN* 2.8 56.7 + - - +
253E GLU* 3.8 23.5 + - - +
255E PHE* 1.4 73.6 - - - +
257E CYS* 1.3 67.0 + - - +
259E GLU* 3.8 8.8 - - - +
266E PHE* 3.9 7.4 - - + -
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Residues in contact with CYS 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.2 38.6 - - - +
188E TYR* 4.2 10.1 - - - -
189E LEU* 3.6 25.4 - - + -
192E ILE* 4.3 2.9 - - + +
213E LYS* 4.0 16.4 - - - -
217E CYS* 3.7 9.2 - - - -
253E GLU 3.0 16.2 + - - +
255E PHE 3.2 0.4 - - - -
256E ARG* 1.3 76.4 - - - +
258E PRO* 1.4 73.1 - - + +
259E GLU 2.9 2.3 + - - -
260E ALA* 3.0 18.0 + - - +
306E TYR* 5.0 0.9 - - - -
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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