Contacts of the helix formed by residues 252 - 257 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D ARG* 5.2 1.2 - - - +
227D MET* 3.3 30.5 - - + +
230D ALA* 4.0 22.8 - - + +
237D GLU* 4.7 2.6 + - - -
251D GLY* 1.4 69.7 - - - -
253D GLU* 1.3 85.6 + - - +
254D ARG 3.4 0.3 + - - -
255D PHE* 3.5 18.2 + - + -
256D ARG* 2.8 59.5 + - - +
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Residues in contact with GLU 253 (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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189D LEU* 4.6 4.2 - - + +
192D ILE* 3.9 25.1 - - + +
193D LEU* 3.9 20.5 - - + +
196D ARG* 3.2 42.7 + - - +
217D CYS* 5.0 0.4 - - - -
250D ILE* 3.6 13.7 - - + -
251D GLY 2.8 23.6 + - - -
252D ASN* 1.3 92.9 + - - +
254D ARG* 1.3 64.2 + - - +
256D ARG* 3.8 21.4 + - - +
257D CYS* 3.0 27.4 + - - +
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Residues in contact with ARG 254 (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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216D LEU* 2.8 44.8 + - + +
217D CYS* 3.0 38.1 - - - +
218D TYR* 3.1 42.1 + - + +
235D SER 4.7 0.2 + - - -
236D LEU* 3.2 36.9 + - - +
238D LYS* 3.7 34.9 - - - +
250D ILE* 3.7 24.7 - - + +
251D GLY 3.0 14.1 + - - +
253D GLU* 1.3 76.6 - - - +
255D PHE* 1.3 60.5 + - + +
258D PRO* 3.3 3.3 - - - +
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Residues in contact with PHE 255 (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 TYR* 3.0 24.6 - - + +
219D VAL* 5.0 0.9 - - - -
220D ALA* 4.2 14.4 - - + +
223D PHE* 3.2 37.0 - + - -
226D GLU* 3.5 47.8 - - + -
227D MET* 3.2 28.9 - - + -
229D THR 4.7 2.0 - - - -
230D ALA* 4.2 7.2 - - + -
236D LEU* 5.3 7.0 - - + -
251D GLY 4.9 2.7 - - - -
252D ASN* 3.7 23.3 - - + -
254D ARG* 1.3 77.3 - - + +
256D ARG* 1.4 63.3 + - - +
257D CYS 3.2 3.7 + - - -
258D PRO* 3.3 9.1 - - - +
259D GLU* 3.2 19.4 + - - +
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Residues in contact with ARG 256 (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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188D TYR* 3.3 24.4 + - - +
192D ILE* 3.8 34.5 + - + +
195D GLU* 5.4 2.8 + - - +
223D PHE* 3.9 20.6 - - + -
227D MET* 3.9 22.4 - - - -
252D ASN* 2.8 57.0 + - - +
253D GLU* 3.8 22.5 + - - +
255D PHE* 1.4 72.7 - - - +
257D CYS* 1.3 65.9 + - - +
259D GLU* 3.8 8.7 - - - +
266D PHE* 3.9 7.8 - - + -
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Residues in contact with CYS 257 (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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185D LEU* 3.2 38.0 - - - +
188D TYR* 4.2 10.6 - - - -
189D LEU* 3.6 25.8 - - + -
192D ILE* 4.3 2.7 - - + +
213D LYS* 4.0 16.8 - - - -
217D CYS* 3.7 9.2 - - - -
253D GLU 3.0 16.5 + - - +
255D PHE 3.2 0.6 - - - -
256D ARG* 1.3 76.5 - - - +
258D PRO* 1.4 73.4 - - + +
259D GLU 2.9 2.3 + - - -
260D ALA* 3.0 17.7 + - - +
306D 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