Contacts of the helix formed by residues 252 - 257 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ARG* 5.2 1.0 - - - +
227C MET* 3.3 31.6 - - + +
230C ALA* 4.0 22.3 - - + +
237C GLU* 4.7 2.8 + - - -
251C GLY* 1.4 70.0 - - - +
253C GLU* 1.3 85.3 + - - +
254C ARG 3.4 0.7 + - - -
255C PHE* 3.5 18.5 + - + -
256C ARG* 2.8 58.2 + - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.6 4.2 - - + +
192C ILE* 3.9 24.3 - - + +
193C LEU* 3.9 19.9 - - + +
196C ARG* 3.2 42.0 + - - +
217C CYS* 5.0 0.2 - - - -
250C ILE* 3.6 13.9 - - + -
251C GLY 2.8 24.4 + - - -
252C ASN* 1.3 93.4 + - - +
254C ARG* 1.3 63.4 + - - +
256C ARG* 3.8 21.0 + - - +
257C CYS* 3.0 28.4 + - - +
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU* 2.8 44.2 + - + +
217C CYS* 3.0 38.3 - - - +
218C TYR* 3.1 43.7 + - + +
235C SER 4.7 0.2 + - - -
236C LEU* 3.2 36.7 + - - +
238C LYS* 3.7 36.4 - - - +
250C ILE* 3.7 25.1 - - + +
251C GLY 3.0 16.1 + - - +
253C GLU* 1.3 76.6 - - - +
255C PHE* 1.3 58.5 + - + +
258C PRO* 3.3 3.1 - - - +
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Residues in contact with PHE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C TYR* 3.0 24.2 - - + +
219C VAL* 5.0 0.9 - - - -
220C ALA* 4.2 15.3 - - + +
223C PHE* 3.2 36.6 - + - -
226C GLU* 3.5 48.7 - - + -
227C MET* 3.2 28.5 - - + -
229C THR 4.7 1.6 - - - -
230C ALA* 4.2 7.0 - - + -
236C LEU* 5.3 7.9 - - + -
251C GLY 4.9 2.7 - - - -
252C ASN* 3.5 24.0 + - + -
253C GLU 3.3 0.2 - - - -
254C ARG* 1.3 77.5 - - + +
256C ARG* 1.4 64.3 + - - +
257C CYS 3.2 2.8 + - - -
258C PRO* 3.3 9.2 - - - +
259C GLU* 3.2 19.1 + - - +
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C TYR* 3.3 24.4 + - - +
192C ILE* 3.8 34.7 + - + +
195C GLU* 5.4 3.2 + - - +
223C PHE* 3.9 20.4 - - + -
227C MET* 3.9 21.5 - - - -
252C ASN* 2.8 57.9 + - - +
253C GLU* 3.8 22.5 + - - +
255C PHE* 1.4 73.8 - - - +
257C CYS* 1.3 65.7 + - - +
259C GLU* 3.8 8.6 - - - +
266C PHE* 3.9 8.2 - - + -
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Residues in contact with CYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.2 38.4 - - - +
188C TYR* 4.2 10.0 - - - -
189C LEU* 3.6 24.9 - - + -
192C ILE* 4.4 2.0 - - + -
213C LYS* 4.0 17.5 - - - -
217C CYS* 3.7 8.7 - - - -
253C GLU 3.0 16.4 + - - +
255C PHE 3.2 0.4 - - - -
256C ARG* 1.3 76.8 - - - +
258C PRO* 1.4 73.2 - - + +
259C GLU 2.9 2.4 + - - -
260C ALA* 3.0 17.5 + - - +
306C TYR* 5.0 0.4 - - - -
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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