Contacts of the helix formed by residues 266 - 272 (chain C) in PDB entry 2X1L
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 ILE 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.8 13.9 - - + -
230C TRP* 3.6 21.8 - - + -
262C ILE* 4.0 6.1 - - + -
263C GLY 3.5 13.0 - - - +
264C LYS 3.2 0.2 - - - -
265C ASP* 1.3 95.8 - - - +
267C ILE* 1.3 64.1 + - - +
268C ARG 3.4 2.5 - - - -
269C PHE* 3.5 17.9 + - + +
270C HIS* 3.1 40.6 + - + -
600C MET* 3.5 29.6 - - + +
601C ADN 3.4 23.1 - - - +
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 3.8 22.9 - - + -
187C GLY 4.9 1.3 - - - +
191C ARG* 3.3 37.2 - - + -
194C GLU* 5.8 1.8 - - - +
195C ILE* 3.9 17.0 - - + -
262C ILE* 3.6 13.9 - - + -
263C GLY 4.0 1.2 + - - -
264C LYS 3.3 19.9 + - - +
265C ASP 3.6 1.0 - - - -
266C ILE* 1.3 77.1 - - - +
268C ARG* 1.3 62.3 + - + +
270C HIS* 3.1 2.6 + - - -
271C THR* 2.7 52.0 + - + +
289C ILE* 5.1 2.2 - - + -
291C ALA* 3.9 15.0 - - + -
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Residues in contact with ARG 268 (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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194C GLU 5.5 1.2 + - - -
195C ILE* 3.8 17.7 - - + +
198C PHE* 3.5 60.6 - - + +
265C ASP 5.6 0.2 + - - -
266C ILE 3.4 0.6 - - - -
267C ILE* 1.3 81.1 - - + +
269C PHE* 1.3 63.6 + - + +
271C THR* 3.9 5.8 - - - -
272C VAL* 3.0 35.6 + - + +
273C TYR* 3.3 16.6 + - + -
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Residues in contact with PHE 269 (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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228C TYR* 4.2 9.2 - + - -
230C TRP* 3.4 76.7 - + + -
234C LEU* 3.5 8.4 - - + +
265C ASP 4.4 5.2 - - - -
266C ILE* 3.7 28.3 - - + +
267C ILE 3.2 0.6 - - - -
268C ARG* 1.3 82.1 - - + +
270C HIS* 1.3 58.9 + - - +
273C TYR* 3.6 33.1 - + + +
274C TRP* 3.0 27.5 + - - +
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Residues in contact with HIS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C TRP* 3.8 11.2 - + - -
234C LEU* 3.6 13.8 - - + +
237C TYR* 2.8 37.4 + + - -
260C HIS* 4.7 9.4 - + + -
262C ILE* 3.5 36.1 - - + +
266C ILE* 3.1 29.4 + - + -
267C ILE 3.1 6.7 + - - +
269C PHE* 1.3 77.7 - - - +
271C THR* 1.3 60.8 + - - +
272C VAL 3.7 0.4 - - - -
274C TRP* 3.4 19.1 - + + +
275C PRO* 3.4 13.2 - - - +
289C ILE* 4.0 20.7 - - + +
600C MET* 3.6 19.5 - - - -
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Residues in contact with THR 271 (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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179C TYR* 2.7 27.5 + - - -
185C PHE* 3.9 6.2 - - + -
186C ILE* 3.7 34.3 - - + -
195C ILE* 3.4 23.6 - - - +
267C ILE* 2.7 37.2 + - + +
268C ARG* 3.9 0.3 - - - -
270C HIS* 1.3 79.7 - - - +
272C VAL* 1.3 57.5 + - - +
275C PRO* 3.3 16.1 - - - +
289C ILE* 3.9 22.2 - - + -
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Residues in contact with VAL 272 (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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168C LEU* 4.2 2.7 - - + -
175C LEU* 3.7 8.8 - - + +
179C TYR* 3.7 13.0 - - - +
195C ILE* 3.9 11.9 - - + -
198C PHE* 4.3 13.2 - - + -
199C VAL* 3.8 13.7 - - + -
203C LEU* 3.9 36.3 - - + -
268C ARG* 3.0 18.1 + - + +
271C THR* 1.3 84.1 - - - +
273C TYR* 1.3 81.2 + - + +
274C TRP 3.5 1.1 - - - -
275C PRO* 3.5 3.3 - - - +
276C ALA* 3.4 22.5 + - - +
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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