Contacts of the helix formed by residues 266 - 272 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 3.7 15.5 - - + -
230B TRP* 3.6 21.5 - - + -
262B ILE* 3.9 7.6 - - + -
263B GLY 3.5 13.2 - - - +
264B LYS 3.2 0.2 - - - -
265B ASP* 1.3 94.0 + - - +
267B ILE* 1.3 62.1 + - - +
268B ARG 3.4 2.6 + - - -
269B PHE* 3.5 15.5 + - + +
270B HIS* 3.0 42.8 + - + -
600B MET* 3.4 28.0 - - + +
601B ADN 3.4 23.8 - - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.9 17.0 - - + -
191B ARG* 4.2 14.6 - - + +
194B GLU* 5.8 2.9 - - - +
195B ILE* 3.8 21.3 - - + -
262B ILE* 3.7 12.2 - - + +
264B LYS* 3.3 21.7 + - - +
265B ASP 3.6 1.7 - - - +
266B ILE* 1.3 77.2 - - - +
268B ARG* 1.3 63.9 + - + +
270B HIS* 3.2 2.8 + - - +
271B THR* 2.7 61.1 + - + +
289B ILE* 4.6 3.1 - - + -
291B ALA* 3.7 25.6 - - + +
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Residues in contact with ARG 268 (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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194B GLU* 5.4 2.0 + - - +
195B ILE* 3.8 19.0 - - + +
198B PHE* 3.6 60.4 - - + +
266B ILE 3.4 0.8 - - - -
267B ILE* 1.3 85.8 - - + +
269B PHE* 1.3 66.9 + - + +
271B THR* 4.0 4.9 - - - -
272B VAL* 3.1 29.5 + - + +
273B TYR* 3.3 17.5 + - + -
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Residues in contact with PHE 269 (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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228B TYR* 3.9 9.9 - + - -
230B TRP* 3.4 83.0 - + + -
234B LEU* 3.6 6.1 - - + +
265B ASP 4.6 4.3 - - - -
266B ILE* 3.8 25.1 - - + +
267B ILE 3.3 0.2 - - - -
268B ARG* 1.3 79.6 - - + +
270B HIS* 1.3 59.1 + - - +
273B TYR* 3.5 36.5 - + + +
274B TRP* 2.9 28.9 + - - +
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Residues in contact with HIS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TRP* 3.8 11.7 - + - -
234B LEU* 3.7 6.4 - - + +
237B TYR* 2.8 42.8 + + - -
260B HIS* 4.7 10.1 - + + -
262B ILE* 3.4 26.3 - - + +
266B ILE* 3.0 45.0 + - + -
267B ILE 3.2 6.7 + - - +
269B PHE* 1.3 79.9 - - - +
271B THR* 1.3 58.5 + - - +
272B VAL 3.7 0.2 - - - -
274B TRP* 3.5 17.2 - + - +
275B PRO* 3.4 12.6 - - - +
289B ILE* 3.9 22.2 - - + +
600B MET* 3.6 13.8 - - - -
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Residues in contact with THR 271 (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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179B TYR* 2.7 28.1 + - - -
185B PHE* 3.9 4.6 - - + -
186B ILE* 3.7 34.3 - - + -
195B ILE* 3.4 23.1 - - - +
267B ILE* 2.7 30.7 + - + +
270B HIS* 1.3 81.3 - - - +
272B VAL* 1.3 57.2 + - - +
275B PRO* 3.3 14.9 - - - +
289B ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 272 (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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168B LEU* 4.1 2.2 - - + +
175B LEU* 3.7 10.2 - - + +
179B TYR* 3.8 12.1 - - - +
195B ILE* 3.9 17.5 - - + -
198B PHE* 4.3 13.9 - - + -
199B VAL* 3.9 8.5 - - + -
203B LEU* 3.8 37.0 - - + -
268B ARG* 3.1 18.1 + - - +
271B THR* 1.3 85.9 - - - +
273B TYR* 1.3 79.8 + - + +
274B TRP 3.5 0.4 - - - -
275B PRO* 3.5 3.4 - - - +
276B ALA* 3.4 22.0 + - - +
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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