Contacts of the helix formed by residues 266 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.6 14.8 - - + -
230A TRP* 3.6 26.5 - - + -
262A ILE* 4.0 6.7 - - + -
263A GLY 3.6 13.0 - - - +
264A LYS 3.2 0.2 - - - -
265A ASP* 1.3 97.1 - - - +
267A ILE* 1.3 61.6 + - - +
268A ARG 3.4 2.5 - - - -
269A PHE* 3.5 17.0 + - + +
270A HIS* 3.0 42.8 + - + -
600A MET* 3.6 25.8 - - + +
601A ADN 3.4 22.4 - - - +
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.9 15.0 - - + -
187A GLY 5.1 0.2 - - - +
191A ARG* 3.5 36.3 - - + +
194A GLU* 6.0 1.8 - - - +
195A ILE* 3.9 19.1 - - + -
262A ILE* 3.6 15.6 - - + +
263A GLY 4.0 0.2 + - - -
264A LYS* 3.4 20.9 - - + +
265A ASP 3.6 1.2 - - - -
266A ILE* 1.3 75.8 - - - +
268A ARG* 1.3 66.2 + - + +
270A HIS* 3.1 2.3 + - - +
271A THR* 2.8 53.4 + - + +
289A ILE* 5.1 1.3 - - + -
291A ALA* 3.9 15.9 - - + -
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.1 32.8 - - - +
138A GLU* 5.2 4.9 + - - -
151A GLU* 3.9 13.6 + - - -
194A GLU 5.6 0.8 + - - -
195A ILE* 3.8 19.2 - - + +
198A PHE* 3.4 59.9 - - + +
266A ILE 3.4 0.6 - - - -
267A ILE* 1.3 81.2 - - + +
269A PHE* 1.3 61.6 + - + +
271A THR* 3.9 5.6 - - - -
272A VAL* 2.9 36.9 + - + +
273A TYR* 3.3 15.4 + - + +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 4.5 3.4 - - - -
131A GLU 4.2 2.2 - - - -
132A ARG* 4.1 32.3 - - + -
228A TYR* 3.6 11.0 - - - -
230A TRP* 3.4 80.3 - + + -
234A LEU* 3.6 8.6 - - + +
265A ASP 4.6 4.9 - - - -
266A ILE* 3.7 23.3 - - + +
267A ILE 3.3 0.4 - - - -
268A ARG* 1.3 79.8 - - + +
270A HIS* 1.3 59.5 + - - +
273A TYR* 3.5 32.8 - + + +
274A TRP* 3.0 28.4 + - - +
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Residues in contact with HIS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 4.4 0.2 - - - -
230A TRP* 4.0 11.0 - + - -
234A LEU* 3.9 4.9 - - + +
237A TYR* 2.8 43.4 + + - -
260A HIS* 4.7 9.4 - + + -
262A ILE* 3.5 36.1 - - + +
266A ILE* 3.0 34.5 + - + -
267A ILE 3.1 7.1 + - - +
269A PHE* 1.3 78.3 - - - +
271A THR* 1.3 59.5 + - - +
274A TRP* 3.4 18.5 - + - +
275A PRO* 3.3 14.0 - - - +
289A ILE* 4.0 21.7 - - + +
600A MET* 3.7 14.6 - - - +
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 2.7 28.6 + - - -
185A PHE* 3.9 4.8 - - + -
186A ILE* 3.7 34.8 - - + -
195A ILE* 3.4 23.6 - - - +
267A ILE* 2.8 36.7 + - + +
268A ARG* 3.9 0.5 - - - -
270A HIS* 1.3 80.1 - - - +
272A VAL* 1.3 56.0 + - - +
275A PRO* 3.3 15.3 - - - +
289A ILE* 3.8 21.1 - - + -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.2 2.0 - - + -
175A LEU* 3.7 9.2 - - + +
179A TYR* 3.8 12.6 - - - +
195A ILE* 4.0 11.0 - - + -
198A PHE* 4.3 12.3 - - + -
199A VAL* 3.9 12.8 - - + -
203A LEU* 3.8 37.0 - - + -
268A ARG* 2.9 22.8 + - + +
271A THR* 1.3 85.0 - - - +
273A TYR* 1.3 80.1 + - + +
274A TRP 3.5 0.9 - - - -
275A PRO* 3.5 3.2 - - - +
276A ALA* 3.4 22.9 + - - +
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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