Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 1XR2
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 GLU 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ASN* 1.3 73.8 - - - +
259A GLU* 1.3 75.1 + - - +
260A ASN 3.4 2.2 - - - -
261A LEU* 3.5 13.2 + - + +
262A LYS* 3.2 21.4 + - - +
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Residues in contact with GLU 259 (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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234A ASP* 3.6 0.7 - - - +
235A SER* 3.0 28.8 + - - +
257A ASN* 3.4 13.2 + - - +
258A GLU* 1.3 88.8 + - - +
260A ASN* 1.3 67.7 + - - +
262A LYS* 3.2 7.2 + - - +
263A ASN* 2.9 37.0 + - - +
591A LYS* 3.4 30.8 + - - +
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Residues in contact with ASN 260 (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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231A THR* 5.2 0.6 + - - -
234A ASP 4.2 2.4 + - - -
235A SER* 3.4 18.0 - - - +
236A VAL* 3.1 24.2 + - - +
239A TYR* 4.4 9.1 - - + -
252A PHE* 3.8 22.9 - - + +
253A ASP 3.0 33.3 + - - +
254A PHE* 3.8 21.1 - - + -
257A ASN* 3.0 13.7 + - - +
259A GLU* 1.3 76.8 - - - +
261A LEU* 1.3 63.9 + - - +
263A ASN* 3.3 6.8 + - - +
264A LEU* 3.0 23.0 + - - +
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Residues in contact with LEU 261 (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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254A PHE* 3.9 17.7 - - + +
257A ASN 5.6 1.1 + - - +
258A GLU* 3.5 13.7 + - + +
259A GLU 3.2 0.6 - - - -
260A ASN* 1.3 78.9 - - - +
262A LYS* 1.3 65.2 + - - +
264A LEU* 3.0 5.4 + - + +
265A GLU* 2.9 36.5 + - + +
296A LEU* 4.1 13.2 - - + -
299A LYS* 4.1 26.9 - - - +
300A LEU* 3.4 31.0 - - + -
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Residues in contact with LYS 262 (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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258A GLU 3.2 11.9 + - - +
259A GLU* 3.7 9.6 - - - +
261A LEU* 1.3 79.8 - - - +
263A ASN* 1.3 60.8 + - - +
265A GLU* 3.1 9.7 + - - +
266A LYS* 2.9 28.8 + - - +
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Residues in contact with ASN 263 (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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235A SER* 5.8 0.2 - - - -
236A VAL 4.8 8.1 + - - -
239A TYR* 3.6 37.2 - - + +
259A GLU* 2.9 29.5 + - - +
260A ASN* 3.7 5.5 + - - +
262A LYS* 1.3 78.4 - - - +
264A LEU* 1.3 58.2 + - - +
266A LYS* 4.5 5.3 - - - +
267A HIS* 2.7 50.9 + - - +
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Residues in contact with LEU 264 (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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239A TYR* 3.6 27.8 - - + +
252A PHE* 6.1 0.4 - - + -
254A PHE* 4.1 13.0 - - + -
260A ASN 3.0 14.0 + - - +
261A LEU* 3.0 9.2 + - - +
263A ASN* 1.3 76.5 - - - +
265A GLU* 1.3 77.0 + - - +
268A GLY* 2.7 37.0 + - - +
269A PHE* 4.4 10.3 - - + +
275A LEU* 3.7 31.0 - - + -
299A LYS 5.0 1.1 - - - +
300A LEU* 4.3 25.8 - - + +
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Residues in contact with GLU 265 (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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261A LEU* 2.9 30.0 + - + +
262A LYS* 3.1 11.6 + - - +
264A LEU* 1.3 93.1 - - - +
266A LYS* 1.3 59.0 + - - +
268A GLY 4.6 0.7 + - - -
299A LYS* 3.8 33.7 - - - +
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Residues in contact with LYS 266 (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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262A LYS 2.9 15.8 + - - +
263A ASN* 3.2 8.9 + - - +
265A GLU* 1.3 80.1 - - - +
267A HIS* 1.3 85.7 + - + +
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Residues in contact with HIS 267 (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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239A TYR* 3.8 21.7 - + + -
240A GLU* 3.7 43.2 - - + +
263A ASN* 2.7 39.9 + - - +
266A LYS* 1.3 104.7 + - + +
268A GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 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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239A TYR* 2.7 31.1 + - - -
240A GLU* 5.6 0.2 - - - +
243A VAL* 5.3 0.5 - - - +
264A LEU* 2.7 27.3 + - - -
265A GLU 4.4 1.0 - - - -
266A LYS 3.6 1.2 - - - -
267A HIS* 1.3 78.5 - - - +
269A PHE* 1.3 55.6 + - - -
270A PRO* 4.4 1.4 - - - +
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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