Contacts of the helix formed by residues 258 - 266 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B ASN* 1.3 77.2 - - - +
259B GLU* 1.3 74.8 + - - +
260B ASN 3.4 3.1 - - - -
261B LEU* 3.3 11.6 + - - +
262B LYS* 3.2 20.5 + - - +
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Residues in contact with GLU 259 (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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234B ASP* 3.5 2.9 - - - +
235B SER* 2.9 30.3 + - - +
257B ASN* 3.3 3.0 + - - +
258B GLU* 1.3 91.0 + - - +
260B ASN* 1.3 65.7 + - - +
262B LYS* 3.9 6.2 - - - +
263B ASN* 3.0 38.3 + - - +
588B LYS* 4.7 0.3 - - - -
591B LYS* 2.6 38.5 + - - -
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Residues in contact with ASN 260 (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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231B THR* 5.0 1.0 + - - -
234B ASP 3.9 3.2 + - - -
235B SER* 3.3 11.0 - - - +
236B VAL* 3.1 33.8 + - - +
239B TYR* 4.2 6.2 - - + -
252B PHE* 3.8 22.7 - - + -
253B ASP 3.0 27.3 + - - +
254B PHE* 3.6 19.6 - - + -
257B ASN* 2.9 24.3 + - - +
259B GLU* 1.3 71.7 - - - +
261B LEU* 1.3 58.8 + - - +
263B ASN* 3.4 6.1 + - - +
264B LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 261 (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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254B PHE* 3.6 21.6 - - + +
257B ASN* 4.8 0.6 + - - +
258B GLU* 3.3 12.4 + - - +
259B GLU 3.3 0.4 - - - -
260B ASN* 1.3 77.0 - - - +
262B LYS* 1.3 65.8 + - - +
264B LEU* 3.2 5.7 + - + -
265B GLU* 2.9 49.0 + - + +
296B LEU* 3.8 22.7 - - + -
300B LEU* 3.6 31.4 - - + -
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Residues in contact with LYS 262 (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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258B GLU 3.2 13.6 + - - +
259B GLU* 3.9 7.4 - - - +
261B LEU* 1.3 76.6 - - - +
263B ASN* 1.3 68.9 + - - +
265B GLU* 3.0 15.2 + - - +
266B LYS* 2.9 25.2 + - - +
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Residues in contact with ASN 263 (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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235B SER* 5.7 0.7 - - - -
236B VAL* 5.0 5.7 - - - +
239B TYR* 3.6 44.2 + - + +
259B GLU* 3.0 29.0 + - - +
260B ASN* 3.7 4.6 - - - +
262B LYS* 1.3 80.2 - - - +
264B LEU* 1.3 62.6 + - - +
266B LYS* 3.2 24.3 + - - +
268B GLY 4.6 0.2 + - - -
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Residues in contact with LEU 264 (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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239B TYR* 3.4 32.2 - - + +
252B PHE* 5.4 0.7 - - + -
254B PHE* 4.2 15.5 - - + -
260B ASN 2.9 17.3 + - - +
261B LEU* 3.7 7.2 - - + +
263B ASN* 1.3 75.7 - - - +
265B GLU* 1.3 71.2 + - + +
268B GLY* 3.1 26.1 - - - +
269B PHE* 3.9 24.9 - - + +
275B LEU* 3.9 22.2 - - + -
300B LEU* 4.6 21.8 - - + +
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Residues in contact with GLU 265 (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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261B LEU* 2.9 45.6 + - + +
262B LYS* 3.5 12.9 - - - +
264B LEU* 1.3 85.3 - - + +
266B LYS* 1.3 58.1 + - + +
268B GLY* 5.1 1.2 - - - -
300B LEU* 5.8 1.9 - - + +
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Residues in contact with LYS 266 (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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262B LYS 2.9 14.0 + - - +
263B ASN* 3.3 13.6 - - - +
265B GLU* 1.3 79.6 - - + +
268B GLY 2.9 30.1 + - - -
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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