Contacts of the helix formed by residues 227 - 236 (chain B) in PDB entry 1XLB
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 PHE 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B PRO* 3.9 9.9 - - + -
216B GLU 3.6 10.3 - - - -
217B THR* 3.4 56.8 - - + +
220B GLU* 4.1 16.2 - - + -
221B GLN* 4.3 18.0 + - + +
225B LEU 3.5 4.6 + - - -
226B ASN* 1.3 72.9 + - - +
228B THR* 1.4 60.8 + - - +
230B GLY* 3.1 2.6 + - - -
231B ILE* 3.0 40.4 + - + +
243B ILE* 3.5 31.9 - - + -
245B LEU* 4.2 1.1 - - + -
266B SER* 4.6 6.8 + - - +
270B THR* 3.3 40.4 - - + +
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Residues in contact with THR 228 (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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226B ASN* 3.1 10.2 + - - -
227B PHE* 1.4 76.0 - - - +
229B HIS* 1.3 64.5 + - + +
231B ILE* 3.6 8.4 + - - +
232B ALA* 3.1 25.7 + - + +
266B SER* 3.6 9.8 + - - -
269B PHE* 3.5 31.4 - - + +
270B THR* 3.0 26.4 + - - +
273B LEU* 3.7 17.7 - - + +
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Residues in contact with HIS 229 (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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226B ASN* 3.2 42.5 + - + +
227B PHE 3.3 0.4 - - - -
228B THR* 1.3 83.8 - - + +
230B GLY* 1.3 58.6 + - - +
232B ALA* 3.6 16.2 - - - +
233B GLN* 3.6 10.7 + - - +
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Residues in contact with GLY 230 (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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195B VAL* 3.4 30.6 - - - +
220B GLU* 5.7 3.6 - - - -
226B ASN 3.1 9.6 + - - -
227B PHE* 3.1 8.0 + - - -
229B HIS* 1.3 72.2 - - - +
231B ILE* 1.3 67.4 + - - +
233B GLN* 3.4 5.7 + - - +
234B ALA 3.2 16.8 + - - -
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Residues in contact with ILE 231 (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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195B VAL* 5.3 0.4 - - + -
215B PRO* 3.8 21.5 - - + -
227B PHE* 3.0 45.7 + - + +
228B THR* 3.7 8.1 - - - +
230B GLY* 1.3 75.9 - - - +
232B ALA* 1.3 54.4 + - - +
234B ALA* 3.1 6.4 + - - +
235B LEU* 2.8 37.1 + - - +
240B LEU* 4.3 11.8 - - + +
243B ILE* 3.7 23.6 - - + -
270B THR* 3.9 25.4 - - + +
273B LEU* 4.2 15.5 - - + -
274B LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 232 (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 THR 3.1 21.0 + - - +
229B HIS* 3.6 11.2 - - - +
231B ILE* 1.3 74.8 - - - +
233B GLN* 1.3 50.5 + - - +
235B LEU* 3.4 2.9 + - - +
236B TRP* 2.8 35.9 + - - +
273B LEU* 3.8 17.3 - - + -
278B PHE* 4.0 20.2 - - + -
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Residues in contact with GLN 233 (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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195B VAL* 5.3 2.3 - - + +
196B GLY* 5.4 9.5 + - - -
199B LEU* 4.1 17.7 - - + +
229B HIS 3.6 8.5 + - - +
230B GLY* 3.4 11.1 + - - +
231B ILE 3.3 0.6 - - - -
232B ALA* 1.3 73.8 - - - +
234B ALA* 1.3 65.1 + - - +
236B TRP* 3.5 24.9 + - + +
237B ALA* 3.1 23.8 + - + +
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Residues in contact with ALA 234 (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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195B VAL* 4.2 11.9 - - + -
199B LEU* 3.9 17.1 - - + +
213B LEU* 4.5 10.5 - - + -
215B PRO* 4.8 0.9 - - + -
230B GLY 3.2 12.8 + - - +
231B ILE* 3.1 11.9 + - - +
233B GLN* 1.3 76.1 - - - +
235B LEU* 1.4 59.0 + - - +
237B ALA* 3.3 4.0 + - - +
238B GLU 3.1 4.5 + - - -
239B LYS 2.9 26.7 + - - -
240B LEU* 4.0 22.2 - - + +
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Residues in contact with LEU 235 (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 ILE 2.8 16.9 + - - +
232B ALA 3.6 4.7 - - - +
234B ALA* 1.4 67.0 - - - +
236B TRP* 1.3 59.4 + - - +
238B GLU* 2.8 43.0 + - - +
240B LEU* 4.0 27.0 - - + +
273B LEU* 3.4 31.4 - - + -
278B PHE* 3.6 18.6 - - + -
283B PRO* 3.9 23.5 - - + +
284B LYS* 3.6 29.6 - - - +
285B TYR* 4.1 11.4 - - + +
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Residues in contact with TRP 236 (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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232B ALA 2.8 21.6 + - - +
233B GLN* 3.5 29.4 - - + +
235B LEU* 1.3 73.5 - - - +
237B ALA* 1.3 64.9 + - + +
238B GLU* 3.6 6.8 + - - +
278B PHE* 5.3 3.3 - - + -
283B PRO* 4.7 13.3 - - + +
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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