Contacts of the helix formed by residues 233 - 240 (chain B) in PDB entry 1XAI
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 GLY 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU 3.3 5.9 + - - -
232B GLN* 1.3 77.5 - - - +
234B VAL* 1.3 58.7 + - - -
235B ARG 3.5 1.3 - - - -
236B LYS* 2.8 43.0 - - - +
237B PHE* 5.3 2.2 - - - -
334B VAL* 5.1 1.9 - - - +
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Residues in contact with VAL 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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224B ILE* 3.9 21.8 - - + +
227B ALA* 4.8 8.7 - - + +
228B ASP* 3.1 26.5 + - + +
232B GLN 4.0 1.2 + - - -
233B GLY* 1.3 66.5 - - - -
235B ARG* 1.3 57.0 + - - +
236B LYS 2.8 5.4 - - - -
237B PHE* 2.6 68.2 + - + +
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Residues in contact with ARG 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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133B VAL 4.1 1.2 + - - -
134B GLY* 2.8 41.8 + - - -
136B LYS* 3.5 26.3 - - - +
151B PHE* 4.4 1.0 - - - -
224B ILE* 3.4 17.5 - - - +
225B VAL* 3.6 22.6 - - - +
228B ASP* 2.9 39.0 + - - +
229B GLU* 3.2 21.7 + - - +
231B GLU* 3.6 21.1 - - + +
234B VAL* 1.3 69.0 - - - +
236B LYS* 1.3 56.2 + - - +
237B PHE 2.8 11.0 + - - -
238B LEU* 3.2 22.3 + - + +
239B ASN* 4.3 1.4 + - - -
501B CRB 2.7 43.4 + - - +
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Residues in contact with LYS 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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90A ARG* 4.8 4.2 - - - +
231B GLU* 3.6 42.2 - - + +
233B GLY* 2.8 31.0 - - - +
234B VAL 2.7 0.2 + - - -
235B ARG* 1.3 78.0 - - - +
237B PHE* 1.3 58.3 + - - +
238B LEU 3.3 0.7 - - - -
239B ASN* 3.2 14.2 - - - +
314B LYS 5.6 0.4 + - - -
315B LYS* 3.9 31.7 + - + +
322B GLN* 4.8 6.3 - - - +
324B VAL* 3.0 25.9 - - - +
334B VAL* 4.1 28.0 - - + -
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Residues in contact with PHE 237 (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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185B LEU* 3.5 26.5 - - + +
224B ILE* 5.0 8.7 - - + -
233B GLY 5.4 1.3 - - - -
234B VAL* 2.6 43.2 + - + +
236B LYS* 1.3 78.3 - - + +
238B LEU* 1.3 61.2 + - + +
239B ASN 3.0 6.6 + - - -
240B LEU* 3.5 12.6 + - - +
324B VAL* 3.7 6.9 - - + +
332B ILE* 3.3 57.2 - - + -
333B VAL* 4.4 1.1 - - - -
334B VAL* 3.6 21.8 - - + -
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Residues in contact with LEU 238 (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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181B LYS* 2.6 30.3 + - - +
182B HIS* 4.7 11.4 - - + +
185B LEU* 4.7 11.4 - - + -
220B THR* 6.0 0.7 - - + -
221B LYS* 3.5 38.4 - - + -
224B ILE* 3.7 33.4 - - + -
225B VAL* 4.0 6.7 - - + -
235B ARG* 3.2 19.2 + - + +
237B PHE* 1.3 77.1 - - + +
239B ASN* 1.3 55.1 + - - +
240B LEU 3.1 6.5 + - - -
242B HIS* 3.4 8.5 - - - -
501B CRB 3.2 39.6 + - + +
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Residues in contact with ASN 239 (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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136B LYS* 4.3 0.6 - - - +
231B GLU* 4.0 20.8 + - - -
235B ARG 4.9 0.6 + - - -
236B LYS* 3.2 16.6 + - - +
237B PHE 3.0 0.4 - - - -
238B LEU* 1.3 77.3 - - - +
240B LEU* 1.3 63.9 + - - +
241B GLY 3.1 1.2 + - - -
242B HIS* 3.0 36.2 + - - +
243B THR* 4.2 4.7 + - - -
246B HIS* 4.6 1.4 + - - -
313B ASP* 5.2 0.5 - - - +
315B LYS* 3.6 36.2 + - + +
324B VAL* 4.0 9.4 + - + +
501B CRB 3.3 39.1 + - - -
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Residues in contact with LEU 240 (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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181B LYS* 3.7 13.8 - - + +
184B LEU* 4.2 24.2 - - + -
185B LEU* 2.9 31.0 - - + -
237B PHE 3.5 14.0 + - - +
238B LEU 3.1 3.0 - - - -
239B ASN* 1.3 74.7 - - - +
241B GLY* 1.3 58.4 + - - +
242B HIS* 3.0 18.0 + - - -
260B VAL* 4.3 0.3 - - - +
264B ILE* 3.4 18.1 - - + +
267B GLN* 3.8 21.5 - - - +
324B VAL* 3.3 37.0 - - + +
325B LEU 4.7 0.2 - - - -
326B MET* 4.8 8.7 - - + +
332B ILE* 4.4 7.9 - - + -
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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