Contacts of the helix formed by residues 236 - 249 (chain B) in PDB entry 1XPM
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 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.4 27.8 - - + -
39B GLN* 3.2 18.2 - - + +
152B THR* 4.3 8.1 - - + -
202B LYS* 4.7 8.1 - - + -
234B VAL* 3.2 8.4 - - - +
235B PRO* 1.3 90.5 - - + +
237B THR* 1.3 58.7 + - - +
238B LYS* 3.4 21.3 - - + -
239B MET* 2.9 76.5 + - + +
240B GLY 3.5 2.9 + - - -
2402B CAA 3.4 56.8 - - + -
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Residues in contact with THR 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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38B GLY* 2.6 41.2 + - - +
39B GLN* 3.1 7.9 + - - +
234B VAL* 4.0 6.1 - - + +
236B PHE* 1.3 71.2 - - - +
238B LYS* 1.3 60.5 + - - +
241B LYS* 3.1 12.6 + - - +
263B TYR* 2.7 29.0 + - - -
267B VAL* 3.6 33.4 - - + +
271B ARG* 3.6 28.4 + - + +
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Residues in contact with LYS 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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35B ILE 4.9 1.6 - - - +
36B GLY 3.2 23.1 - - - +
37B ILE 2.9 24.6 + - - +
38B GLY* 5.2 0.2 - - - -
236B PHE* 3.1 14.3 + - + -
237B THR* 1.3 77.5 + - - +
239B MET* 1.3 63.7 + - - +
241B LYS* 3.6 6.7 + - - +
242B LYS* 3.4 25.6 + - - +
2402B CAA 5.4 5.4 - - - +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 3.7 35.7 - - + +
205B TYR* 3.8 32.8 - - + -
206B ILE* 3.9 24.0 - - + -
235B PRO* 3.4 23.6 - - + -
236B PHE* 2.9 39.1 + - + +
238B LYS* 1.3 74.0 - - - +
240B GLY* 1.3 66.6 + - - +
241B LYS 3.1 1.0 + - - -
242B LYS* 3.1 8.2 + - + +
243B ALA* 3.1 11.2 + - - +
2402B CAA 4.0 11.0 - - - -
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 4.6 9.4 - - - -
232B PHE* 5.1 5.2 - - - -
233B HIS 5.1 4.3 - - - -
234B VAL* 6.2 0.7 - - - -
235B PRO* 5.2 1.4 - - - +
236B PHE 3.5 3.0 + - - -
237B THR 3.3 3.2 + - - -
239B MET* 1.3 81.7 - - - +
241B LYS* 1.3 55.8 + - - +
243B ALA* 3.8 7.5 - - - +
244B LEU* 2.9 29.1 + - - +
263B TYR* 3.0 27.5 + - - -
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Residues in contact with LYS 241 (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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237B THR 3.1 15.6 + - - +
238B LYS* 3.8 8.3 - - - +
239B MET 3.1 1.2 - - - -
240B GLY* 1.3 75.1 - - - +
242B LYS* 1.3 67.6 + - + +
244B LEU* 3.2 13.9 + - + +
245B GLU* 2.9 58.9 + - + +
260B ARG* 3.6 25.5 + - - +
263B TYR* 3.3 15.1 + - + -
264B GLU* 5.1 9.1 + - - +
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Residues in contact with LYS 242 (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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202B LYS* 6.2 4.0 - - + -
206B ILE* 4.2 16.3 - - + +
238B LYS 3.4 14.1 + - - +
239B MET* 3.1 11.9 + - + +
241B LYS* 1.3 78.3 - - + +
243B ALA* 1.3 63.5 + - - +
245B GLU* 3.5 6.6 + - - +
246B SER* 3.2 21.8 + - - -
2402B CAA 5.2 10.3 - - - +
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Residues in contact with ALA 243 (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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205B TYR* 3.5 36.6 - - + +
206B ILE* 4.1 13.1 - - + +
209B PHE* 3.7 21.1 - - + -
232B PHE* 4.8 5.2 - - + -
239B MET 3.1 11.9 + - - +
240B GLY* 3.8 5.6 - - - +
242B LYS* 1.3 77.0 - - - +
244B LEU* 1.3 61.7 + - - +
246B SER* 2.5 26.9 + - - -
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Residues in contact with LEU 244 (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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209B PHE* 5.0 1.1 - - - -
230B LEU* 4.6 5.6 - - + -
232B PHE* 4.0 30.9 - - + -
240B GLY 2.9 19.0 + - - +
241B LYS* 3.4 13.7 - - + +
243B ALA* 1.3 78.6 - - - +
245B GLU* 1.3 75.0 + - - +
246B SER 3.2 1.2 + - - -
247B ILE* 3.3 11.7 + - + +
248B ILE* 3.4 41.5 - - + +
259B LEU* 4.5 15.3 - - + +
260B ARG* 4.1 18.4 - - + -
263B TYR* 4.0 26.9 - - + -
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Residues in contact with GLU 245 (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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241B LYS* 2.9 56.0 + - + +
242B LYS* 4.0 6.1 - - - +
243B ALA 3.4 0.2 - - - -
244B LEU* 1.3 77.4 - - - +
246B SER* 1.3 61.3 + - - +
247B ILE 3.1 1.6 + - - -
248B ILE* 3.0 23.7 + - - +
249B ASP* 4.1 10.6 + - - +
260B ARG* 2.8 38.0 + - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 3.7 19.4 - - - +
209B PHE* 4.3 1.6 - - - -
210B GLN* 3.5 31.3 + - - +
242B LYS 3.2 12.6 + - - -
243B ALA 2.5 21.0 + - - -
244B LEU 3.1 0.2 - - - -
245B GLU* 1.3 76.7 - - - +
247B ILE* 1.3 63.2 + - - +
249B ASP* 5.1 3.5 - - - +
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Residues in contact with ILE 247 (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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209B PHE* 3.3 38.1 - - + -
210B GLN* 4.1 17.9 - - + +
213B TRP* 4.3 21.5 - - + +
214B ASN* 6.0 0.2 - - - +
224B LEU* 3.7 39.2 - - + +
230B LEU* 4.5 5.2 - - + -
244B LEU* 3.6 10.1 - - - +
245B GLU 3.1 0.2 + - - -
246B SER* 1.3 93.8 + - - +
248B ILE* 1.3 63.4 + - + +
249B ASP* 2.8 14.0 + - - +
250B ASN* 3.2 17.7 + - - +
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Residues in contact with ILE 248 (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 LEU* 4.0 4.0 - - + -
230B LEU* 5.6 0.2 - - + -
244B LEU* 3.4 39.7 - - + +
245B GLU* 3.0 47.1 - - - +
247B ILE* 1.3 81.0 - - + +
249B ASP* 1.3 55.2 + - - +
250B ASN 3.3 0.2 - - - -
251B ALA* 2.9 29.2 + - + +
256B GLN* 2.6 33.1 + - + +
259B LEU* 4.3 22.9 - - + -
260B ARG* 3.4 22.0 - - + +
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Residues in contact with ASP 249 (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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245B GLU 4.1 10.3 + - - +
246B SER 5.3 2.2 - - - +
247B ILE* 2.8 4.3 + - - +
248B ILE* 1.3 81.1 - - - +
250B ASN* 1.3 61.0 + - - +
251B ALA 3.1 9.4 + - - +
256B GLN* 3.4 11.1 + - - +
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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