Contacts of the helix formed by residues 222 - 232 (chain B) in PDB entry 1B43
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 ARG 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B LEU 3.9 3.8 - - - +
177B LEU* 3.0 29.7 + - - -
178B PHE 3.5 8.4 + - - -
179B GLY* 3.7 22.6 - - - +
211B LEU* 3.9 22.9 - - + -
215B LEU* 3.6 16.9 - - + +
221B THR* 1.3 73.1 - - - +
223B GLU* 1.3 57.2 + - - +
225B LEU* 3.4 3.8 + - + +
226B ILE* 2.9 38.4 + - + +
278B PHE 3.1 18.8 + - - -
279B LEU* 3.4 35.8 + - + +
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Residues in contact with GLU 223 (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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221B THR* 3.1 9.7 + - - +
222B ARG* 1.3 79.9 - - - +
224B LYS* 1.3 57.5 + - + +
226B ILE* 3.2 13.1 + - - +
227B GLU* 2.9 40.9 + - - +
257B LYS 5.8 0.2 - - - +
275B LYS* 2.8 40.4 + - - -
279B LEU* 4.2 18.3 - - + +
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Residues in contact with LYS 224 (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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219B LYS 5.1 0.7 - - - +
220B LEU* 3.4 34.1 - - + -
221B THR* 3.1 36.7 + - + +
223B GLU* 1.3 73.7 - - + +
225B LEU* 1.3 55.9 - - - +
226B ILE 3.1 1.1 - - - -
227B GLU* 3.0 17.8 + - - +
228B LEU* 2.8 32.8 + - - +
253B VAL* 3.0 27.6 + - + +
254B ARG* 4.5 10.2 + - + +
256B SER 4.2 11.9 + - - -
257B LYS* 5.6 2.4 - - - +
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Residues in contact with LEU 225 (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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4B ILE* 4.2 20.6 - - + -
7B ILE* 5.6 1.1 - - + -
8B ILE* 5.2 5.4 - - + -
176B LEU* 5.2 5.4 - - + +
177B LEU* 3.6 17.9 - - + -
211B LEU* 4.2 16.6 - - + -
214B VAL* 4.4 11.7 - - + -
215B LEU* 3.6 25.1 - - + -
218B LEU* 4.2 20.4 - - + -
220B LEU* 4.5 7.1 - - + +
221B THR 2.8 15.5 + - - +
222B ARG* 3.7 6.1 - - + +
224B LYS* 1.3 76.0 - - - +
226B ILE* 1.3 57.2 + - - +
228B LEU* 3.6 16.1 + - + +
229B ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 226 (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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177B LEU* 3.3 37.2 - - + +
222B ARG* 2.9 30.6 + - - +
223B GLU* 3.3 7.6 - - - +
224B LYS 3.1 0.2 - - - -
225B LEU* 1.3 75.0 - - - +
227B GLU* 1.3 59.7 + - - +
229B ALA* 3.1 7.9 + - - +
230B ILE* 2.8 48.7 + - + +
275B LYS* 4.0 12.3 - - + +
278B PHE* 3.6 34.8 - - + -
279B LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 227 (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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223B GLU* 2.9 42.4 + - - +
224B LYS* 3.0 29.1 + - - +
226B ILE* 1.3 76.2 - - - +
228B LEU* 1.3 50.7 + - - +
230B ILE* 2.8 16.7 + - - +
231B LEU* 2.8 39.1 + - + +
253B VAL* 3.2 19.0 - - + +
257B LYS 4.4 8.1 - - - +
259B PRO* 4.3 25.5 - - + +
260B LEU* 4.6 9.3 - - + +
275B LYS* 3.9 21.0 + - + -
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Residues in contact with LEU 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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4B ILE* 3.8 17.0 - - + -
7B ILE* 4.1 7.9 - - + -
220B LEU* 3.9 16.8 - - + -
224B LYS 2.8 19.1 + - - +
225B LEU* 3.6 11.7 - - + +
227B GLU* 1.3 71.9 - - - +
229B ALA* 1.3 67.1 + - - +
231B LEU* 3.0 15.6 + - - +
232B VAL* 3.0 39.7 + - + +
246B LEU* 4.1 9.9 - - + +
249B ALA* 4.0 15.5 - - + +
250B LEU* 3.6 34.3 - - + +
253B VAL* 3.7 9.3 - - + +
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Residues in contact with ALA 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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2B VAL* 3.8 11.9 - - + +
4B ILE* 4.2 14.6 - - + -
177B LEU* 3.5 32.5 - - + -
225B LEU 2.9 19.5 + - - +
226B ILE* 3.2 7.0 - - + +
228B LEU* 1.3 75.1 - - - +
230B ILE* 1.3 57.1 + - - +
232B VAL* 3.9 1.4 - - - +
233B GLY 3.0 22.5 + - - -
234B THR* 3.2 15.7 + - + +
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Residues in contact with ILE 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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226B ILE* 2.8 34.3 + - + +
227B GLU* 2.8 10.4 + - - +
229B ALA* 1.3 75.9 - - - +
231B LEU* 1.3 65.5 + - - +
233B GLY 3.5 0.9 + - - -
234B THR* 3.7 15.9 - - + -
237B ASN* 3.0 38.7 + - - +
240B GLY* 3.9 0.5 - - - -
241B ILE* 4.4 3.1 + - - +
260B LEU* 3.5 29.8 - - + -
271B LEU* 4.2 15.7 - - + +
274B ILE* 4.6 8.3 - - + -
275B LYS* 3.5 41.5 - - + +
278B PHE* 4.9 0.4 - - + -
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Residues in contact with LEU 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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227B GLU 2.8 23.7 + - - +
228B LEU* 3.4 10.8 - - - +
230B ILE* 1.3 69.5 - - - +
232B VAL* 1.3 68.5 + - - +
241B ILE* 2.9 32.2 + - + +
244B ILE* 3.7 12.4 - - + +
249B ALA* 3.2 37.5 - - + +
252B ILE* 4.0 15.3 - - + -
253B VAL* 4.0 11.7 - - + +
259B PRO* 4.5 10.3 - - + -
260B LEU* 4.3 13.0 - - + -
263B PHE* 3.7 35.0 - - + -
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Residues in contact with VAL 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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3B PRO* 4.0 35.4 - - + -
4B ILE* 4.3 8.7 - - + -
228B LEU* 3.0 32.6 + - + +
229B ALA 3.9 3.8 - - - +
231B LEU* 1.3 80.3 - - - +
233B GLY* 1.3 59.1 + - - +
239B GLY 3.0 20.1 - - - +
241B ILE 4.0 0.2 + - - -
244B ILE 3.9 16.4 - - - +
245B GLY* 4.2 10.3 - - - +
246B LEU* 4.4 10.8 - - + +
249B ALA* 3.6 18.8 - - + +
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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