Contacts of the helix formed by residues 224 - 245 (chain B) in PDB entry 6A69
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 LEU 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 4.3 26.8 - - + +
222B ALA 3.3 4.4 + - - -
223B PRO* 1.3 81.5 - - + +
225B TRP* 1.3 70.1 + - + +
226B PRO 3.5 0.2 - - - -
227B PHE* 3.1 23.8 + - + +
228B LEU* 3.5 27.1 + - + -
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Residues in contact with TRP 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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1043A TRP* 5.6 5.2 - - + -
221B LEU* 4.2 24.1 - - + +
222B ALA 5.1 2.5 - - - -
223B PRO 3.3 0.4 + - - -
224B LEU* 1.3 81.6 - - + +
226B PRO* 1.3 65.6 - - + +
227B PHE 3.3 0.3 + - - -
228B LEU* 3.3 9.6 + - - +
229B GLY* 3.0 18.5 + - - -
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Residues in contact with PRO 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039A GLU* 3.2 29.4 - - + +
1042A LEU* 3.5 13.5 - - + +
1043A TRP* 3.4 47.6 - - + +
1046A PHE* 4.8 6.9 - - + -
223B PRO 3.4 7.6 - - - +
225B TRP* 1.3 89.0 - - + +
227B PHE* 1.3 58.5 + - - -
229B GLY* 3.3 6.5 - - - +
230B ILE* 2.8 31.9 + - - +
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039A GLU* 6.1 0.2 - - - +
1042A LEU* 3.6 27.3 - - + +
223B PRO 4.6 1.7 + - - +
224B LEU* 3.1 18.6 + - + +
226B PRO* 1.3 78.7 - - - +
228B LEU* 1.3 70.4 + - + +
230B ILE* 3.3 11.8 + - + +
231B LEU* 3.0 50.5 + - + +
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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
----------------------------------------------------------
224B LEU* 3.5 31.4 + - + +
225B TRP* 3.3 10.7 + - - +
227B PHE* 1.3 88.3 - - + +
229B GLY* 1.3 56.6 + - - +
231B LEU* 3.3 15.2 + - + +
232B ALA* 2.9 31.0 + - - +
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Residues in contact with GLY 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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1046A PHE* 3.8 19.0 - - - -
225B TRP 3.0 13.3 + - - -
226B PRO* 3.1 9.1 + - - -
228B LEU* 1.3 75.7 - - - +
230B ILE* 1.3 60.9 + - - +
232B ALA* 3.3 6.2 + - - +
233B GLU* 3.0 25.3 + - - +
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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
----------------------------------------------------------
1042A LEU* 3.8 20.6 - - + -
1045A ILE* 4.0 15.9 - - + +
1046A PHE* 3.6 37.4 - - + +
1049A MET* 4.0 15.8 - - + +
226B PRO 2.8 19.9 + - - +
227B PHE* 3.4 15.0 - - + +
229B GLY* 1.3 70.1 - - - +
231B LEU* 1.3 63.8 + - + +
233B GLU* 3.2 4.2 + - - +
234B ILE* 2.9 50.9 + - + +
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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
----------------------------------------------------------
227B PHE* 3.0 45.9 + - + +
228B LEU* 3.9 16.6 - - + +
229B GLY 3.3 0.2 - - - -
230B ILE* 1.3 77.9 - - + +
232B ALA* 1.3 61.8 + - - +
234B ILE* 3.5 20.7 + - + +
235B ILE* 3.0 37.7 + - + +
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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 LEU 2.9 17.7 + - - +
229B GLY* 3.7 6.7 - - - +
230B ILE 3.3 0.2 - - - -
231B LEU* 1.3 75.9 - - - +
233B GLU* 1.3 58.2 + - - +
235B ILE* 3.2 10.6 + - - +
236B ILE* 2.9 35.7 + - + +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A PHE* 3.2 33.7 - - + +
1049A MET* 2.9 48.1 - - + +
1050A GLY* 3.2 9.2 - - - -
1053A LEU* 3.4 23.3 - - + +
229B GLY 3.0 15.8 + - - +
230B ILE 3.8 2.9 - - - +
232B ALA* 1.3 74.4 - - - +
234B ILE* 1.3 66.8 + - - +
236B ILE* 3.2 12.6 + - + +
237B LEU* 3.1 25.5 + - + +
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Residues in contact with ILE 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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1000A PHE* 6.4 1.8 - - + -
1049A MET* 3.6 22.9 - - + -
230B ILE* 2.9 37.9 + - + +
231B LEU* 3.6 19.3 - - + +
233B GLU* 1.3 77.0 - - - +
235B ILE* 1.3 61.6 + - + +
237B LEU* 3.4 10.8 + - + +
238B VAL* 3.0 46.4 + - + +
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Residues in contact with ILE 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 LEU* 3.0 26.7 + - + +
232B ALA* 3.2 8.5 + - - +
234B ILE* 1.3 80.5 - - + +
236B ILE* 1.3 62.0 + - + +
238B VAL* 3.9 4.6 - - - +
239B VAL* 2.9 40.8 + - + +
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Residues in contact with ILE 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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1053A LEU* 4.4 17.3 - - + -
232B ALA* 2.9 22.5 + - + +
233B GLU* 3.2 15.0 + - + +
235B ILE* 1.3 77.8 - - + +
237B LEU* 1.3 65.0 + - - +
239B VAL* 3.2 6.7 + - - +
240B ILE* 3.0 44.1 + - + +
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Residues in contact with LEU 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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999A VAL 5.6 0.4 - - - +
1000A PHE* 4.6 18.8 - - + -
1049A MET* 4.1 22.7 - - + +
1052A LEU* 3.7 31.2 - - + -
1053A LEU* 3.7 23.8 - - + -
1056A GLN* 6.3 2.9 - - + -
233B GLU* 3.1 18.7 + - + +
234B ILE* 3.4 18.4 - - + +
236B ILE* 1.3 77.1 - - - +
238B VAL* 1.3 75.2 + - + +
240B ILE* 3.3 7.5 + - - +
241B ILE* 3.0 39.3 + - + +
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Residues in contact with VAL 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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1000A PHE* 5.4 8.5 - - + -
234B ILE* 3.0 33.0 + - + +
235B ILE* 4.0 4.9 - - - +
237B LEU* 1.3 90.6 - - + +
239B VAL* 1.3 58.0 + - + +
241B ILE* 3.3 9.1 + - + +
242B VAL* 2.9 38.4 + - + +
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Residues in contact with VAL 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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235B ILE* 2.9 33.8 + - + +
236B ILE* 3.6 5.4 - - - +
238B VAL* 1.3 76.8 - - + +
240B ILE* 1.3 59.5 + - + +
242B VAL* 3.2 8.6 + - + +
243B VAL* 2.9 40.3 + - + +
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Residues in contact with ILE 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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997A ARG* 5.2 10.8 - - + +
1053A LEU* 4.8 6.7 - - + -
1056A GLN* 3.5 41.1 - - - +
236B ILE* 3.0 34.3 + - + +
237B LEU* 3.3 9.8 + - - +
239B VAL* 1.3 80.1 - - + +
241B ILE* 1.3 59.1 + - + +
243B VAL* 3.2 8.3 + - + +
244B TYR* 3.0 29.3 + - + +
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Residues in contact with ILE 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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997A ARG* 4.4 15.5 - - + +
998A ASN* 3.7 22.3 + - - +
999A VAL 4.3 26.5 - - - +
1000A PHE* 4.9 7.6 - - + +
1056A GLN* 6.2 3.6 - - + -
237B LEU* 3.0 32.0 + - + +
238B VAL* 3.3 8.7 + - + +
240B ILE* 1.3 78.1 - - + +
242B VAL* 1.3 63.3 + - + +
244B TYR* 4.2 3.8 - - - +
245B GLU* 3.4 24.9 + - + +
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Residues in contact with VAL 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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238B VAL* 2.9 31.1 + - + +
239B VAL* 3.2 9.2 + - + +
241B ILE* 1.3 79.6 - - + +
243B VAL* 1.3 65.1 + - + +
245B GLU* 3.7 8.2 + - - +
246B LYS* 3.9 15.0 + - + +
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Residues in contact with VAL 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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239B VAL* 2.9 31.8 + - + +
240B ILE* 3.2 7.6 + - + +
242B VAL* 1.3 82.3 - - + +
244B TYR* 1.3 63.1 + - - +
245B GLU 3.4 0.3 + - - -
246B LYS* 3.5 18.0 - - - +
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Residues in contact with TYR 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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996A GLU 4.2 17.8 + - - -
997A ARG* 3.6 54.3 - - + +
998A ASN* 5.0 10.1 - - - +
240B ILE* 3.0 17.1 + - + +
241B ILE* 4.3 4.0 - - - +
242B VAL 3.4 0.2 - - - -
243B VAL* 1.3 79.7 - - - +
245B GLU* 1.3 62.9 + - + +
246B LYS 3.2 6.7 + - - +
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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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998A ASN* 5.2 10.1 - - - +
241B ILE* 3.4 18.5 + - + +
242B VAL* 4.1 3.6 - - - +
243B VAL 3.4 0.8 - - - -
244B TYR* 1.3 78.4 - - + +
246B LYS* 1.3 59.7 + - - +
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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
------------------------------------------------------------
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