Contacts of the helix formed by residues 231 - 246 (chain B) in PDB entry 3DYQ
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 ASN 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B SER 3.3 6.2 + - - +
230B ILE* 1.3 73.9 - - - +
232B PRO* 1.3 65.4 - - - +
233B VAL* 3.2 17.2 - - - +
234B THR* 3.0 40.9 + - - +
235B LEU 2.9 24.1 + - - -
237B ARG* 4.5 2.6 - - - +
340B ILE* 5.3 0.8 + - - +
342B SER* 5.6 5.0 + - - +
343B ASN* 4.6 8.2 - - - +
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Residues in contact with PRO 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLU* 4.8 3.4 - - - +
220B HIS* 4.4 20.9 - - + +
225B VAL* 4.5 10.8 - - + -
230B ILE 3.3 9.6 - - - +
231B ASN* 1.3 89.0 - - - +
233B VAL* 1.3 63.0 + - + +
235B LEU* 3.5 11.2 - - + +
236B ARG* 3.4 24.4 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 3.2 11.6 - - - +
232B PRO* 1.3 77.8 - - + +
234B THR* 1.3 62.7 + - - +
236B ARG* 3.1 19.2 + - + +
237B ARG* 2.9 54.6 + - + +
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 3.0 31.8 + - - +
233B VAL* 1.3 77.0 - - - +
235B LEU* 1.3 58.6 + - - +
237B ARG* 3.1 18.1 + - - +
238B TRP* 2.7 29.5 + - - +
336B PRO 4.6 3.2 + - - +
337B GLU 3.4 18.7 + - - +
338B CYS 3.5 3.6 - - - -
339B ASN 3.5 35.7 - - - +
340B ILE* 3.8 5.2 - - + +
342B SER* 5.6 1.1 - - - +
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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
----------------------------------------------------------
216B GLU* 4.0 20.2 - - + +
219B TYR* 3.7 34.3 - - + -
220B HIS* 4.0 11.0 - - + +
225B VAL* 3.7 28.3 - - + -
230B ILE* 3.9 9.6 - - + -
231B ASN 2.9 11.7 + - - +
232B PRO* 3.5 10.8 - - + +
233B VAL 3.2 0.2 - - - -
234B THR* 1.3 74.9 - - - +
236B ARG* 1.3 57.5 + - - +
238B TRP* 3.6 20.1 + - + +
239B LEU* 3.0 39.4 + - + +
340B ILE* 3.6 13.8 - - + +
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Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLU* 3.3 39.1 + - - +
232B PRO 3.4 12.5 + - - +
233B VAL* 3.1 21.4 + - + +
234B THR 3.1 0.8 - - - -
235B LEU* 1.3 76.8 - - - +
237B ARG* 1.3 66.3 + - + +
239B LEU* 3.3 7.6 + - - +
240B PHE* 3.0 24.3 + - - +
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 4.5 2.0 - - - +
233B VAL* 2.9 35.8 + - + +
234B THR* 3.2 31.7 + - - +
236B ARG* 1.3 75.1 - - + +
238B TRP* 1.3 57.6 + - - +
240B PHE* 3.1 7.7 + - - +
241B CYS* 2.8 31.0 + - - +
337B GLU* 2.9 46.5 + - - +
338B CYS* 4.2 6.2 - - - -
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Residues in contact with TRP 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.6 30.1 - + - -
234B THR 2.7 20.2 + - - +
235B LEU* 3.7 11.4 - - + +
237B ARG* 1.3 74.1 - - - +
239B LEU* 1.3 89.0 + - + +
241B CYS* 3.1 2.9 + - - +
242B VAL* 2.8 46.3 + - + +
287B THR* 3.6 24.5 - - + -
290B ILE* 3.8 15.3 - - + -
291B CYS* 3.9 16.8 - - - -
329B ALA 5.3 0.2 + - - -
332B ILE* 3.7 16.7 - - + +
333B LEU* 3.4 19.7 - - + +
338B CYS* 3.4 34.7 - - - +
340B ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 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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212B LEU* 3.4 30.9 - - + +
215B LEU* 3.8 27.6 - - + -
216B GLU* 3.4 40.4 - - + +
219B TYR* 5.5 0.7 - - + -
235B LEU* 3.0 30.3 + - + +
236B ARG* 3.3 5.6 + - - +
238B TRP* 1.3 103.3 - - + +
240B PHE* 1.3 56.0 + - - +
242B VAL* 3.4 5.2 + - + +
243B HIS 2.8 23.9 + - - -
254B PHE* 5.2 0.6 - - + -
290B ILE* 4.4 11.7 - - + -
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Residues in contact with PHE 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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212B LEU* 4.3 20.6 - - + +
236B ARG 3.0 14.1 + - - +
237B ARG* 3.4 10.5 - - - +
239B LEU* 1.3 75.4 - - - +
241B CYS* 1.3 61.6 + - - +
243B HIS* 3.3 20.7 + + - +
244B ASP* 2.9 36.1 + - + +
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Residues in contact with CYS 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 ARG 2.8 17.0 + - - +
238B TRP 3.5 3.6 - - - +
240B PHE* 1.3 77.8 - - + +
242B VAL* 1.3 64.9 - - - +
244B ASP* 3.0 14.3 + - - +
245B ASN* 2.9 36.5 + - - -
332B ILE* 3.8 22.0 - - + -
335B GLU* 6.1 2.9 - - - -
337B GLU* 5.8 0.4 - - - -
338B CYS* 3.7 20.2 - - - -
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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
----------------------------------------------------------
238B TRP* 2.8 56.1 + - + +
239B LEU* 3.6 10.1 - - + +
241B CYS* 1.3 71.7 - - - +
243B HIS* 1.3 66.2 + - - +
245B ASN* 3.0 12.6 + - - -
246B TYR* 3.2 37.1 + - + -
254B PHE* 5.1 2.7 - - + -
257B CYS* 4.9 2.5 - - - -
290B ILE* 3.7 22.0 - - + +
291B CYS* 4.6 6.7 - - - -
294B LEU* 3.8 5.7 - - + +
332B ILE* 4.1 17.5 - - + -
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Residues in contact with HIS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PRO* 4.0 21.5 - - + +
212B LEU* 3.9 22.4 - - + +
239B LEU 2.8 15.3 + - - +
240B PHE* 3.4 25.3 + + - +
242B VAL* 1.3 79.3 - - - +
244B ASP* 1.3 71.9 + - - +
245B ASN 3.2 0.3 + - - -
246B TYR* 3.3 15.9 + - - +
254B PHE* 3.6 43.9 - + + +
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Residues in contact with ASP 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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240B PHE* 2.9 25.4 + - + +
241B CYS* 3.0 12.7 + - - +
243B HIS* 1.3 86.5 + - - +
245B ASN* 1.3 61.3 + - - +
246B TYR 3.4 9.9 - - - +
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Residues in contact with ASN 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 CYS* 2.9 32.3 + - - -
242B VAL 3.0 5.0 + - - +
244B ASP* 1.3 80.8 + - - +
246B TYR* 1.3 61.0 + - - +
247B ARG* 5.4 0.2 - - - -
294B LEU* 3.6 22.2 - - + -
295B ASP* 2.8 37.2 + - + +
328B VAL* 4.4 9.6 - - + +
332B ILE* 3.3 22.1 - - + +
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Residues in contact with TYR 246 (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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242B VAL* 3.2 36.6 + - + -
243B HIS 3.3 12.2 + - - +
244B ASP 3.4 10.2 - - - +
245B ASN* 1.3 80.3 - - - +
247B ARG* 1.3 61.0 + - - +
248B ASN* 4.9 2.9 - - - +
252B HIS 4.6 3.1 - - - -
253B ASN* 3.8 20.0 - - - -
254B PHE* 3.8 28.7 - + + +
257B CYS* 3.3 23.8 - - + +
290B ILE 2.6 30.4 + - - -
291B CYS 3.5 2.3 - - - -
292B HIS* 3.6 1.6 + - - -
293B ASP* 3.2 51.2 + - + +
294B LEU* 3.7 14.8 - - + -
295B ASP 4.4 1.1 - - - +
296B HIS 5.8 0.2 - - - -
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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