Contacts of the helix formed by residues 231 - 245 (chain C) in PDB entry 3SWD
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 ASP 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.4 3.3 - - + +
19C SER* 3.0 20.7 + - - +
20C GLY 3.7 3.1 - - - +
21C ALA* 3.5 16.7 - - - +
22C LYS* 3.1 17.3 + - - +
47C LEU* 5.9 0.2 - - - +
230C PRO* 1.3 69.0 - - - +
232C ARG* 1.3 54.1 + - - +
233C ILE* 2.8 14.2 + - - +
234C GLU* 2.8 40.1 + - + +
235C THR* 2.8 34.5 + - - -
371C ARG* 3.1 25.9 + - - -
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Residues in contact with ARG 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C GLU* 3.5 20.2 + - - +
189C PRO* 3.7 17.0 - - - +
190C GLU* 2.8 42.8 + - - +
230C PRO 3.3 5.6 + - - +
231C ASP* 1.3 70.0 + - - +
233C ILE* 1.3 76.8 + - + +
235C THR* 3.4 5.2 + - - -
236C GLY* 2.9 23.7 + - - -
258C THR* 2.9 42.7 + - + -
259C LEU* 3.4 22.8 - - + +
299C HIS* 4.1 15.4 + - - +
303C PRO* 3.9 29.1 - - + +
305C ASP* 5.8 1.8 + - - -
306C MET* 4.9 0.5 - - - +
501C EPZ 5.0 6.5 + - - -
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN* 6.0 0.9 - - - +
231C ASP* 2.8 8.5 + - - +
232C ARG* 1.3 97.0 - - + +
234C GLU* 1.3 60.2 + - - +
236C GLY 3.5 0.2 + - - -
237C THR* 2.7 33.6 + - - -
259C LEU* 6.0 0.9 - - + -
303C PRO* 4.4 11.4 - - + -
305C ASP* 3.5 50.0 - - + +
306C MET* 3.6 22.5 - - + +
309C GLN* 4.2 0.4 - - - +
371C ARG* 4.1 26.0 - - - +
399C TYR* 4.1 13.2 - - - +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.6 9.0 - - + +
19C SER* 2.9 36.4 + - - +
231C ASP* 2.8 25.7 + - - +
233C ILE* 1.3 74.7 - - - +
235C THR* 1.3 64.9 + - - +
237C THR* 3.2 5.5 + - - -
238C PHE* 3.2 48.6 + - + -
371C ARG* 5.1 0.6 - - - +
399C TYR* 4.3 22.7 - - + +
400C GLU 4.3 13.7 + - - +
402C ILE* 6.1 0.7 - - - +
405C LYS* 3.1 24.5 + - - +
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Residues in contact with THR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 3.3 26.0 - - + +
230C PRO* 5.3 0.9 - - - +
231C ASP 2.8 20.2 + - - -
232C ARG* 3.5 9.2 - - - -
234C GLU* 1.3 76.0 - - - +
236C GLY* 1.3 62.2 + - - +
238C PHE* 3.2 5.4 + - - +
239C LEU* 3.0 27.7 + - + +
251C CYS* 4.4 16.9 - - + -
254C ALA* 4.6 7.6 - - + +
255C GLN 5.6 0.5 + - - -
259C LEU* 3.5 24.0 - - + -
280C ILE* 3.9 17.0 - - + -
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ARG 2.9 14.5 + - - -
233C ILE 3.5 0.2 + - - -
234C GLU 3.3 0.2 - - - -
235C THR* 1.3 76.0 - - - +
237C THR* 1.3 62.0 + - - +
239C LEU* 3.3 11.2 + - - +
240C VAL* 3.0 28.9 + - - +
259C LEU* 4.6 2.4 - - - +
262C VAL* 4.5 11.4 - - - -
306C MET* 3.4 23.3 - - - -
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Residues in contact with THR 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ILE 2.7 22.4 + - - -
234C GLU 3.5 5.6 - - - -
235C THR 3.2 0.2 - - - -
236C GLY* 1.3 77.9 - - - +
238C PHE* 1.3 64.7 + - + +
240C VAL* 3.4 3.2 + - - +
241C ALA* 2.9 25.6 + - - +
306C MET* 3.8 4.7 - - - -
309C GLN* 3.1 27.0 + - + -
374C ALA* 4.3 8.5 - - + -
378C LEU* 3.6 29.7 - - + +
399C TYR* 3.3 21.8 + - + +
402C ILE* 5.1 4.9 - - + -
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Residues in contact with PHE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.2 19.3 - - + -
18C ILE* 4.6 2.5 - - + -
234C GLU* 3.2 53.8 + - + -
235C THR 3.2 4.9 + - - +
237C THR* 1.3 79.5 - - + +
239C LEU* 1.3 66.6 + - - +
241C ALA* 3.2 7.6 + - + +
242C ALA* 3.2 16.5 + - - +
249C ILE* 3.9 23.9 - - + +
251C CYS* 4.5 2.7 - - - -
378C LEU* 6.1 0.9 - - + -
399C TYR* 5.6 1.1 - + - -
402C ILE* 4.3 20.2 - - + -
405C LYS* 3.7 35.0 - - + -
406C LEU* 3.9 26.7 - - + -
409C LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C THR* 3.0 37.4 + - + +
236C GLY* 3.8 8.3 - - - +
238C PHE* 1.3 74.9 - - - +
240C VAL* 1.3 63.1 + - - +
242C ALA* 3.1 5.7 + - - +
243C ALA* 3.0 22.4 + - - +
249C ILE* 4.2 7.0 - - + -
251C CYS* 4.0 17.0 - - - -
259C LEU* 4.6 2.0 - - + -
262C VAL* 5.2 0.9 - - + -
263C LEU* 3.8 28.3 - - + -
266C LEU* 3.7 16.8 - - + -
273C ILE* 5.9 0.2 - - + -
280C ILE* 4.0 22.9 - - + +
282C LEU* 3.8 32.8 - - + +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLY 3.0 20.6 + - - +
237C THR 3.6 4.9 - - - +
239C LEU* 1.3 75.8 - - - +
241C ALA* 1.3 63.7 + - - +
243C ALA* 3.2 6.0 + - - -
244C ILE* 3.0 39.5 + - + +
266C LEU* 4.3 8.3 - - + -
306C MET* 3.8 7.2 - - + -
309C GLN* 3.8 24.0 - - + +
310C PHE* 3.7 35.9 - - + -
312C LEU* 5.5 0.7 - - + -
313C LEU* 4.6 5.6 - - + -
378C LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.6 27.1 - - + +
237C THR 2.9 14.5 + - - +
238C PHE* 3.2 16.8 + - + +
240C VAL* 1.3 75.5 - - - +
242C ALA* 1.3 59.8 + - - +
244C ILE* 3.4 15.4 - - - +
245C SER* 2.9 18.7 + - - -
378C LEU* 4.0 22.0 - - + -
406C LEU* 4.7 7.0 - - + -
409C LEU* 5.5 2.5 - - + -
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.2 13.7 - - - +
238C PHE 3.2 4.7 + - - +
239C LEU 3.1 8.6 + - - +
240C VAL 3.1 0.4 - - - -
241C ALA* 1.3 76.3 - - - +
243C ALA* 1.3 67.2 + - - +
245C SER* 3.1 10.8 + - - -
247C GLY 3.1 22.9 + - - -
248C LYS 4.3 7.0 - - - +
249C ILE* 3.6 34.8 - - + -
282C LEU* 4.0 10.1 - - + -
284C MET* 4.0 2.2 - - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LEU 3.0 15.4 + - - +
240C VAL 3.2 4.9 + - - +
242C ALA* 1.3 78.4 - - - +
244C ILE* 1.3 58.6 + - - +
245C SER 3.7 0.2 + - - -
246C ARG* 3.8 2.6 + - - -
266C LEU* 4.2 13.0 - - + -
269C ALA* 6.1 1.1 - - + -
271C ALA* 5.2 1.1 - - + -
282C LEU* 4.1 6.0 - - + +
284C MET* 3.5 42.7 - - + +
289C PRO* 3.7 12.4 - - - +
313C LEU* 4.1 20.6 - - + -
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 5.9 0.9 - - + -
240C VAL* 3.0 24.3 + - + +
241C ALA* 3.4 12.3 - - - +
243C ALA* 1.3 76.4 - - - +
245C SER* 1.3 62.3 + - - +
246C ARG* 3.4 7.2 + - - +
289C PRO* 4.6 9.0 - - - +
312C LEU* 3.8 23.1 - - + -
313C LEU* 3.8 39.0 - - + +
316C VAL* 4.2 11.7 - - + +
378C LEU* 4.1 20.4 - - + +
382C ILE* 3.6 40.2 - - + +
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR 3.6 7.2 - - - -
11C LYS* 3.3 15.8 - - - +
12C LEU* 2.8 37.1 + - - +
241C ALA 2.9 18.7 + - - -
242C ALA 3.1 4.2 + - - -
244C ILE* 1.3 78.4 - - - +
246C ARG* 1.3 74.4 + - - +
247C GLY 3.3 0.7 + - - -
382C ILE* 3.6 21.8 - - - -
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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
------------------------------------------------------------
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