Contacts of the helix formed by residues 215 - 234 (chain C) in PDB entry 1JIQ
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 THR 215 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 3.4 35.2 - - + -
210C SER* 2.9 22.6 + - - -
211C LYS 5.2 0.2 + - - -
212C THR* 3.7 8.0 + - - -
213C PHE 3.7 1.2 - - - -
214C THR* 1.3 74.1 + - - +
216C GLN* 1.3 68.5 + - - +
217C GLU 3.4 1.3 + - - +
218C THR* 3.8 18.8 - - - +
219C ILE* 2.9 26.2 + - - +
519C LYS* 5.0 7.6 - - - +
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Residues in contact with GLN 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C THR 3.0 8.8 + - - +
215C THR* 1.3 73.1 - - - +
217C GLU* 1.3 63.8 + - + +
219C ILE* 3.9 2.3 - - - +
220C THR* 2.8 43.1 + - - +
519C LYS* 5.9 1.2 - - - +
523C LYS* 2.9 27.0 - - - +
526C GLU* 2.9 31.6 + - - +
424D ILE* 3.9 26.8 - - + +
428D ASN* 4.7 4.0 + - - -
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Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ILE* 3.9 15.7 - - + -
185C SER 4.1 4.3 - - - +
187C ILE* 3.4 38.6 + - + +
215C THR* 3.4 1.8 - - - +
216C GLN* 1.3 85.2 - - + +
218C THR* 1.3 64.8 + - - +
220C THR* 3.3 2.1 + - - -
221C ASN* 3.0 29.3 + - - +
385D THR* 2.4 35.7 + - - +
388D GLN* 4.4 2.4 - - - +
389D HIS* 2.6 34.5 + - + -
424D ILE* 4.8 2.5 - - + -
428D ASN* 4.4 7.7 + - - +
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Residues in contact with THR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE* 3.6 31.5 - - + +
156C GLY* 3.5 2.2 - - - -
157C ILE* 3.4 29.4 + - - +
208C ILE* 4.1 16.4 - - + -
209C ALA 3.6 15.9 + - - +
210C SER* 4.2 6.5 - - - -
215C THR* 3.4 21.4 + - - +
216C GLN 3.4 0.6 - - - -
217C GLU* 1.3 75.4 - - - +
219C ILE* 1.3 59.7 + - + +
221C ASN* 3.3 5.3 + - - +
222C ALA* 2.8 26.9 + - - +
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Residues in contact with ILE 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 4.1 16.8 - - + -
210C SER* 4.7 0.9 - - - -
213C PHE* 3.6 58.3 - - + +
214C THR* 4.0 3.1 - - - +
215C THR* 2.9 25.3 + - - +
216C GLN* 4.1 2.2 - - - +
218C THR* 1.3 76.8 - - + +
220C THR* 1.3 60.0 + - - +
222C ALA* 3.5 3.3 - - + +
223C GLU* 2.9 50.1 + - + +
256C PHE* 5.2 6.7 - - + -
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Residues in contact with THR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ILE* 3.7 20.2 - - + -
216C GLN* 2.8 29.0 + - - +
217C GLU 3.6 3.8 - - - -
219C ILE* 1.3 76.1 - - - +
221C ASN* 1.3 62.3 + - - +
223C GLU* 3.2 10.6 + - - +
224C THR* 3.0 26.1 + - - -
417D ARG* 3.4 5.6 + - - +
420D LEU* 4.0 25.8 - - + +
421D HIS* 3.8 15.9 - - + +
424D ILE* 3.9 15.7 - - + +
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Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE* 3.5 26.2 - - + +
184C VAL* 3.7 19.7 - - + +
185C SER* 3.9 8.9 + - - +
186C ASN 3.0 29.4 + - - +
187C ILE* 4.2 2.3 - - - +
192C ILE* 3.7 16.1 - - + +
217C GLU 3.0 19.9 + - - +
218C THR* 5.0 0.6 - - - +
220C THR* 1.3 75.0 - - - +
222C ALA* 1.3 57.9 + - - +
224C THR* 3.2 3.5 + - - -
225C ALA* 2.9 27.7 + - - +
421D HIS* 3.1 25.9 + - - -
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Residues in contact with ALA 222 (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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155C ILE* 3.9 11.1 - - + +
208C ILE* 3.7 34.5 - - + -
218C THR 2.8 20.4 + - - +
219C ILE* 3.5 7.6 - - + +
220C THR 3.3 0.2 - - - -
221C ASN* 1.3 73.5 - - - +
223C GLU* 1.3 57.5 + - - +
225C ALA* 3.3 3.8 + - - +
226C LYS 2.9 23.7 + - - -
243C PHE* 4.1 1.0 - - - -
256C PHE* 3.6 23.4 - - + -
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Residues in contact with GLU 223 (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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219C ILE* 2.9 36.3 + - + +
220C THR* 3.2 10.1 + - - +
222C ALA* 1.3 71.5 - - - +
224C THR* 1.3 61.8 + - - +
226C LYS* 3.8 10.8 - - - +
227C GLU* 2.9 29.5 + - - +
256C PHE* 4.2 18.4 - - + -
417D ARG* 3.7 27.0 + - - +
420D LEU* 5.5 0.9 - - - +
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Residues in contact with THR 224 (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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192C ILE* 4.0 21.5 - - + -
196C LEU* 4.4 6.5 - - + -
220C THR 3.0 6.1 + - - -
221C ASN* 3.2 8.7 + - - -
223C GLU* 1.3 74.5 - - - +
225C ALA* 1.3 66.6 + - - +
227C GLU* 3.3 7.7 + - - +
228C TRP* 3.1 22.6 + - + +
416D ILE* 4.0 11.0 - - + -
417D ARG* 2.8 31.9 + - + +
421D HIS* 2.7 31.2 + - - +
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Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE* 4.0 8.1 - - + -
192C ILE* 4.5 5.1 - - + +
196C LEU* 4.2 12.1 - - + +
206C PHE* 3.7 34.8 - - + -
221C ASN 2.9 14.2 + - - +
222C ALA 3.3 8.5 + - - +
224C THR* 1.3 77.6 - - - +
226C LYS* 1.3 55.9 + - - +
228C TRP* 3.3 6.6 + - - +
229C PHE* 2.9 28.4 + - - +
243C PHE* 3.8 6.9 - - + -
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Residues in contact with LYS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ALA 2.9 15.9 + - - +
223C GLU* 3.8 11.0 - - - +
224C THR 3.3 0.4 - - - -
225C ALA* 1.3 73.1 - - - +
227C GLU* 1.3 60.6 + - - +
229C PHE* 3.6 2.0 - - - +
230C LEU* 2.8 47.8 + - + +
239C VAL* 3.9 22.2 - - + -
243C PHE* 3.6 15.1 - - + -
255C GLU 4.8 2.0 + - - -
256C PHE* 2.7 60.2 + - + +
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Residues in contact with GLU 227 (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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223C GLU 2.9 18.0 + - - +
224C THR* 3.6 8.1 - - - +
225C ALA 3.3 0.2 - - - -
226C LYS* 1.3 76.2 - - - +
228C TRP* 1.3 58.5 + - - +
230C LEU* 3.3 5.5 + - - +
231C GLN* 2.9 52.5 + - + +
417D ARG* 3.5 33.7 + - - +
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Residues in contact with TRP 228 (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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196C LEU* 3.6 51.4 + - + +
199C LEU* 3.6 33.0 - - + -
200C ASN 3.8 4.7 - - - -
201C PRO* 3.4 45.4 - - + +
204C SER* 4.4 2.0 - - - -
206C PHE* 3.7 24.9 - + - -
224C THR* 3.1 12.9 + - + +
225C ALA 3.5 12.1 - - - +
227C GLU* 1.3 77.5 + - - +
229C PHE* 1.3 78.7 + - + +
231C GLN* 3.4 28.7 + - - +
232C ALA* 3.7 6.1 + - - +
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Residues in contact with PHE 229 (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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144C TYR* 3.7 14.6 - + - -
201C PRO* 3.5 27.6 - - + -
206C PHE* 5.2 2.5 - + + -
225C ALA 2.9 18.0 + - - +
226C LYS 3.6 3.4 - - - +
227C GLU 3.3 0.2 - - - -
228C TRP* 1.3 89.1 - + + +
230C LEU* 1.3 67.8 + - + +
232C ALA* 3.0 9.5 + - - +
233C ALA* 2.9 44.4 + - + -
238C ALA* 3.6 24.2 - - + -
239C VAL* 3.9 8.1 - - + -
242C HIS* 3.2 44.0 - + + -
243C PHE* 4.0 21.3 - + + -
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Residues in contact with LEU 230 (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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226C LYS* 2.8 41.5 + - + +
227C GLU* 4.0 4.9 - - - +
229C PHE* 1.3 76.8 - - + +
231C GLN* 1.3 61.0 + - - +
232C ALA 3.0 2.2 - - - -
233C ALA* 4.1 0.4 - - + +
234C LYS* 2.8 41.0 + - - +
235C ASP 3.4 35.0 - - - +
236C PRO* 4.0 9.2 - - + -
239C VAL* 3.9 20.4 - - + -
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Residues in contact with GLN 231 (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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227C GLU* 2.9 39.0 + - + +
228C TRP* 3.5 23.0 + - - +
229C PHE 3.2 0.2 - - - -
230C LEU* 1.3 76.8 - - - +
232C ALA* 1.3 56.8 + - - +
234C LYS* 2.8 29.1 + - - +
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Residues in contact with ALA 232 (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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144C TYR* 3.4 7.6 + - - -
201C PRO* 3.8 26.2 - - + -
202C GLU* 3.8 14.4 - - - +
228C TRP 3.7 2.8 + - - +
229C PHE 3.0 8.3 + - - +
231C GLN* 1.3 81.6 - - - +
233C ALA* 1.3 62.9 + - - +
234C LYS* 3.6 10.2 + - - +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TYR* 3.6 36.4 - - + -
229C PHE* 2.9 41.7 + - + +
230C LEU* 4.4 2.2 - - + -
232C ALA* 1.3 75.6 - - - +
234C LYS* 1.3 62.1 + - - +
235C ASP* 2.7 21.5 + - - +
238C ALA* 4.2 7.2 - - + -
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LEU* 2.8 32.5 + - - +
231C GLN* 2.8 27.3 + - - +
232C ALA* 4.0 8.3 - - - +
233C ALA* 1.3 74.0 - - - +
235C ASP* 1.3 56.8 + - + +
236C PRO* 3.3 13.5 - - - +
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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
------------------------------------------------------------
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