Contacts of the helix formed by residues 214 - 232 (chain C) in PDB entry 1JLH
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 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C ILE* 3.3 35.2 - - + -
209C SER* 2.8 22.6 + - - -
210C LYS 5.2 0.3 + - - -
211C THR* 4.0 6.3 + - - -
212C PHE 3.7 1.2 - - - -
213C THR* 1.3 74.5 + - - +
215C GLN* 1.3 58.9 + - - +
216C GLU* 3.8 6.3 - - - +
217C THR* 3.6 19.3 - - - +
218C ILE* 2.8 35.0 + - - +
518C LYS* 5.6 8.3 - - - +
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Residues in contact with GLN 215 (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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213C THR 3.1 7.6 + - - +
214C THR* 1.3 70.0 - - - +
216C GLU* 1.3 70.3 + - - +
218C ILE* 3.9 2.8 - - - +
219C THR* 2.6 46.3 + - - +
518C LYS* 5.5 17.5 - - - +
521C ALA* 6.0 1.8 - - - +
522C LYS* 3.5 16.7 + - - +
525C GLU* 3.0 20.7 + - - +
423D ILE* 3.0 44.7 - - + +
427D ASN* 4.9 3.6 - - - +
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Residues in contact with GLU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ILE* 3.6 18.8 - - + +
184C SER 4.6 3.1 - - - +
186C ILE* 3.7 37.1 - - + +
214C THR* 3.8 8.8 - - - +
215C GLN* 1.3 94.6 + - - +
217C THR* 1.3 62.9 + - - +
219C THR* 3.6 1.7 - - - -
220C ASN* 3.0 31.2 + - - -
518C LYS* 5.6 5.9 - - - +
384D THR* 4.7 4.2 - - - +
388D HIS* 3.0 36.7 + - - +
423D ILE* 5.5 2.5 - - + -
427D ASN* 4.7 11.9 + - - +
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Residues in contact with THR 217 (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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154C ILE* 3.4 36.7 - - + +
155C GLY* 3.5 1.6 - - - -
156C ILE* 3.5 25.4 + - - +
207C ILE* 4.0 17.0 - - + -
208C ALA 3.6 15.6 + - - +
209C SER* 4.1 4.7 - - - -
214C THR* 3.3 26.6 + - - +
216C GLU* 1.3 77.1 - - - +
218C ILE* 1.3 57.7 + - + +
220C ASN* 3.4 1.8 + - - +
221C ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 218 (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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207C ILE* 4.4 13.9 - - + -
209C SER* 4.7 3.6 - - - +
212C PHE* 3.3 50.7 - - + +
213C THR* 3.8 5.2 - - - -
214C THR 2.8 32.2 + - - +
215C GLN* 4.1 2.7 - - - +
217C THR* 1.3 72.5 - - - +
219C THR* 1.3 60.2 + - - +
221C ALA* 3.3 5.2 - - + +
222C GLU* 2.8 59.0 + - + +
255C PHE* 5.3 4.9 - - + -
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Residues in contact with THR 219 (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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186C ILE* 3.7 15.5 - - + +
215C GLN* 2.6 35.1 + - - +
216C GLU 3.6 4.7 - - - -
218C ILE* 1.3 76.8 - - - +
220C ASN* 1.3 61.6 + - - +
222C GLU* 3.4 7.4 + - - -
223C THR* 3.0 26.7 + - - -
416D ARG* 3.6 4.6 + - - +
419D LEU* 4.2 23.9 - - + +
420D HIS* 3.4 28.7 - - + +
423D ILE* 5.4 3.4 - - + +
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Residues in contact with ASN 220 (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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154C ILE* 3.5 26.3 - - + +
156C ILE* 5.7 0.2 - - - +
183C VAL* 4.0 15.6 - - + +
184C SER* 4.1 7.1 + - - +
185C ASN 3.3 28.0 + - - +
186C ILE* 4.2 2.4 - - - +
191C ILE* 3.7 18.5 - - + +
216C GLU 3.0 26.1 + - - +
217C THR* 4.7 0.4 - - - +
219C THR* 1.3 76.4 - - - +
221C ALA* 1.3 57.3 + - - +
223C THR* 3.4 3.8 + - - -
224C ALA* 2.9 29.1 + - - +
420D HIS* 3.3 25.7 + - - -
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Residues in contact with ALA 221 (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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154C ILE* 4.3 10.3 - - + +
207C ILE* 3.6 30.7 - - + -
217C THR 2.9 15.9 + - - +
218C ILE* 3.3 13.0 - - + +
220C ASN* 1.3 76.7 - - - +
222C GLU* 1.3 58.1 + - - +
224C ALA* 3.0 5.3 + - - +
225C LYS 2.8 24.9 + - - -
242C PHE* 4.1 0.7 - - - -
255C PHE* 3.6 22.3 - - + -
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Residues in contact with GLU 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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218C ILE* 2.8 42.5 + - + +
219C THR* 4.7 4.0 - - - -
221C ALA* 1.3 71.7 - - - +
223C THR* 1.3 59.0 + - - +
225C LYS* 3.2 13.8 + - - +
226C GLU* 2.9 30.1 + - - +
255C PHE* 4.2 14.5 - - + -
416D ARG* 3.4 20.9 + - - +
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Residues in contact with THR 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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191C ILE* 4.0 19.1 - - + -
195C LEU* 4.6 5.6 - - + -
219C THR 3.0 13.0 + - - -
220C ASN* 3.6 5.4 - - - -
221C ALA 3.2 0.2 - - - -
222C GLU* 1.3 77.2 - - - +
224C ALA* 1.3 61.8 + - - +
226C GLU* 3.5 4.4 + - - +
227C TRP* 3.1 22.4 + - + +
415D ILE* 4.1 20.4 - - + -
416D ARG* 2.9 25.6 + - + +
420D HIS* 2.9 28.6 - - - -
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 4.0 7.2 - - + -
191C ILE* 4.4 4.7 - - + +
195C LEU* 4.4 11.4 - - - -
205C PHE* 3.7 34.1 - - + -
220C ASN 2.9 15.0 + - - +
221C ALA 3.0 9.4 + - - +
223C THR* 1.3 75.2 - - - +
225C LYS* 1.3 60.5 + - - +
227C TRP* 3.4 7.8 + - - +
228C PHE* 3.0 27.4 + - - +
242C PHE* 3.8 6.6 - - + -
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Residues in contact with LYS 225 (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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221C ALA 2.8 12.3 + - - +
222C GLU* 3.6 14.0 + - - +
224C ALA* 1.3 74.3 - - - +
226C GLU* 1.3 55.1 + - - +
228C PHE* 2.9 2.4 + - - +
229C LEU* 2.6 57.0 + - + +
238C VAL* 4.1 17.9 - - + -
242C PHE* 3.5 16.4 - - + -
254C GLU 4.5 2.6 + - - -
255C PHE* 2.8 63.8 + - + +
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Residues in contact with GLU 226 (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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222C GLU 2.9 15.7 + - - +
223C THR* 3.8 3.8 - - - +
225C LYS* 1.3 77.0 - - - +
227C TRP* 1.3 63.4 + - - +
229C LEU* 3.3 8.5 + - - +
230C GLN* 3.1 24.5 + - + +
416D ARG* 3.4 31.6 + - - -
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Residues in contact with TRP 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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195C LEU* 3.5 48.2 + - + +
196C ALA* 5.8 0.2 - - - +
198C LEU* 3.5 32.8 - - + -
199C ASN 4.1 0.2 - - - -
200C PRO* 3.3 45.9 - - + +
203C SER* 4.5 1.3 - - - -
205C PHE* 3.4 29.8 - + - -
223C THR* 3.1 16.5 + - + +
224C ALA 3.5 9.4 - - - +
226C GLU* 1.3 78.3 - - - +
228C PHE* 1.3 78.0 + - + +
230C GLN* 3.3 17.4 - - + +
231C ALA* 3.9 6.2 + - - +
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Residues in contact with PHE 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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143C TYR* 3.9 17.0 - + - -
200C PRO* 3.4 35.7 - - + -
205C PHE* 5.4 2.2 - + - -
224C ALA 3.0 13.8 + - - +
225C LYS* 2.9 9.1 + - - +
227C TRP* 1.3 84.3 - + + +
229C LEU* 1.3 62.2 + - + +
230C GLN 2.9 9.3 + - - -
231C ALA* 3.1 5.5 + - - +
232C ALA* 3.0 29.7 + - + +
237C ALA* 3.5 27.6 - - + -
238C VAL* 3.8 18.4 - - + -
241C HIS* 3.2 37.7 - + + -
242C PHE* 3.7 21.1 - + + -
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Residues in contact with LEU 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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225C LYS* 2.6 45.6 + - + +
226C GLU* 4.0 6.7 - - - +
228C PHE* 1.3 75.3 - - + +
230C GLN* 1.3 60.2 + - - +
232C ALA 3.2 29.1 - - - +
233C LYS* 3.4 19.0 + - + +
234C ASP 3.8 16.6 - - - +
235C PRO* 4.1 8.5 - - + -
238C VAL* 3.6 25.6 - - + -
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Residues in contact with GLN 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 GLU* 3.1 13.3 + - + +
227C TRP* 3.3 16.3 - - + +
228C PHE 2.9 0.8 - - - -
229C LEU* 1.3 80.5 - - - +
231C ALA* 1.3 69.0 + - - +
233C LYS* 4.1 23.5 - - - +
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Residues in contact with ALA 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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143C TYR* 3.1 24.6 + - - +
200C PRO* 3.9 26.2 - - + -
227C TRP 3.9 2.0 + - - +
228C PHE 3.1 4.0 + - - +
230C GLN* 1.3 88.1 - - - +
232C ALA* 1.3 59.0 + - - +
233C LYS* 3.9 1.5 + - - -
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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
----------------------------------------------------------
143C TYR* 3.4 45.3 - - + -
228C PHE* 3.0 22.9 + - + +
229C LEU* 3.2 21.1 - - - +
231C ALA* 1.3 77.0 - - - +
233C LYS* 1.3 52.3 + - - +
234C ASP* 2.6 21.1 + - + +
237C ALA* 4.7 4.9 - - + -
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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