Contacts of the helix formed by residues 214 - 232 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D ILE* 3.4 34.3 - - + -
209D SER* 2.7 27.2 + - - -
210D LYS 5.2 0.2 + - - -
211D THR* 3.7 7.0 + - - -
212D PHE 3.7 1.0 - - - -
213D THR* 1.3 75.3 + - - +
215D GLN* 1.3 63.4 + - - +
216D GLU* 3.8 6.1 - - - +
217D THR* 3.3 17.0 + - - +
218D ILE* 2.8 31.5 + - - +
518D LYS* 4.7 8.7 - - - +
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Residues in contact with GLN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ILE* 3.6 30.3 - - + +
427C ASN* 4.7 4.2 - - - +
213D THR 3.0 8.7 + - - +
214D THR* 1.3 70.9 - - - +
216D GLU* 1.3 70.4 + - - +
218D ILE* 3.7 2.1 - - - +
219D THR* 2.7 47.2 + - - +
518D LYS* 4.0 24.4 - - - +
521D ALA* 6.0 1.4 - - - +
522D LYS* 3.6 14.1 + - - +
525D GLU* 2.9 36.6 + - - +
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Residues in contact with GLU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C THR* 4.6 5.4 - - - +
387C GLN* 4.6 0.3 - - - +
388C HIS* 3.1 34.5 + - - +
423C ILE* 5.5 1.1 - - + -
427C ASN* 4.5 14.4 + - - +
156D ILE* 3.7 29.1 - - + +
184D SER 4.5 3.8 - - - +
186D ILE* 3.7 35.7 - - + +
214D THR* 3.8 5.7 - - - +
215D GLN* 1.3 90.2 + - - +
217D THR* 1.3 64.9 + - - +
219D THR* 3.3 2.4 + - - -
220D ASN* 3.0 30.0 + - - -
518D LYS* 4.7 8.1 + - - +
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ILE* 3.7 24.9 - - + +
155D GLY* 3.3 18.5 - - - -
156D ILE* 3.5 18.3 + - - +
207D ILE* 4.1 17.3 - - + -
208D ALA 3.7 20.8 + - - +
209D SER* 4.1 7.0 - - - -
214D THR* 3.3 16.9 + - - +
216D GLU* 1.3 78.7 - - - +
218D ILE* 1.3 58.7 + - - +
220D ASN* 3.3 4.8 + - - +
221D ALA* 2.9 26.5 + - - +
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Residues in contact with ILE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ILE* 4.3 14.8 - - + -
209D SER* 4.9 0.4 - - - -
212D PHE* 3.4 59.0 - - + +
213D THR* 3.8 7.2 - - - +
214D THR* 2.8 25.5 + - - +
215D GLN* 4.1 2.2 - - - +
217D THR* 1.3 73.0 - - + +
219D THR* 1.3 60.7 + - - +
221D ALA* 3.5 4.9 - - + +
222D GLU* 2.9 49.9 + - + +
255D PHE* 5.1 5.4 - - + -
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ARG* 3.4 4.2 + - - +
419C LEU* 4.2 22.0 - - + +
420C HIS* 3.7 25.8 - - + +
423C ILE* 4.0 15.6 - - + +
186D ILE* 3.7 14.4 - - + -
215D GLN* 2.7 34.3 + - - +
216D GLU 3.7 3.8 - - - -
218D ILE* 1.3 72.1 - - - +
220D ASN* 1.3 63.1 + - - +
222D GLU* 3.3 10.0 + - - +
223D THR* 3.1 22.3 + - - -
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Residues in contact with ASN 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C HIS* 3.3 25.3 + - - -
154D ILE* 3.6 26.0 - - + +
183D VAL* 3.9 18.6 - - + +
184D SER 3.9 11.7 + - - -
185D ASN 3.2 26.1 + - - +
186D ILE* 4.3 1.6 - - - +
191D ILE* 3.7 18.2 - - + +
216D GLU 3.0 20.3 + - - +
217D THR* 4.9 0.2 - - - +
219D THR* 1.3 76.5 - - - +
221D ALA* 1.3 62.5 + - - +
223D THR* 3.3 4.6 + - - -
224D ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ILE* 4.1 10.9 - - - +
207D ILE* 3.7 32.8 - - + -
217D THR 2.9 17.9 + - - +
218D ILE* 3.5 8.3 - - + +
219D THR 3.2 0.2 - - - -
220D ASN* 1.3 77.4 - - - +
222D GLU* 1.3 56.6 + - - +
224D ALA* 3.2 4.7 + - - +
225D LYS* 3.0 23.2 + - - +
242D PHE* 4.1 1.2 - - - -
255D PHE* 3.6 24.2 - - + -
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Residues in contact with GLU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ARG* 3.0 25.1 + - - +
419C LEU* 5.7 1.4 - - - +
218D ILE* 2.9 38.6 + - + +
219D THR* 3.3 6.4 + - - -
221D ALA* 1.3 71.9 - - - +
223D THR* 1.3 60.4 + - - +
225D LYS* 3.8 9.8 - - - +
226D GLU* 3.0 28.4 + - - +
255D PHE* 4.1 16.6 - - + -
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Residues in contact with THR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ILE* 4.2 12.1 - - + -
416C ARG* 2.7 31.6 + - + +
420C HIS* 2.8 24.1 - - - -
191D ILE* 4.1 26.2 - - + -
195D LEU* 4.4 6.5 - - + -
219D THR 3.1 6.2 + - - -
220D ASN* 3.6 8.5 - - - -
221D ALA 3.2 0.2 - - - -
222D GLU* 1.3 75.8 - - - +
224D ALA* 1.3 59.5 + - - +
226D GLU* 3.3 6.9 + - - +
227D TRP* 3.0 27.4 + - + +
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ILE* 4.2 6.5 - - + -
191D ILE* 4.5 5.1 - - + +
195D LEU* 4.3 11.9 - - + -
205D PHE* 3.8 33.4 - - + -
220D ASN 3.0 13.2 + - - +
221D ALA 3.2 8.9 + - - +
223D THR* 1.3 78.9 - - - +
225D LYS* 1.3 56.8 + - - +
227D TRP* 3.5 6.5 + - - +
228D PHE* 2.8 28.6 + - - +
242D PHE* 3.8 7.6 - - + -
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Residues in contact with LYS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ALA 3.0 15.0 + - - +
222D GLU* 3.8 10.1 - - - +
223D THR 3.3 0.2 - - - -
224D ALA* 1.3 74.7 - - - +
226D GLU* 1.3 60.5 + - - +
228D PHE* 3.7 1.2 - - - +
229D LEU* 2.8 47.6 + - + +
238D VAL* 4.0 20.9 - - + -
242D PHE* 3.5 15.7 - - + -
254D GLU 4.7 1.8 + - - -
255D PHE* 2.8 63.5 + - + +
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ARG* 3.3 31.1 + - - +
222D GLU 3.0 18.1 + - - +
223D THR* 3.5 7.7 - - - +
225D LYS* 1.3 78.0 - - - +
227D TRP* 1.3 61.6 + - - +
229D LEU* 3.8 5.0 - - - +
230D GLN* 3.0 30.8 + - - +
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Residues in contact with TRP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 3.5 46.8 + - + +
196D ALA* 5.8 0.2 - - - +
198D LEU* 3.5 35.6 + - + -
199D ASN 3.9 0.4 - - - -
200D PRO* 3.5 47.4 - - + +
203D SER* 4.3 0.9 - - - -
205D PHE* 3.3 32.8 - + - -
223D THR* 3.0 16.9 + - + +
224D ALA 3.5 9.9 - - - +
226D GLU* 1.3 77.2 - - - +
228D PHE* 1.3 76.7 + - + +
230D GLN* 3.0 32.7 - - - +
231D ALA* 3.7 2.3 + - - +
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Residues in contact with PHE 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR* 3.9 11.0 - + - -
200D PRO* 3.5 27.8 - - + -
205D PHE* 5.1 2.2 - + + -
224D ALA 2.8 18.7 + - - +
225D LYS 3.7 2.9 - - - +
227D TRP* 1.3 84.1 - + + +
229D LEU* 1.3 78.3 + - + +
230D GLN 2.9 4.7 - - - -
231D ALA* 2.8 22.5 + - - +
232D ALA* 2.8 36.6 + - + +
237D ALA* 3.6 21.3 - - + -
238D VAL* 3.9 3.8 - - + -
241D HIS* 3.2 44.4 - + + -
242D PHE* 4.0 20.4 - + + -
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LYS* 2.8 37.8 + - + +
226D GLU* 4.0 4.9 - - - +
228D PHE* 1.3 89.3 - - + +
230D GLN* 1.3 61.9 + - - +
232D ALA 2.7 29.8 - - - +
233D LYS* 3.5 12.5 + - - +
234D ASP 4.0 8.5 - - - +
235D PRO* 4.3 16.4 - - + -
238D VAL* 3.4 30.1 - - + -
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Residues in contact with GLN 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D GLU* 3.0 20.2 + - - +
227D TRP* 3.0 29.8 - - - +
228D PHE 2.9 0.6 + - - -
229D LEU* 1.3 78.4 - - - +
231D ALA* 1.3 55.2 + - - +
233D LYS* 3.1 23.8 - - - +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR* 3.5 9.0 + - - +
200D PRO* 3.8 21.8 - - + -
201D GLU* 3.7 20.2 - - - +
227D TRP 3.7 0.8 + - - +
228D PHE 2.8 6.9 + - - +
230D GLN* 1.3 79.0 - - - +
232D ALA* 1.3 60.0 + - - +
233D LYS* 3.4 17.1 + - - +
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR* 3.4 36.3 - - + -
228D PHE* 2.8 38.6 + - + +
229D LEU* 2.7 30.4 - - - +
231D ALA* 1.3 73.0 - - - +
233D LYS* 1.3 58.9 + - - +
234D ASP 3.0 5.6 + - - +
237D ALA* 4.2 5.4 - - + -
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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