Contacts of the helix formed by residues 207 - 220 (chain B) in PDB entry 1JXQ
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B ASP 4.3 0.2 + - - -
206B LEU* 1.3 74.4 - - - +
208B ALA* 1.3 58.8 + - - +
209B LYS* 3.2 24.0 - - + +
210B LYS* 2.9 22.5 + - + +
211B MET* 2.5 38.6 + - - +
246B THR* 3.6 10.5 + - - -
247B ASP* 3.2 30.7 + - + +
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Residues in contact with ALA 208 (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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207B THR* 1.3 69.3 - - - +
209B LYS* 1.3 63.1 + - - +
211B MET* 3.3 5.2 + - - +
212B VAL* 3.0 31.1 + - - +
245B GLY* 3.9 2.4 - - - -
247B ASP* 2.8 12.4 + - - +
254B CYS* 3.6 39.7 - - + +
255B PRO 4.0 3.1 - - - +
256B VAL* 3.7 20.9 - - + -
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Residues in contact with LYS 209 (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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207B THR* 3.1 12.3 - - + +
208B ALA* 1.3 81.4 - - - +
210B LYS* 1.3 70.5 + - - +
212B VAL* 3.3 4.9 + - - +
213B LEU* 2.9 44.1 + - + +
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Residues in contact with LYS 210 (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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205B ASP 5.6 1.3 - - - +
206B LEU* 4.0 18.6 - - + +
207B THR* 2.9 30.1 + - + +
209B LYS* 1.3 84.0 - - + +
211B MET* 1.3 65.2 + - - +
213B LEU* 3.2 9.3 + - + +
214B ALA* 3.0 24.1 + - - +
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Residues in contact with MET 211 (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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168B ILE* 4.0 15.3 - - + +
170B ASN* 3.9 6.1 - - - +
206B LEU* 3.5 27.1 - - + +
207B THR 2.5 24.3 + - - +
208B ALA* 3.6 3.6 - - - +
210B LYS* 1.3 71.3 - - - +
212B VAL* 1.3 64.0 + - - +
214B ALA* 3.2 4.2 + - - +
215B LEU* 2.9 32.8 + - + +
234B ILE* 3.8 41.1 - - + -
243B VAL* 4.0 13.9 - - + -
244B TYR 4.7 1.1 - - - +
245B GLY* 3.6 30.1 - - - -
256B VAL* 4.0 19.7 - - + -
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Residues in contact with VAL 212 (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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208B ALA 3.0 17.8 + - - +
209B LYS* 3.6 7.2 - - - +
211B MET* 1.3 77.3 - - - +
213B LEU* 1.3 62.1 + - + +
215B LEU* 3.2 10.6 + - - +
216B LEU* 2.9 40.4 + - + +
256B VAL* 4.1 15.5 - - + -
260B LYS* 3.6 39.5 - - + -
264B ILE* 4.2 11.2 - - + -
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Residues in contact with LEU 213 (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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209B LYS* 2.9 49.4 + - + +
210B LYS* 3.6 11.2 - - + +
211B MET 3.2 0.2 - - - -
212B VAL* 1.3 82.1 - - + +
214B ALA* 1.3 52.7 + - - +
216B LEU* 3.3 9.9 + - + +
217B GLU* 2.7 35.6 + - - +
220B ARG* 4.7 21.5 + - - +
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Residues in contact with ALA 214 (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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166B LEU* 4.2 14.0 - - + +
168B ILE* 4.6 0.4 - - + -
203B LYS* 4.1 26.1 + - + +
206B LEU* 4.1 16.4 - - + -
210B LYS 3.0 12.7 + - - +
211B MET 3.5 8.5 - - - +
213B LEU* 1.3 75.9 - - - +
215B LEU* 1.3 58.2 + - - +
217B GLU* 3.3 11.4 + - - +
218B LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 215 (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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166B LEU* 4.2 11.9 - - + -
168B ILE* 5.3 5.8 - - + -
211B MET* 2.9 22.1 + - + +
212B VAL* 3.5 11.9 - - - +
213B LEU 3.2 0.2 - - - -
214B ALA* 1.3 73.4 - - - +
216B LEU* 1.3 60.8 + - - +
218B LEU* 2.8 22.4 + - - +
219B ALA* 3.0 10.7 + - - +
232B VAL* 3.9 31.4 - - + -
234B ILE* 5.1 5.4 - - + -
256B VAL* 5.0 4.5 - - + -
261B ILE* 3.7 35.2 - - + -
264B ILE* 3.9 21.8 - - + -
265B PHE* 3.8 22.2 - - + -
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Residues in contact with LEU 216 (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 VAL* 2.9 31.7 + - + +
213B LEU* 3.6 13.9 - - + +
215B LEU* 1.3 74.9 - - - +
217B GLU* 1.3 63.1 + - - +
219B ALA* 3.1 4.8 + - + +
220B ARG* 2.9 58.2 + - + +
264B ILE* 3.5 31.2 - - + +
269B SER* 6.3 1.8 - - - -
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Residues in contact with GLU 217 (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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201B GLU* 6.0 1.3 - - - +
203B LYS* 5.1 8.7 - - - +
213B LEU 2.7 17.7 + - - +
214B ALA* 3.3 12.3 - - - +
216B LEU* 1.3 77.1 - - - +
218B LEU* 1.3 62.4 + - - +
220B ARG* 3.6 26.0 + - - +
221B GLN* 3.2 26.8 + - - +
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Residues in contact with LEU 218 (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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164B HIS* 3.9 29.4 - - + -
165B CYS 5.6 0.4 - - - +
166B LEU* 4.1 23.8 - - + +
214B ALA 3.0 11.3 + - - +
215B LEU* 2.8 11.3 + - - +
217B GLU* 1.3 78.4 - - - +
219B ALA* 1.3 59.1 + - - +
221B GLN* 3.0 19.7 - - + +
224B HIS* 3.0 25.4 + - + -
230B CYS* 3.7 15.0 - - - -
231B VAL 4.4 2.2 - - - +
232B VAL* 4.0 12.8 - - + -
265B PHE* 3.5 27.1 - - + -
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Residues in contact with ALA 219 (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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215B LEU 3.0 9.7 + - - +
216B LEU* 3.1 7.8 + - + +
218B LEU* 1.3 73.1 - - - +
220B ARG* 1.3 58.6 + - + +
221B GLN 2.9 17.0 + - - +
224B HIS* 4.2 5.2 - - - -
264B ILE* 3.4 31.0 - - + +
265B PHE* 4.1 9.4 - - + -
269B SER 4.5 8.1 - - - +
270B CYS* 3.7 28.1 - - + +
272B SER* 5.2 0.5 - - - -
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Residues in contact with ARG 220 (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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213B LEU* 4.7 14.5 + - - +
216B LEU* 2.9 54.5 + - + +
217B GLU* 3.8 23.7 + - - +
218B LEU 3.2 0.4 - - - -
219B ALA* 1.3 72.8 - - + +
221B GLN* 1.3 66.7 + - - +
269B SER 5.9 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