Contacts of the helix formed by residues 251 - 269 (chain B) in PDB entry 1JQO
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TYR* 3.0 13.4 + - - -
248B ILE 3.4 0.2 + - - -
249B HIS 3.4 0.2 - - - -
250B GLU* 1.3 89.8 + - - +
252B VAL* 1.3 64.4 + - + +
253B TRP 3.0 3.2 + - - -
254B LYS* 3.1 7.8 + - - +
255B GLY* 2.8 24.5 + - - -
681B PHE 4.2 13.6 + - - +
682B GLY 4.5 7.4 + - - -
683B GLU 4.0 9.5 + - - +
684B GLU* 4.2 18.9 - - + +
687B CYS* 3.6 33.0 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 4.7 1.8 - - + -
247B TYR 3.0 17.7 + - - +
248B ILE* 3.7 15.7 - - + +
251B THR* 1.3 73.5 - - - +
253B TRP* 1.3 61.7 + - - +
255B GLY* 3.7 2.0 - - - +
256B VAL* 3.1 27.4 + - + +
285B PHE* 3.2 43.7 - - + -
446B PHE* 4.0 8.5 - - + -
681B PHE* 3.4 36.8 - - + -
687B CYS* 4.5 7.9 - - - -
691B LEU* 6.0 0.2 - - + -
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Residues in contact with TRP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE 2.7 20.9 + - - +
249B HIS* 3.9 12.1 - - - -
251B THR 3.0 0.6 + - - -
252B VAL* 1.3 74.6 - - - +
254B LYS* 1.3 87.8 + - + +
257B PRO* 3.4 7.4 - - - +
315B ALA 5.2 0.2 - - - -
318B LEU* 3.4 43.3 + - + +
319B TYR* 3.5 46.0 - + - -
322B GLN* 4.0 15.1 + - + +
442B GLN* 2.9 53.0 + - + +
446B PHE* 3.4 48.9 - + + -
450B LEU* 3.8 15.3 - - + -
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B HIS 2.9 25.8 + - - +
250B GLU* 4.9 6.2 + - - +
251B THR* 3.1 7.1 + - - +
253B TRP* 1.3 100.3 - - + +
255B GLY* 1.3 65.9 + - - +
257B PRO* 3.0 15.2 - - - +
258B LYS* 3.7 26.2 + - - +
318B LEU* 5.2 6.5 - - - +
322B GLN* 6.3 0.4 - - - +
442B GLN* 4.7 1.6 - - - +
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 2.8 16.9 + - - -
252B VAL* 3.9 3.6 - - - -
253B TRP 3.4 0.2 - - - -
254B LYS* 1.3 78.1 - - - +
256B VAL* 1.3 61.4 + - - +
258B LYS* 3.1 11.9 + - - +
259B PHE* 3.0 24.1 + - - +
687B CYS* 4.6 11.0 - - - -
688B PHE* 5.6 0.7 - - - -
691B LEU* 4.6 7.1 - - - +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 3.1 29.0 + - + +
255B GLY* 1.3 75.2 - - - +
257B PRO* 1.3 73.2 - - + +
259B PHE* 3.4 6.8 + - - +
260B LEU* 3.1 40.8 + - + +
283B ILE* 4.4 11.4 - - + -
285B PHE* 4.0 13.2 - - + -
441B ARG 4.7 4.7 - - - +
445B THR* 4.2 21.3 - - + +
446B PHE* 3.4 22.7 - - + -
691B LEU* 4.8 6.0 - - + +
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Residues in contact with PRO 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TRP 3.4 9.2 - - - +
254B LYS* 3.0 22.4 - - - +
256B VAL* 1.3 90.4 - - + +
258B LYS* 1.3 63.3 + - + +
260B LEU* 3.3 8.3 + - + +
261B ARG* 3.0 28.5 + - - +
438B ASP* 3.5 36.2 - - + +
441B ARG* 4.4 5.0 + - + +
442B GLN* 3.6 31.2 - - + +
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Residues in contact with LYS 258 (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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212A GLU* 5.5 0.7 - - - +
254B LYS* 3.8 23.6 - - - +
255B GLY* 3.1 12.6 + - - +
257B PRO* 1.3 78.1 - - + +
259B PHE* 1.3 66.8 + - - +
260B LEU 2.9 1.4 + - - -
261B ARG* 2.9 20.2 + - - +
262B ARG* 3.1 12.1 + - - +
684B GLU* 4.0 19.0 + - - -
688B PHE* 4.8 8.1 - - + -
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Residues in contact with PHE 259 (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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143B ILE* 3.4 19.3 - - + -
255B GLY 3.0 11.8 + - - +
256B VAL 3.8 3.1 - - - +
258B LYS* 1.3 78.6 - - - +
260B LEU* 1.3 83.3 + - + +
262B ARG* 3.4 3.5 + - - +
263B VAL* 3.1 25.2 + - + +
282B LEU* 4.1 12.1 - - + -
283B ILE* 4.5 10.8 - - + -
688B PHE* 3.6 21.4 - + + -
691B LEU* 3.7 35.9 - - + -
692B GLN* 3.4 39.7 - - - -
695B THR* 2.9 30.7 - - + -
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Residues in contact with LEU 260 (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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256B VAL* 3.1 32.6 + - + +
257B PRO 3.5 7.9 - - - +
258B LYS 3.0 0.8 - - - -
259B PHE* 1.3 100.1 - - + +
261B ARG* 1.3 66.5 + - - +
263B VAL* 2.9 15.6 + - - +
264B ASP* 2.9 17.1 + - - +
276B LEU* 5.1 8.8 - - + +
280B VAL 5.4 5.8 - - - +
281B SER* 6.1 1.1 - - - -
282B LEU* 4.3 20.2 - - + +
283B ILE* 4.7 9.2 - - + -
441B ARG* 3.5 46.4 - - + +
445B THR* 5.1 4.0 - - - +
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Residues in contact with ARG 261 (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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212A GLU* 4.6 21.2 - - + +
215A GLU* 5.4 0.6 + - - -
219A ARG* 3.4 21.2 - - - +
257B PRO 3.0 21.0 + - - +
258B LYS* 2.9 9.2 + - - +
260B LEU* 1.3 73.0 - - - +
262B ARG* 1.3 52.7 + - - +
264B ASP* 2.7 34.5 + - + +
265B THR* 2.8 20.1 + - - -
275B ARG* 3.3 34.1 + - - +
433B ASP 2.5 30.3 + - - -
434B GLY 3.3 10.1 + - - -
437B LEU* 4.8 5.3 - - - +
438B ASP* 2.9 33.7 + - - +
441B ARG* 4.2 4.8 - - - +
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Residues in contact with ARG 262 (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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206A THR* 4.8 1.8 + - - -
208A ASP* 3.7 24.7 + - - +
209A ASP* 3.2 37.6 + - - +
212A GLU* 2.8 38.1 + - - +
143B ILE* 6.5 0.2 - - + -
144B GLU* 6.5 1.1 - - - -
258B LYS 3.1 8.2 + - - +
259B PHE* 3.4 10.1 - - + +
261B ARG* 1.3 78.2 - - - +
263B VAL* 1.3 59.7 + - + +
265B THR* 3.0 11.1 + - - -
266B ALA* 2.8 28.8 + - + +
688B PHE* 3.8 35.6 - - + -
692B GLN* 5.0 7.6 - - - +
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Residues in contact with VAL 263 (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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143B ILE* 3.8 33.2 - - + -
147B LEU* 5.6 0.2 - - + -
165B LEU* 4.0 27.8 - - + -
259B PHE* 3.1 28.1 + - + +
260B LEU* 2.9 10.8 + - - +
262B ARG* 1.3 76.6 - - + +
264B ASP* 1.3 63.1 + - - +
266B ALA* 3.3 6.6 + - + +
267B LEU* 2.9 27.0 + - + +
276B LEU* 4.2 18.4 - - + -
282B LEU* 4.1 10.8 - - + -
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Residues in contact with ASP 264 (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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260B LEU 2.9 18.5 + - - +
261B ARG* 2.7 19.5 + - - +
263B VAL* 1.3 77.6 - - - +
265B THR* 1.3 60.6 + - - +
267B LEU* 3.4 9.0 + - - +
268B LYS* 3.2 22.8 + - - +
272B ILE 5.2 0.2 - - - +
274B GLU 5.1 2.6 - - - +
275B ARG* 2.8 39.8 + - + +
276B LEU* 2.6 34.6 + - - -
441B ARG* 2.6 25.8 + - - -
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Residues in contact with THR 265 (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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208A ASP* 3.4 21.3 - - + +
211A GLN* 4.2 16.1 - - - +
212A GLU* 2.7 34.8 + - - +
215A GLU* 5.6 1.2 + - - -
144B GLU* 5.6 0.4 - - + +
261B ARG 2.8 8.5 + - - -
262B ARG* 3.2 11.2 - - - +
264B ASP* 1.3 77.1 - - - +
266B ALA* 1.3 59.3 + - - +
268B LYS* 2.9 17.0 + - - +
269B ASN* 2.8 45.9 + - - +
275B ARG* 5.9 1.0 + - - -
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Residues in contact with ALA 266 (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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143B ILE* 4.3 3.4 - - + -
144B GLU* 3.6 34.8 - - + +
147B LEU* 3.5 23.6 - - + -
262B ARG* 2.8 16.7 + - + +
263B VAL* 3.6 10.5 - - - +
265B THR* 1.3 74.6 - - - +
267B LEU* 1.3 62.2 + - - +
269B ASN* 3.0 11.0 + - - +
270B ILE* 3.0 20.6 - - - +
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Residues in contact with LEU 267 (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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147B LEU* 4.3 8.1 - - + -
162B PHE* 3.6 38.4 - - + -
165B LEU* 3.8 25.8 - - + -
263B VAL* 2.9 20.7 + - + +
264B ASP* 3.7 6.5 - - - +
265B THR 3.3 0.2 - - - -
266B ALA* 1.3 75.4 - - - +
268B LYS* 1.3 55.7 + - - +
270B ILE* 3.6 10.5 - - + +
271B GLY 3.6 2.3 + - - -
272B ILE* 2.6 60.4 + - + +
274B GLU 4.4 8.3 - - - +
276B LEU* 4.0 26.0 - - + +
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Residues in contact with LYS 268 (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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211A GLN* 4.2 20.6 - - - +
215A GLU* 2.8 29.1 + - - -
264B ASP 3.2 10.1 + - - +
265B THR* 2.9 19.4 + - - +
267B LEU* 1.3 74.3 - - - +
269B ASN* 1.3 55.7 + - - +
270B ILE 2.5 18.4 + - - -
271B GLY* 2.9 14.7 + - - +
272B ILE 3.0 12.1 + - - +
273B ASN* 4.6 16.4 - - + -
275B ARG* 5.3 7.3 - - - +
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Residues in contact with ASN 269 (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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208A ASP* 3.0 27.9 + - - -
211A GLN* 4.1 17.2 + - - +
144B GLU* 3.1 28.6 + - - +
148B LYS* 3.8 14.6 - - - +
265B THR* 2.8 25.4 + - - +
266B ALA 3.0 7.5 + - - +
268B LYS* 1.3 75.9 - - - +
270B ILE* 1.3 63.7 + - - +
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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