Contacts of the helix formed by residues 267 - 285 (chain Z) in PDB entry 5JPQ
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 ILE 267 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266Z SER* 1.3 75.7 - - - +
268Z PRO* 1.4 65.3 - - - +
269Z GLU* 4.7 3.8 - - + +
270Z GLU* 3.1 29.1 + - + +
271Z LEU* 3.2 11.8 + - - +
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Residues in contact with PRO 268 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204Z LEU* 3.6 32.3 - - + +
207Z ARG* 3.9 12.1 - - + -
208Z MET* 3.4 14.8 - - + +
241Z TRP* 6.5 1.3 - - + -
266Z SER 3.8 4.2 - - - -
267Z ILE* 1.4 70.3 - - - +
269Z GLU* 1.3 62.8 + - - +
271Z LEU* 3.2 9.6 + - + +
272Z GLY 3.1 18.0 + - - -
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Residues in contact with GLU 269 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Z ARG* 3.5 23.6 + - + +
210Z ASP* 5.7 2.2 - - + -
211Z GLY* 3.3 15.5 - - - +
267Z ILE* 3.3 4.4 - - + -
268Z PRO* 1.3 75.7 - - - +
270Z GLU* 1.3 57.4 + - - +
272Z GLY 3.3 1.6 + - - -
273Z GLU* 3.0 26.7 + - - +
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Residues in contact with GLU 270 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267Z ILE* 3.1 25.2 + - + +
269Z GLU* 1.3 75.8 - - - +
271Z LEU* 1.4 59.3 + - - +
273Z GLU* 3.4 7.7 + - - +
274Z LYS* 3.0 29.9 + - - +
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Residues in contact with LEU 271 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Z MET* 5.6 3.4 - - + -
243Z ILE* 5.9 4.0 - - + -
260Z ASP* 6.1 4.6 - - + +
261Z ILE 5.6 2.9 - - - +
262Z GLY* 5.2 15.9 - - - +
266Z SER* 6.4 0.9 - - - -
267Z ILE 3.2 9.0 + - - +
268Z PRO* 3.2 11.0 + - + +
270Z GLU* 1.4 76.3 - - - +
272Z GLY* 1.3 64.1 + - - +
274Z LYS* 3.3 6.4 + - - +
275Z VAL* 3.0 27.1 + - - +
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Residues in contact with GLY 272 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Z MET* 3.3 30.4 - - - +
212Z ALA* 3.4 20.9 - - - +
243Z ILE* 5.5 5.2 - - - -
268Z PRO 3.1 10.5 + - - -
269Z GLU 3.3 2.2 + - - -
271Z LEU* 1.3 77.0 - - - +
273Z GLU* 1.4 54.0 + - - +
275Z VAL* 3.6 4.0 + - - +
276Z ALA 3.0 23.4 + - - -
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Residues in contact with GLU 273 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211Z GLY* 3.5 17.3 - - - +
214Z LYS* 6.3 0.2 - - + -
215Z VAL* 4.4 8.2 - - + +
269Z GLU 3.0 14.0 + - - +
270Z GLU* 3.5 11.2 - - - +
272Z GLY* 1.4 75.1 - - - +
274Z LYS* 1.4 52.8 + - - +
276Z ALA* 3.3 5.0 + - - +
277Z CYS* 2.9 33.3 + - - +
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Residues in contact with LYS 274 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270Z GLU 3.0 17.7 + - - +
271Z LEU* 3.3 6.9 + - - +
273Z GLU* 1.4 74.4 - - - +
275Z VAL* 1.3 51.7 + - - +
277Z CYS* 3.1 9.3 + - - +
278Z GLN* 2.8 35.0 + - - +
95a PHE* 4.7 21.1 - - + +
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Residues in contact with VAL 275 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243Z ILE* 4.5 23.3 - - + +
245Z LEU* 4.9 7.5 - - + +
258Z ALA* 3.7 12.8 - - - +
259Z GLU 5.0 2.7 - - - -
260Z ASP* 4.9 14.1 - - + +
271Z LEU 3.0 16.7 + - - +
272Z GLY* 4.2 3.4 - - - +
274Z LYS* 1.3 74.5 - - - +
276Z ALA* 1.4 57.9 + - - +
278Z GLN* 3.2 8.9 + - - +
279Z LEU* 2.8 30.0 + - - +
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Residues in contact with ALA 276 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Z ALA* 3.7 19.5 - - + +
215Z VAL* 3.7 23.1 - - + -
216Z LEU* 4.9 5.6 - - + +
245Z LEU* 5.3 4.9 - - - +
272Z GLY 3.0 18.6 + - - +
273Z GLU 3.5 5.2 - - - +
274Z LYS 3.3 0.2 - - - -
275Z VAL* 1.4 74.9 - - - +
277Z CYS* 1.4 59.9 + - - +
279Z LEU* 3.3 7.5 + - - +
280Z LEU* 3.2 22.5 + - - +
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Residues in contact with CYS 277 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Z VAL* 4.8 4.4 - - + +
273Z GLU 2.9 14.3 + - - +
274Z LYS* 3.4 11.2 - - - +
276Z ALA* 1.4 73.1 - - - +
278Z GLN* 1.3 57.8 + - - +
280Z LEU* 3.5 4.4 + - - +
281Z GLU* 3.0 28.5 + - - +
95a PHE* 5.5 1.6 - - - +
98a LEU* 4.0 34.3 - - + +
99a ALA* 4.6 6.7 - - + +
102a TRP* 4.8 14.3 - - + +
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Residues in contact with GLN 278 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258Z ALA* 3.8 14.1 - - + +
274Z LYS 2.8 16.7 + - - +
275Z VAL* 3.6 8.5 - - - +
277Z CYS* 1.3 73.7 - - - +
279Z LEU* 1.3 59.8 + - - +
281Z GLU* 3.4 7.1 + - - +
282Z GLU* 2.8 29.5 + - - +
92a PHE* 5.3 13.7 - - + -
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Residues in contact with LEU 279 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245Z LEU* 4.4 19.5 - - + +
247Z ALA* 6.1 5.8 - - + +
256Z TYR* 5.7 3.5 - - - +
257Z PHE* 5.1 1.8 - - - -
258Z ALA* 3.6 17.4 - - + +
275Z VAL 2.8 19.6 + - - +
276Z ALA* 3.3 6.9 + - - +
278Z GLN* 1.3 70.5 - - - +
280Z LEU* 1.4 59.6 + - - +
282Z GLU* 3.2 6.5 + - - +
283Z ILE* 2.8 29.0 + - - +
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Residues in contact with LEU 280 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276Z ALA 3.2 12.9 + - - +
277Z CYS* 3.8 8.1 - - - +
278Z GLN 3.4 0.2 - - - -
279Z LEU* 1.4 74.5 - - - +
281Z GLU* 1.3 57.2 + - - +
283Z ILE* 3.3 8.7 + - - +
284Z SER* 3.0 29.3 + - - -
102a TRP* 4.7 16.4 - - + -
105a VAL* 6.4 2.2 - - + -
108a ILE* 5.3 5.4 - - + +
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Residues in contact with GLU 281 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277Z CYS 3.0 18.4 + - - +
278Z GLN* 3.6 9.0 - - - +
280Z LEU* 1.3 76.1 - - - +
282Z GLU* 1.4 62.1 + - - +
284Z SER* 3.2 9.4 + - - -
285Z LYS* 3.1 23.0 + - - +
92a PHE* 6.3 2.9 - - + -
98a LEU* 5.6 6.5 - - + -
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Residues in contact with GLU 282 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256Z TYR* 5.5 4.5 - - + -
257Z PHE 4.3 20.9 - - - +
258Z ALA* 5.3 1.1 - - + -
278Z GLN 2.8 21.8 + - - +
279Z LEU* 3.2 6.9 + - - +
281Z GLU* 1.4 70.5 - - - +
283Z ILE* 1.4 63.0 + - - +
285Z LYS* 3.2 8.9 + - - +
286Z SER* 3.1 24.1 + - - -
290Z GLY* 5.3 7.2 - - - -
291Z ARG 6.1 1.3 - - - +
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Residues in contact with ILE 283 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247Z ALA* 5.6 6.5 - - + -
256Z TYR* 5.1 12.7 - - + +
279Z LEU 2.8 17.3 + - - +
280Z LEU* 3.3 11.2 + - - +
282Z GLU* 1.4 72.7 - - - +
284Z SER* 1.4 56.8 + - - +
286Z SER* 3.0 29.7 + - - +
108a ILE* 5.2 11.0 - - + -
111a ARG* 5.7 7.0 - - + -
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Residues in contact with SER 284 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Z LEU 3.0 13.4 + - - -
281Z GLU* 3.2 12.3 + - - -
283Z ILE* 1.4 74.6 - - - +
285Z LYS* 1.3 57.8 + - - +
286Z SER 3.7 3.5 + - - +
314Z ASN* 5.3 1.7 - - - +
316Z GLU* 5.3 0.9 - - - +
107a ALA* 5.7 7.4 - - - -
108a ILE* 5.2 12.7 - - - +
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Residues in contact with LYS 285 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281Z GLU 3.1 14.4 + - - +
282Z GLU* 3.6 7.6 - - - +
283Z ILE 3.2 0.4 - - - -
284Z SER* 1.3 74.8 - - - +
286Z SER* 1.3 58.3 + - - +
291Z ARG* 5.8 5.3 + - + -
314Z ASN* 3.2 18.1 - - - +
316Z GLU* 3.8 28.3 - - + +
317Z GLN* 4.2 10.4 + - - +
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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