Contacts of the helix formed by residues 259 - 278 (chain B) in PDB entry 5JJA
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 SER 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.8 26.0 - - - -
216B GLU 4.8 4.5 + - - -
257B VAL* 3.2 4.4 + - - +
258B LYS* 1.3 82.2 - - - +
260B LEU* 1.3 63.5 + - - +
261B SER* 3.1 6.6 + - - -
262B VAL* 3.1 27.2 + - - +
263B TYR* 3.5 9.8 - - - -
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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
----------------------------------------------------------
254B LEU 3.8 9.9 - - - +
255B HIS* 3.4 23.3 - - + +
257B VAL 3.0 17.6 + - - +
258B LYS 3.2 3.5 + - - +
259B SER* 1.3 76.3 - - - +
261B SER* 1.3 58.6 + - - +
263B TYR* 3.0 33.9 + - + +
264B HIS* 2.8 61.2 + - + +
267B LEU* 3.9 13.7 - - + -
304B PHE* 3.5 25.1 - - + -
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Residues in contact with SER 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LYS 4.9 1.2 + - - -
259B SER* 3.1 4.0 + - - -
260B LEU* 1.3 79.4 - - - +
262B VAL* 1.3 68.6 + - - +
263B TYR 3.3 0.5 + - - -
264B HIS* 3.8 14.8 + - - +
265B PRO* 4.1 8.0 - - - +
300B LYS* 3.7 32.6 + - - +
303B MET* 6.0 2.3 - - - +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASN 5.9 2.7 - - - +
222B ALA* 4.3 11.4 - - + +
259B SER* 3.1 23.8 + - - +
260B LEU 3.1 0.8 + - - -
261B SER* 1.3 83.7 + - - +
263B TYR* 1.3 64.7 + - + +
265B PRO* 4.8 2.1 - - - +
266B GLN* 4.2 5.5 + - - +
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.6 30.2 - + - -
221B ILE* 3.7 15.9 - - + -
222B ALA* 3.8 27.6 - - + +
225B LEU* 3.7 15.3 - - + -
254B LEU* 2.7 36.1 + - + +
257B VAL* 3.4 19.9 - - - +
259B SER* 3.5 21.1 - - - -
260B LEU* 3.0 28.0 + - + -
262B VAL* 1.3 82.1 - - + +
264B HIS* 1.3 67.0 + - - +
265B PRO* 3.4 4.0 - - - -
266B GLN* 3.1 12.3 + - - +
267B LEU* 3.0 21.2 + - + -
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Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B HIS* 4.1 4.0 - + - -
260B LEU* 2.8 55.6 + - + +
261B SER* 4.2 7.6 - - - -
262B VAL 3.8 0.4 - - - -
263B TYR* 1.3 75.6 - - - +
265B PRO* 1.4 67.5 - - + +
267B LEU* 3.2 3.9 + - + +
268B ALA* 2.8 26.9 + - + +
300B LYS 5.3 0.2 + - - -
303B MET* 3.4 31.7 + - + +
304B PHE* 3.7 37.3 - + - -
307B GLU* 2.8 30.4 + - - -
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Residues in contact with PRO 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B SER 4.1 9.4 - - - +
262B VAL 4.8 1.6 - - - +
263B TYR* 3.5 4.5 - - - -
264B HIS* 1.4 94.3 - - + +
266B GLN* 1.3 72.8 + - - +
268B ALA* 3.5 3.1 + - + +
269B TYR* 3.2 22.5 + - - +
303B MET* 3.8 26.0 - - + -
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Residues in contact with GLN 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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222B ALA* 3.5 30.7 - - - +
225B LEU* 3.8 22.7 - - + +
226B GLU* 4.5 23.6 + - + +
262B VAL 4.2 2.5 + - - +
263B TYR* 3.1 23.1 + - - +
265B PRO* 1.3 83.5 - - - +
267B LEU* 1.3 65.7 + - - +
269B TYR* 3.4 8.2 + - - +
270B CYS* 3.3 25.8 + - - -
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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
----------------------------------------------------------
225B LEU* 3.8 12.2 - - + +
251B LEU* 3.5 42.6 - - + +
254B LEU* 3.9 22.0 - - + -
255B HIS* 3.5 40.4 - - + +
260B LEU* 3.9 18.4 - - + -
263B TYR* 3.0 15.4 + - + +
264B HIS* 3.4 10.1 - - + +
266B GLN* 1.3 74.5 - - - +
268B ALA* 1.3 66.4 + - - +
270B CYS* 3.1 4.4 + - + +
271B VAL* 3.0 24.8 + - + +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS* 2.8 19.2 + - - +
265B PRO* 3.8 5.4 - - + +
267B LEU* 1.3 73.2 - - - +
269B TYR* 1.3 62.2 + - - +
271B VAL* 3.2 2.1 + - - +
272B VAL* 3.0 28.9 + - + +
303B MET* 4.3 9.6 - - + -
307B GLU* 3.7 40.2 - - + -
310B GLU* 4.2 13.9 - - - +
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Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU 5.8 0.2 - - - -
226B GLU* 6.5 0.2 - - - -
229B GLY* 3.8 30.7 + - - -
230B SER* 5.8 0.3 - - - -
233B ASN* 3.9 14.6 + - - +
265B PRO 3.2 11.2 + - - +
266B GLN* 3.7 10.5 - - - +
267B LEU 3.2 0.6 - - - -
268B ALA* 1.3 79.5 - - - +
270B CYS* 1.3 64.4 + - - +
272B VAL* 3.3 6.8 + - + +
273B GLN* 3.0 65.3 + - + +
310B GLU* 5.4 1.5 + - - -
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.3 41.7 - - - -
228B LEU* 4.2 2.7 - - - -
229B GLY* 3.8 15.9 - - - -
232B ILE* 3.7 18.6 - - + +
251B LEU* 3.9 15.0 - - + -
266B GLN 3.3 13.9 + - - -
267B LEU* 3.1 9.2 + - - +
269B TYR* 1.3 80.7 - - - +
271B VAL* 1.3 62.0 + - - +
273B GLN* 3.4 5.0 + - - +
274B PHE* 3.2 27.8 + - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 4.6 17.7 - - + +
251B LEU* 4.7 4.0 - - + -
252B LEU* 4.6 4.7 - - + -
255B HIS* 4.0 17.0 - - + -
267B LEU* 3.0 21.5 + - + +
268B ALA 3.6 7.0 - - - +
270B CYS* 1.3 74.6 - - - +
272B VAL* 1.3 63.5 + - + +
274B PHE* 3.2 14.9 + - - +
275B LEU* 3.3 12.6 + - + +
285B VAL* 3.6 33.7 - - + -
307B GLU* 3.8 21.5 - - - +
311B ILE* 4.2 11.2 - - + -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA* 3.0 21.7 + - - +
269B TYR* 3.9 7.6 - - + +
271B VAL* 1.3 75.4 - - + +
273B GLN* 1.3 67.5 + - - +
275B LEU* 3.1 9.7 + - - +
276B GLU* 3.0 28.7 + - - +
307B GLU* 4.5 3.1 - - + +
310B GLU* 3.9 40.2 - - + +
311B ILE* 4.0 22.0 - - + +
314B VAL* 4.3 17.3 - - + -
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Residues in contact with GLN 273 (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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229B GLY 4.7 4.0 - - - +
232B ILE* 3.7 18.6 - - + -
233B ASN* 3.0 29.2 + - - +
269B TYR* 3.0 63.1 + - + +
270B CYS* 3.7 6.3 - - - +
272B VAL* 1.3 79.6 - - - +
274B PHE* 1.3 63.0 + - - +
276B GLU* 3.2 30.4 + - - +
277B LYS* 3.1 29.6 + - - +
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Residues in contact with PHE 274 (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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232B ILE* 3.6 28.9 - - + +
235B PHE* 3.9 17.9 - + - -
239B LEU* 3.8 24.2 - - + -
243B HIS* 3.1 42.6 - - + -
244B LYS* 4.2 0.9 - - - -
246B PHE* 4.2 7.4 - + - -
247B LEU* 3.9 35.4 - - + -
251B LEU* 3.7 20.6 - - + -
270B CYS 3.2 18.9 + - - -
271B VAL 3.2 10.8 + - - +
273B GLN* 1.3 78.8 - - - +
275B LEU* 1.3 58.8 + - + +
277B LYS* 3.2 6.7 + - - +
278B ASP* 3.0 27.7 + - - +
281B LEU* 4.1 3.1 - - + +
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Residues in contact with LEU 275 (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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271B VAL 3.3 10.1 + - - +
272B VAL* 3.1 8.9 + - - +
274B PHE* 1.3 75.8 - - + +
276B GLU* 1.3 66.7 + - - +
277B LYS 3.5 0.2 + - - -
278B ASP 3.5 17.5 + - - +
279B SER* 3.7 8.1 + - - -
281B LEU* 3.7 19.5 - - + +
282B THR* 3.7 41.1 - - + +
285B VAL* 4.1 20.9 - - + -
311B ILE* 3.7 42.4 - - + -
314B VAL* 4.2 19.0 - - + +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 5.8 0.7 - - - +
272B VAL* 3.0 23.3 + - - +
273B GLN* 3.2 32.1 + - - +
275B LEU* 1.3 77.1 - - - +
277B LYS* 1.3 63.1 + - + +
314B VAL* 3.8 32.4 - - + +
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Residues in contact with LYS 277 (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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232B ILE* 3.5 18.2 - - + +
233B ASN* 2.8 31.4 + - - +
234B GLY 4.1 0.6 - - - -
235B PHE* 2.7 30.0 + - + +
237B LEU* 3.3 45.2 - - + +
239B LEU* 4.1 19.3 - - + -
273B GLN* 3.1 19.6 + - - +
274B PHE* 3.6 8.5 - - - +
275B LEU 3.2 0.2 - - - -
276B GLU* 1.3 80.9 - - - +
278B ASP* 1.3 60.0 + - - +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 5.5 0.7 - - + -
239B LEU* 3.8 23.4 + - + +
244B LYS* 3.6 26.5 + - - -
274B PHE 3.0 11.9 + - - +
275B LEU* 3.6 7.0 - - - +
276B GLU 3.5 0.8 - - - -
277B LYS* 1.3 80.4 - - - +
279B SER* 1.3 63.5 + - - +
280B THR* 2.5 37.4 + - - +
281B LEU* 3.3 20.7 + - + +
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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
------------------------------------------------------------
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