Contacts of the helix formed by residues 267 - 281 (chain B) in PDB entry 4JU5
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 ASP 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL 3.6 1.2 + - - -
266B SER* 1.3 78.8 + - - +
268B TYR* 1.3 64.6 + - - +
269B ASP 3.4 2.2 - - - -
270B GLY* 3.6 24.3 + - - -
271B LYS* 3.0 29.3 + - - +
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Residues in contact with TYR 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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261B LEU* 3.5 29.6 - - + +
262B PRO 3.3 18.2 - - - -
263B LYS* 3.6 51.2 - - + +
265B VAL* 3.6 22.8 + - + +
266B SER 3.2 1.0 - - - -
267B ASP* 1.3 75.8 - - - +
269B ASP* 1.3 76.8 + - - +
271B LYS* 3.3 4.8 + - - +
272B LEU* 3.0 49.4 + - + +
290B PHE* 3.7 23.9 - - - -
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP 3.4 0.4 - - - -
268B TYR* 1.3 96.0 - - - +
270B GLY* 1.3 56.8 + - - +
272B LEU* 3.9 8.6 - - - +
273B SER* 2.9 32.9 + - - -
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 3.3 28.0 + - - -
268B TYR 3.2 0.6 - - - -
269B ASP* 1.3 76.8 - - - +
271B LYS* 1.3 58.8 + - - +
273B SER* 3.5 4.8 + - - -
274B ASN* 2.9 36.6 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 5.3 1.6 - - - +
259B LEU* 4.6 4.8 - - + +
261B LEU* 4.2 26.7 - - + -
265B VAL* 4.2 14.1 - - + -
266B SER* 3.1 26.7 - - - +
267B ASP* 3.0 23.9 + - - +
268B TYR 3.3 4.7 + - - +
270B GLY* 1.3 76.7 - - - +
272B LEU* 1.3 60.9 + - - +
274B ASN* 3.5 11.1 - - - +
275B PHE* 3.3 20.1 + - - +
313B PRO* 4.4 14.5 - - + +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 4.4 7.6 - - + +
259B LEU* 4.9 3.8 - - + -
261B LEU* 3.7 18.3 - - + +
268B TYR* 3.0 42.7 + - + +
269B ASP* 4.0 9.4 - - - +
271B LYS* 1.3 76.0 - - - +
273B SER* 1.3 59.0 + - - +
275B PHE* 3.3 7.9 + - + +
276B LYS* 3.0 25.6 + - - +
290B PHE* 3.7 47.6 - - + -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASP 2.9 21.7 + - - -
270B GLY* 3.8 6.5 - - - -
271B LYS 3.4 0.2 - - - -
272B LEU* 1.3 76.7 - - - +
274B ASN* 1.3 55.6 + - - +
276B LYS* 3.1 9.2 + - - +
277B THR* 2.7 41.5 + - - -
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Residues in contact with ASN 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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335A THR* 3.4 15.3 - - - +
336A ALA* 3.1 48.0 - - - +
339A ILE* 4.1 4.2 - - + +
270B GLY 2.9 20.4 + - - +
271B LYS* 3.5 13.8 - - - +
272B LEU 3.3 0.2 - - - -
273B SER* 1.3 77.1 - - - +
275B PHE* 1.3 56.0 + - - +
277B THR* 4.4 1.1 - - - -
278B ALA* 3.0 26.3 + - - +
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Residues in contact with PHE 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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339A ILE* 3.9 21.7 - - + +
237B VAL* 4.0 17.3 - - + -
257B ILE* 3.5 38.8 - - + -
259B LEU* 3.7 42.0 - - + -
271B LYS 3.3 10.4 + - - +
272B LEU* 3.4 11.0 - - + +
274B ASN* 1.3 77.6 - - - +
276B LYS* 1.3 57.6 + - - +
278B ALA* 3.5 0.7 + - - -
279B ALA* 2.9 28.1 + - - +
288B PHE* 3.4 50.2 - + + -
289B ILE 3.6 19.7 - - - -
290B PHE* 4.3 3.1 - - + -
315B VAL* 5.4 1.6 - - + -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.6 8.0 - - + +
237B VAL* 3.5 23.1 - - + +
272B LEU* 3.0 14.1 + - + +
273B SER* 3.1 12.1 + - - +
275B PHE* 1.3 74.3 - - - +
277B THR* 1.3 63.0 + - - +
279B ALA* 3.2 4.2 + - - +
280B GLU* 3.2 25.4 + - - +
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Residues in contact with THR 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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336A ALA* 4.2 17.0 - - + -
273B SER* 2.7 24.3 + - - -
274B ASN* 3.8 5.5 + - - -
276B LYS* 1.3 72.4 - - - +
278B ALA* 1.3 62.8 + - - +
280B GLU* 3.2 26.7 - - + +
281B SER* 4.3 2.9 + - - -
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Residues in contact with ALA 278 (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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336A ALA 3.6 10.7 + - - +
339A ILE* 3.6 26.5 - - + -
340A THR* 3.4 23.6 - - - +
274B ASN 3.0 19.0 + - - +
275B PHE 3.8 2.9 - - - +
277B THR* 1.3 74.3 - - - +
279B ALA* 1.3 63.1 + - - +
280B GLU 3.3 0.3 + - - -
281B SER* 3.6 4.7 + - - -
282B PHE* 2.9 28.4 - - - -
288B PHE* 3.8 2.5 - - + -
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Residues in contact with ALA 279 (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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236B LEU* 3.4 32.1 - - + +
237B VAL* 3.9 8.5 - - + -
275B PHE 2.9 18.4 + - - +
276B LYS 3.2 8.2 + - - +
278B ALA* 1.3 74.4 - - - +
280B GLU* 1.3 64.5 + - - +
282B PHE* 3.2 13.3 + - - +
283B LYS 3.6 5.5 + - - -
288B PHE* 3.5 31.1 - - + -
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Residues in contact with GLU 280 (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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210B ASP* 5.4 1.6 - - - +
236B LEU* 3.5 16.6 - - - +
276B LYS* 3.2 15.1 + - - +
277B THR* 3.2 19.1 - - + +
278B ALA 3.2 0.2 - - - -
279B ALA* 1.3 77.3 - - - +
281B SER* 1.3 59.0 + - - +
282B PHE 3.3 3.6 + - - -
283B LYS* 3.4 45.9 + - - +
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 4.0 13.9 + - - +
344A HIS* 4.9 5.8 + - - -
277B THR 5.0 1.3 + - - -
278B ALA 3.6 5.4 + - - -
279B ALA 3.3 0.8 - - - -
280B GLU* 1.3 77.6 - - - +
282B PHE* 1.3 85.9 + - - +
283B LYS 3.8 0.7 - - - -
285B LYS* 5.2 5.9 + - - -
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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