Contacts of the helix formed by residues 274 - 292 (chain B) in PDB entry 4XZC
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 GLY 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 3.7 27.9 - - - +
269B LEU* 4.1 14.1 - - - +
270B GLU 4.2 3.4 + - - -
272B GLY* 3.1 1.4 - - - -
273B LYS* 1.3 77.0 - - - +
275B ASP* 1.3 62.5 + - - +
277B LEU* 3.8 4.2 - - - +
278B VAL* 3.1 31.5 + - - +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 5.5 2.9 - - - +
263B GLU* 6.1 1.2 - - - +
272B GLY* 3.1 15.8 + - - +
274B GLY* 1.3 73.1 - - - +
276B GLU* 1.3 61.5 + - - +
277B LEU 2.9 10.5 + - - -
278B VAL* 3.3 6.5 + - - +
279B LYS* 3.0 29.9 + - + +
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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
----------------------------------------------------------
222B ASN* 4.6 13.3 + - - +
272B GLY 3.1 12.8 + - - +
273B LYS* 2.8 46.6 + - - +
275B ASP* 1.3 77.8 - - - +
277B LEU* 1.3 52.1 + - - +
279B LYS* 4.0 8.7 - - - +
280B THR* 2.7 37.4 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 3.8 16.6 - - + +
214B PHE* 3.6 32.3 - - + -
221B ILE* 3.9 31.6 - - + -
258B LEU* 4.6 1.6 - - + -
262B ILE* 4.4 13.2 - - + -
269B LEU* 6.2 0.4 - - + -
273B LYS 3.3 16.5 + - - +
274B GLY* 3.8 5.6 - - - +
275B ASP 2.9 1.4 + - - -
276B GLU* 1.3 75.9 - - - +
278B VAL* 1.3 68.1 + - - +
279B LYS 3.1 1.3 - - - -
280B THR* 3.1 3.4 + - - -
281B LEU* 2.9 49.3 + - + +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.9 7.1 - - + +
258B LEU* 4.8 8.5 - - + -
259B LYS* 4.3 39.3 - - + -
262B ILE* 3.7 21.5 - - + -
274B GLY 3.1 17.9 + - - +
275B ASP* 3.9 6.3 - - - +
277B LEU* 1.3 75.2 - - - +
279B LYS* 1.3 58.3 + - - +
281B LEU* 4.0 4.6 - - - +
282B THR* 2.4 41.7 + - - +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP* 3.0 23.0 + - + +
276B GLU* 4.0 8.3 - - - +
278B VAL* 1.3 76.4 - - - +
280B THR* 1.3 63.8 + - - +
282B THR* 3.2 7.4 + - - -
283B LYS* 3.1 21.0 + - - +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 4.7 11.8 - - + +
222B ASN* 3.4 30.0 + - - +
276B GLU* 2.7 25.7 + - - +
277B LEU* 3.1 6.8 + - - -
279B LYS* 1.3 77.8 - - - +
281B LEU* 1.3 58.0 + - - +
283B LYS* 3.0 9.7 + - - +
284B GLN* 2.9 52.9 + - + +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 4.2 16.6 - - + -
205B LEU* 4.5 0.9 - - + -
213B VAL* 3.5 43.1 - - + -
221B ILE* 4.3 9.2 - - + -
236B MET* 4.3 9.9 - - + +
255B LEU* 3.5 30.4 - - + +
258B LEU* 3.7 12.8 - - + -
277B LEU* 2.9 36.7 + - + +
278B VAL* 4.1 4.0 - - - +
280B THR* 1.3 78.0 - - - +
282B THR* 1.3 56.6 + - - +
283B LYS 3.3 0.2 - - - -
284B GLN* 3.3 21.1 - - - +
285B LEU* 3.2 19.4 + - - +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.5 9.8 - - + +
278B VAL* 2.4 34.9 + - - +
279B LYS* 3.5 6.7 - - - -
280B THR 3.1 0.2 - - - -
281B LEU* 1.3 74.3 - - - +
283B LYS* 1.3 64.2 + - - +
285B LEU* 3.7 9.4 + - + +
286B ALA* 3.2 21.3 + - - +
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Residues in contact with LYS 283 (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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279B LYS 3.1 10.8 + - - +
280B THR* 3.0 12.2 + - - +
282B THR* 1.3 74.5 - - - +
284B GLN* 1.3 63.5 + - + +
286B ALA* 3.4 6.9 + - + +
287B ASP* 3.0 59.2 + - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.0 28.6 + - - +
222B ASN* 4.5 2.0 + - - -
230B PRO* 4.2 14.0 - - + +
232B ALA* 3.3 18.2 - - + +
233B VAL* 3.3 31.5 - - + +
236B MET* 4.0 10.0 - - + +
280B THR* 2.9 30.6 + - + +
281B LEU* 3.3 36.0 - - - +
283B LYS* 1.3 80.7 - - + +
285B LEU* 1.3 56.6 + - - +
287B ASP* 3.3 1.2 - - - +
288B ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B MET* 3.9 24.1 - - - -
248B LEU* 3.6 33.0 - - + +
251B ILE* 4.1 6.3 - - + -
252B ARG* 3.7 48.2 - - + +
255B LEU* 3.9 14.6 - - + -
281B LEU 3.2 15.4 + - - +
282B THR* 3.8 8.7 - - + +
284B GLN* 1.3 77.5 - - - +
286B ALA* 1.3 59.2 + - - +
288B ALA* 3.1 1.2 + - - +
289B ILE* 2.8 43.5 + - + +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 5.6 2.2 - - - +
282B THR 3.2 15.3 + - - +
283B LYS* 3.6 11.2 - - + +
284B GLN 3.4 0.2 - - - -
285B LEU* 1.3 78.3 - - - +
287B ASP* 1.3 59.7 + - - +
289B ILE* 3.4 13.1 + - - +
290B GLU* 3.0 32.2 + - - +
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PRO* 5.4 4.9 - - - +
233B VAL* 4.0 18.4 - - + +
283B LYS* 3.0 46.2 + - - +
284B GLN* 3.3 10.0 - - - +
286B ALA* 1.3 75.4 - - - +
288B ALA* 1.3 63.4 + - - +
290B GLU* 3.5 7.4 + - - +
291B LEU* 3.1 33.7 + - + +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 4.1 4.9 - - - +
236B MET* 3.7 29.4 - - + -
237B VAL* 3.9 18.9 - - + +
248B LEU* 3.9 11.0 - - + -
284B GLN 2.9 14.5 + - - +
285B LEU* 3.1 9.6 + - - +
287B ASP* 1.3 72.9 - - - +
289B ILE* 1.3 67.2 + - - +
290B GLU 3.2 0.3 + - - -
291B LEU* 3.2 1.9 + - - +
292B ALA* 3.0 28.0 + - - +
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Residues in contact with ILE 289 (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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245B HIS* 4.3 4.1 + - + -
248B LEU* 4.1 29.1 - - + +
249B GLU* 4.7 2.9 - - - +
252B ARG* 3.2 41.3 - - - +
285B LEU* 2.8 29.6 + - + +
286B ALA* 3.5 9.0 - - - +
288B ALA* 1.3 76.8 - - - +
290B GLU* 1.3 63.5 + - - +
292B ALA* 3.7 1.9 + - - +
293B LYS* 3.1 39.3 + - + +
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Residues in contact with GLU 290 (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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286B ALA 3.0 19.2 + - - +
287B ASP* 3.7 7.6 - - - +
288B ALA 3.1 0.4 - - - -
289B ILE* 1.3 78.8 - - + +
291B LEU* 1.3 67.0 + - + +
293B LYS* 3.0 47.1 + - - +
294B LYS* 3.8 4.0 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 4.1 28.5 - - + -
233B VAL* 3.5 27.1 - - + -
234B THR* 6.0 0.4 - - + -
237B VAL* 3.9 16.6 - - + +
287B ASP* 3.1 23.6 + - + +
288B ALA 3.8 2.7 - - - +
290B GLU* 1.3 79.9 - - + +
292B ALA* 1.3 55.9 + - - +
293B LYS 3.2 0.4 - - - -
294B LYS* 3.1 22.1 + - + +
295B SER* 3.2 11.6 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 4.6 11.2 - - + +
240B ALA* 4.4 11.2 - - + -
245B HIS* 3.7 25.5 - - + +
248B LEU* 4.0 11.0 - - + -
288B ALA 3.0 17.2 + - - +
289B ILE 4.0 1.6 - - - +
290B GLU 3.2 0.2 - - - -
291B LEU* 1.3 73.5 - - - +
293B LYS* 1.3 60.3 + - - +
294B LYS 3.0 7.6 + - - -
295B SER* 3.8 7.9 + - - +
298B LEU* 3.1 28.2 - - + +
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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
------------------------------------------------------------
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