Contacts of the helix formed by residues 269 - 288 (chain B) in PDB entry 4L6V
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 TRP 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ASP* 3.8 37.2 - - + -
239B THR 3.7 19.3 - - - -
240B ALA* 5.0 2.0 - - - -
258B LEU* 3.5 24.0 - - + +
259B GLY 3.8 14.0 + - - -
260B GLY 3.6 15.5 - - - -
261B PHE 3.3 20.6 + - - -
262B HIS* 3.5 44.0 - + - -
263B PRO* 3.9 9.9 - - + -
268B LEU* 1.3 71.5 - - - +
270B LEU* 1.3 61.0 + - - +
271B THR* 3.6 14.8 - - + +
272B ASP* 2.8 41.1 + - - +
273B ILE* 2.9 12.5 + - - +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 3.7 37.9 - - + +
194B LEU* 4.9 11.5 - - + +
198B ALA* 3.8 30.1 - - + +
199B ILE* 3.6 19.0 - - + +
202B ALA* 4.1 5.2 - - + -
244B PHE* 4.0 22.4 - - + -
267B SER* 5.7 0.9 - - - +
268B LEU 3.4 6.6 + - - +
269B TRP* 1.3 72.9 - - - +
271B THR* 1.3 58.2 + - + +
273B ILE* 3.8 22.0 - - + +
274B ALA* 2.9 31.5 + - - +
355B SER 4.8 0.7 - - - +
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 4.1 10.1 - - + -
203B ARG* 3.7 13.7 - - - +
237B PRO* 6.0 0.2 - - + -
238B ASP* 4.0 9.6 - - - +
253B ALA 3.5 25.4 - - - +
254B ILE 3.5 17.5 - - - +
256B THR* 2.4 52.8 + - + +
258B LEU* 4.0 5.6 - - + +
269B TRP* 3.6 14.4 - - + +
270B LEU* 1.3 79.1 - - + +
272B ASP* 1.3 58.7 + - - +
274B ALA 4.2 0.2 - - - -
275B HIS* 3.5 12.0 + - - +
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Residues in contact with ASP 272 (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 THR* 3.0 26.6 + - - +
257B PHE* 4.2 9.6 - - + -
258B LEU 3.0 15.4 + - - -
259B GLY* 3.1 25.1 + - - -
260B GLY 4.7 1.0 - - - +
268B LEU* 5.6 2.9 - - + +
269B TRP* 2.8 32.6 + - - +
271B THR* 1.3 77.4 + - - +
273B ILE* 1.3 55.6 + - + +
274B ALA 3.3 0.2 - - - -
275B HIS* 3.3 2.5 + - - +
276B HIS* 2.8 36.0 + - - +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TRP* 5.1 2.5 - - - +
194B LEU* 3.7 18.4 - - + -
268B LEU* 4.0 32.5 - - + +
269B TRP 2.9 11.3 + - - +
270B LEU* 3.8 22.4 - - + +
272B ASP* 1.3 77.0 - - + +
274B ALA* 1.3 57.4 + - - +
276B HIS* 3.4 6.3 - - - +
277B HIS* 2.4 56.2 + - + -
355B SER* 3.8 31.2 - - - +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA* 3.6 11.7 - - - +
194B LEU* 3.4 32.2 - - + +
195B VAL* 4.0 21.3 - - + -
199B ILE* 4.3 1.6 - - + -
254B ILE 4.2 6.3 - - - +
255B LEU* 4.1 6.5 - - + -
270B LEU 2.9 17.2 + - - +
273B ILE* 1.3 74.4 - - - +
275B HIS* 1.3 65.3 + - - +
276B HIS 3.2 0.2 + - - -
277B HIS 3.2 2.1 + - - -
278B LEU* 3.2 19.4 + - - +
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Residues in contact with HIS 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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255B LEU* 3.8 35.2 + - + +
256B THR 3.2 21.5 + - - +
257B PHE* 4.4 22.2 - + + +
271B THR 3.5 17.5 + - - +
272B ASP 3.3 3.5 + - - +
274B ALA* 1.3 78.6 - - - +
276B HIS* 1.3 61.4 + - - +
278B LEU* 3.5 7.3 + - + +
279B ALA* 3.2 27.8 + - + +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP 2.8 17.6 + - - +
273B ILE* 3.4 9.4 - - - +
274B ALA 3.1 0.2 - - - -
275B HIS* 1.3 79.6 - - - +
277B HIS* 1.3 83.5 + + - +
279B ALA* 3.3 2.8 + - - +
280B ILE* 3.0 61.0 + - + +
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Residues in contact with HIS 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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187B SER* 3.1 37.0 + - - +
190B TRP* 3.3 36.8 + + + -
191B ALA* 3.7 13.0 - - + -
194B LEU* 4.5 0.9 - - + -
273B ILE* 2.4 49.0 + - + +
274B ALA 3.2 2.6 + - - +
276B HIS* 1.3 94.6 - + - +
278B LEU* 1.3 57.5 + - - +
280B ILE* 4.2 0.9 - - - -
281B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.4 29.6 - - + -
191B ALA* 3.7 12.5 - - + +
225B PHE* 5.8 9.9 - - + -
255B LEU* 3.7 31.9 - - + -
274B ALA 3.2 15.3 + - - +
275B HIS* 3.8 10.3 - - + +
276B HIS 3.2 0.2 - - - -
277B HIS* 1.3 76.2 - - - +
279B ALA* 1.3 63.9 + - - +
281B ALA* 3.4 3.9 + - - +
282B VAL* 3.4 31.9 + - + +
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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
----------------------------------------------------------
275B HIS* 3.2 24.0 + - + +
276B HIS* 3.7 4.3 - - - +
278B LEU* 1.3 76.6 - - - +
280B ILE* 1.3 71.5 + - + +
282B VAL* 3.4 9.6 + - - +
283B ILE* 3.4 25.6 + - + +
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B PHE 5.4 0.2 - - - +
187B SER* 3.3 24.9 - - - +
276B HIS* 3.0 53.4 + - + +
277B HIS* 3.7 3.6 - - - +
279B ALA* 1.3 80.2 - - + +
281B ALA* 1.3 67.1 + - - +
283B ILE* 3.0 23.6 - - + +
284B PHE* 2.9 45.6 + - + -
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLY* 3.2 29.9 - - - +
187B SER* 4.1 0.4 - - - -
188B LEU* 3.5 26.2 - - + +
277B HIS 2.9 18.8 + - - +
278B LEU 3.7 5.6 - - - +
279B ALA 3.3 0.2 - - - -
280B ILE* 1.3 79.3 - - - +
282B VAL* 1.3 58.0 + - - +
284B PHE* 3.7 1.2 - - - +
285B ILE* 2.9 38.8 + - + +
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Residues in contact with VAL 282 (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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188B LEU* 6.0 1.1 - - + -
278B LEU* 3.4 22.0 - - + +
279B ALA* 3.4 9.6 + - - +
280B ILE 3.1 0.6 - - - -
281B ALA* 1.3 74.4 - - + +
283B ILE* 1.3 63.3 + - + +
284B PHE 3.0 4.0 - - - -
285B ILE* 2.9 24.2 + - + +
286B ILE* 3.0 26.6 + - + +
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Residues in contact with ILE 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 ALA 3.5 10.5 - - - +
280B ILE* 3.0 41.1 - - + +
282B VAL* 1.3 84.1 - - + +
284B PHE* 1.3 66.2 + - + +
286B ILE* 3.2 32.2 - - + +
287B ALA* 3.4 12.5 - - - +
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Residues in contact with PHE 284 (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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179B LEU* 2.9 42.5 - - + +
183B PHE* 3.2 48.0 - + + -
184B GLY* 3.8 9.4 - - - -
280B ILE* 2.9 45.6 + - + +
281B ALA 3.7 4.0 - - - +
283B ILE* 1.3 88.7 - - + +
285B ILE* 1.3 63.1 + - - +
287B ALA* 3.5 8.3 - - + +
288B GLY 3.4 8.7 + - - -
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Residues in contact with ILE 285 (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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180B ALA* 3.8 26.7 - - + +
184B GLY* 4.1 9.9 - - - -
185B VAL* 4.6 8.7 - - + +
188B LEU* 4.8 17.3 - - + -
281B ALA* 2.9 27.6 + - + +
282B VAL* 2.9 8.3 + - + +
284B PHE* 1.3 76.0 - - - +
286B ILE* 1.3 67.0 + - + +
288B GLY* 3.0 10.9 + - - -
289B HIS* 2.8 39.7 + - + -
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Residues in contact with ILE 286 (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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282B VAL* 3.0 21.4 + - + +
283B ILE* 3.2 34.5 - - + +
285B ILE* 1.3 79.8 - - + +
287B ALA* 1.3 66.1 + - - +
289B HIS* 3.2 25.8 + - - +
290B MET* 4.1 1.4 + - - +
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Residues in contact with ALA 287 (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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176B ASN* 4.5 0.9 - - - +
179B LEU* 3.9 24.7 - - + +
283B ILE 3.4 15.9 + - - +
284B PHE* 3.5 13.9 - - + +
285B ILE 3.1 0.2 - - - -
286B ILE* 1.3 84.9 - - - +
288B GLY* 1.3 56.2 + - - +
289B HIS 3.1 4.7 + - - -
290B MET* 3.3 23.4 + - - +
291B TYR* 4.8 0.3 - - - -
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Residues in contact with GLY 288 (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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176B ASN* 2.9 52.2 + - - +
179B LEU* 3.9 12.8 - - - -
180B ALA* 4.0 3.8 - - - +
284B PHE 3.4 3.2 + - - -
285B ILE 3.0 9.2 + - - -
287B ALA* 1.3 77.6 - - - +
289B HIS* 1.3 67.6 + - - +
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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