Contacts of the helix formed by residues 256 - 277 (chain B) in PDB entry 4R8U
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 HIS 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 4.6 0.2 - - - +
255B HIS* 1.3 94.1 - - + +
257B TRP* 1.3 64.5 + - - +
258B SER* 4.0 16.1 + - - +
259B GLU* 3.1 37.4 + - + +
260B CYS 3.4 4.2 + - - -
321B TRP* 3.4 8.2 - - - -
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Residues in contact with TRP 257 (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 HIS* 1.3 71.6 - - - +
258B SER* 1.3 67.3 + - - +
260B CYS* 2.9 29.4 + - + +
261B GLU* 2.9 50.4 + - + -
264B ILE* 4.5 6.7 - - + -
314B ILE* 3.7 19.1 - - + -
317B ALA* 3.7 16.6 - - + -
318B ARG* 3.3 76.5 - - + +
321B TRP* 3.3 37.8 - + + +
322B ASP* 5.8 1.1 - - - +
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 4.0 13.5 + - - +
257B TRP* 1.3 83.0 - - - +
259B GLU* 1.3 59.0 + - - +
261B GLU* 3.5 9.4 + - - +
262B ALA* 3.0 28.2 + - - +
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.5 23.5 - - + +
255B HIS 3.5 11.1 + - - -
256B HIS* 3.1 42.4 + - + +
257B TRP 3.1 0.6 - - - -
258B SER* 1.3 77.5 + - - +
260B CYS* 1.3 65.5 + - - +
262B ALA* 3.4 5.5 + - - +
263B ILE* 3.1 32.2 + - + +
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Residues in contact with CYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.8 8.8 - - + +
256B HIS 3.4 2.2 + - - -
257B TRP* 2.9 35.7 + - + +
259B GLU* 1.3 77.5 - - - +
261B GLU* 1.3 63.8 + - - +
263B ILE* 3.4 5.2 + - - +
264B ILE* 3.1 39.4 + - - +
291B LEU* 4.4 11.0 - - - -
317B ALA* 4.7 2.7 - - - -
321B TRP* 3.8 28.7 - - + -
333B VAL* 4.3 16.3 - - - +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TRP* 2.9 41.1 + - + +
258B SER* 3.7 10.8 - - - +
260B CYS* 1.3 76.4 - - - +
262B ALA* 1.3 65.2 + - - +
264B ILE* 3.0 13.0 + - - +
265B GLU* 3.0 38.1 + - + +
314B ILE* 4.3 30.5 - - + +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B SER 3.0 17.5 + - - +
259B GLU* 3.8 6.7 - - - +
260B CYS 3.3 0.2 - - - -
261B GLU* 1.3 78.4 - - - +
263B ILE* 1.3 62.9 + - + +
265B GLU* 3.3 11.0 + - - +
266B ARG* 3.2 30.6 + - - +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG* 5.3 6.3 - - + +
250B MET* 3.6 46.4 - - + -
254B ILE* 4.0 24.9 - - + -
259B GLU* 3.1 20.1 + - + +
260B CYS 3.7 3.6 - - - +
261B GLU 3.2 0.2 - - - -
262B ALA* 1.3 73.7 - - + +
264B ILE* 1.3 61.5 + - - +
266B ARG* 3.2 11.1 + - - +
267B LEU* 2.9 41.9 + - + +
333B VAL* 3.8 18.2 - - + -
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TRP* 4.5 3.1 - - + -
260B CYS* 3.1 32.4 + - - +
261B GLU* 3.0 12.1 + - - +
263B ILE* 1.3 78.1 - - - +
265B GLU* 1.3 56.0 + - - +
267B LEU* 3.1 7.1 + - - +
268B TYR* 2.9 28.9 + - - +
289B VAL* 5.5 0.2 - - + -
310B LYS* 5.1 4.9 - - + -
313B LEU* 5.0 3.4 - - + +
314B ILE* 3.6 31.4 - - + +
317B ALA* 3.4 33.4 - - + -
333B VAL* 3.9 17.5 - - + -
335B LEU* 4.2 24.6 - - + +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU* 3.0 34.8 + - + +
262B ALA* 3.3 11.4 + - - +
264B ILE* 1.3 76.9 - - - +
266B ARG* 1.3 59.9 + - + +
268B TYR* 4.1 4.4 - - - +
269B PRO* 3.1 23.9 - - - +
310B LYS* 2.4 38.7 + - - +
314B ILE* 3.8 20.2 - - + +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG* 5.0 12.7 - - - +
262B ALA* 3.2 18.3 + - - +
263B ILE* 3.7 11.2 - - - +
264B ILE 3.1 0.6 - - - -
265B GLU* 1.3 80.3 - - + +
267B LEU* 1.3 66.8 + - + +
268B TYR 3.3 0.2 - - - -
269B PRO* 3.5 9.0 - - - +
270B GLU* 4.6 8.1 + - - +
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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
----------------------------------------------------------
246B VAL* 3.8 37.4 - - + +
247B GLU* 4.3 1.3 - - - -
248B ARG* 4.3 21.8 - - + +
263B ILE* 2.9 31.8 + - + +
264B ILE* 3.7 4.3 - - - +
266B ARG* 1.3 79.9 - - + +
268B TYR* 1.3 64.6 + - - +
270B GLU* 3.2 10.3 + - + +
271B LEU 3.1 16.5 + - - -
333B VAL* 3.4 36.1 - - + +
334B GLY* 4.6 1.6 - - - -
335B LEU* 4.0 16.2 - - + -
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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
----------------------------------------------------------
264B ILE 2.9 16.6 + - - +
265B GLU 4.1 0.9 - - - +
267B LEU* 1.3 76.5 - - - +
269B PRO* 1.4 76.7 - - + +
271B LEU* 3.0 5.3 + - + +
272B GLU* 2.9 49.7 + - + -
282B LEU* 5.5 0.5 - - - +
307B ARG* 5.7 0.5 + - - -
308B LEU* 3.6 43.8 + - + +
309B ASN* 4.3 0.2 - - - -
310B LYS* 3.6 63.2 + - + -
313B LEU* 3.9 15.9 - - + -
335B LEU* 3.9 9.9 - - + -
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Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU 3.1 19.7 - - - +
266B ARG* 3.5 11.7 - - - +
268B TYR* 1.4 101.3 - - + +
270B GLU* 1.3 55.7 + - - +
272B GLU* 3.8 6.5 - - + +
273B ARG* 2.9 32.8 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.3 15.3 - - + -
266B ARG 4.6 6.3 + - - +
267B LEU* 3.2 13.4 + - + +
268B TYR 3.1 0.6 - - - -
269B PRO* 1.3 78.1 - - - +
271B LEU* 1.3 63.4 + - - +
273B ARG* 2.4 45.7 + - - +
274B ARG* 3.1 48.3 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.8 39.3 - - + +
245B GLY* 4.5 2.5 - - - -
246B VAL* 3.6 22.6 - - + +
267B LEU 3.1 6.8 + - - +
268B TYR* 3.0 11.5 + - + +
270B GLU* 1.3 74.7 - - - +
272B GLU* 1.3 64.4 - - - +
274B ARG* 3.3 3.0 + - - +
275B LEU* 2.9 24.0 + - + +
308B LEU* 3.7 28.7 - - + -
313B LEU* 4.3 5.2 - - + -
335B LEU* 3.8 30.5 - - + -
336B HIS 4.6 0.2 - - - +
337B VAL* 4.0 14.6 - - + -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 2.9 45.0 + - + +
269B PRO* 3.8 7.4 - - + +
271B LEU* 1.3 76.7 - - - +
273B ARG* 1.3 54.0 + - - +
275B LEU* 3.2 1.4 + - - +
276B ALA* 2.7 39.6 + - + +
282B LEU* 3.8 21.6 - - + +
308B LEU* 3.6 20.4 - - + +
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Residues in contact with ARG 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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269B PRO 2.9 16.7 + - - +
270B GLU* 2.4 44.8 + - - +
272B GLU* 1.3 79.5 - - - +
274B ARG* 1.3 83.3 + - - +
276B ALA* 3.5 7.9 - - + +
277B LYS* 3.0 65.8 + - - +
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Residues in contact with ARG 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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241B ARG* 4.7 7.6 + - - +
244B VAL* 4.0 20.4 - - + -
245B GLY 3.2 15.5 + - - -
246B VAL* 4.2 10.8 - - - +
270B GLU* 3.1 38.7 + - - +
271B LEU* 3.8 4.9 - - - +
273B ARG* 1.3 93.6 - - - +
275B LEU* 1.3 65.1 + - - +
277B LYS* 3.3 15.9 + - - +
278B VAL* 3.7 12.1 - - - +
22C G 3.0 43.6 + - - -
23C G 4.6 6.6 + - - -
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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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244B VAL* 4.5 7.2 - - + +
271B LEU* 2.9 21.7 + - + +
272B GLU 3.6 3.6 - - - +
274B ARG* 1.3 73.1 - - - +
276B ALA* 1.3 57.3 + - - +
278B VAL* 3.1 12.8 + - + +
279B LYS* 2.8 39.4 + - + +
282B LEU* 3.8 21.1 - - + -
284B ILE* 3.7 23.6 - - + -
308B LEU* 3.7 29.4 - - + -
337B VAL* 4.3 11.9 - - + -
339B LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU* 2.7 24.6 + - + +
273B ARG* 3.5 13.0 - - + +
274B ARG 3.2 0.2 - - - -
275B LEU* 1.3 73.8 - - - +
277B LYS* 1.3 63.2 + - + +
278B VAL 3.1 1.6 + - - -
279B LYS 4.0 7.4 - - - -
280B PRO* 3.4 27.7 - - + +
282B LEU* 3.9 8.7 - - + +
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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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273B ARG* 3.0 51.8 + - - +
274B ARG* 3.3 10.0 + - - +
275B LEU 3.2 1.0 - - - -
276B ALA* 1.3 78.0 - - + +
278B VAL* 1.3 65.0 + - + +
280B PRO* 5.6 0.4 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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