Contacts of the helix formed by residues 249 - 272 (chain B) in PDB entry 4R0C
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 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLN* 3.2 3.3 - - - -
248B ILE* 1.3 91.2 + - + +
250B SER* 1.3 63.0 + - - +
251B ARG* 3.0 8.3 + - - +
252B ALA* 3.2 17.4 + - + +
253B MET* 3.1 23.5 + - - +
310B TYR* 4.4 9.1 - - - +
313B VAL 5.2 1.0 + - - -
314B SER* 3.5 41.8 + - - -
53C GLU* 3.0 29.4 + - + +
54C THR* 4.8 14.7 + - - -
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Residues in contact with SER 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLN* 3.2 18.5 + - - -
248B ILE 2.9 7.4 + - - -
249B HIS* 1.3 77.7 - - - +
251B ARG* 1.3 55.2 + - - +
253B MET* 3.1 9.4 + - - +
254B LYS* 2.6 74.5 + - - +
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE 4.5 0.9 + - - +
249B HIS* 3.0 6.0 + - - +
250B SER* 1.3 85.9 + - - +
252B ALA* 1.3 57.9 + - - +
254B LYS* 3.3 14.5 + - - +
255B TRP* 2.7 48.8 + - + +
313B VAL* 4.5 22.9 + - + +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B HIS* 3.2 10.9 + - + +
250B SER 3.2 0.4 - - - -
251B ARG* 1.3 77.4 - - - +
253B MET* 1.3 56.1 + - - +
255B TRP* 2.8 2.3 + - - +
256B THR* 2.4 40.5 + - - -
310B TYR* 3.7 23.8 - - + +
313B VAL* 3.0 32.5 - - + -
314B SER* 3.7 13.7 - - - +
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 16.4 - - + -
104B VAL* 3.4 31.6 - - + -
105B SER* 3.9 24.2 - - - +
108B SER* 5.3 1.6 - - - +
247B GLN* 4.0 19.5 - - + +
249B HIS 3.1 10.8 + - - +
250B SER* 3.1 11.3 + - - +
252B ALA* 1.3 76.4 - - - +
254B LYS* 1.3 55.7 + - - +
256B THR* 3.7 7.4 - - - -
257B GLY* 2.8 32.4 + - - -
310B TYR* 3.8 18.1 - - + +
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B SER* 2.6 46.3 + - - +
251B ARG* 3.3 16.7 - - + +
253B MET* 1.3 73.3 - - - +
255B TRP* 1.3 64.2 + - + +
257B GLY* 4.1 0.7 - - - -
258B LEU* 3.2 22.7 + - - +
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Residues in contact with TRP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ARG* 2.7 38.1 + - + +
252B ALA* 2.8 10.5 + - - +
254B LYS* 1.3 71.8 - - + +
256B THR* 1.3 64.9 + - - +
258B LEU* 3.4 36.4 + - + +
259B THR* 3.2 26.2 + - + +
309B VAL* 4.3 7.0 - - + -
313B VAL* 3.8 34.2 - - + +
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Residues in contact with THR 256 (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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101B LEU* 4.1 17.5 - - + -
252B ALA 2.4 30.9 + - - -
253B MET* 3.7 11.0 - - - -
255B TRP* 1.3 68.9 - - - +
257B GLY* 1.3 52.8 + - - +
259B THR* 2.2 27.6 + - - -
260B LEU* 2.8 23.2 + - + +
306B CYS* 4.0 31.6 - - + +
309B VAL* 3.5 3.8 - - - +
310B TYR* 3.3 32.6 + - - +
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Residues in contact with GLY 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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253B MET 2.8 19.7 + - - -
254B LYS 4.1 0.9 - - - -
256B THR* 1.3 74.3 - - - +
258B LEU* 1.3 61.3 + - - +
260B LEU* 3.4 12.6 + - - +
261B ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 258 (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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254B LYS 3.2 15.1 + - - +
255B TRP* 3.5 40.4 - - + +
256B THR 3.2 0.6 - - - -
257B GLY* 1.3 74.8 - - - +
259B THR* 1.3 64.3 + - + +
261B ALA* 3.4 8.1 + - + +
262B ILE* 3.0 51.2 + - + +
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Residues in contact with THR 259 (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 TRP* 3.2 14.2 + - + +
256B THR* 2.2 33.1 + - - -
258B LEU* 1.3 73.9 - - + +
260B LEU* 1.3 57.4 + - - +
261B ALA 3.0 1.6 - - - -
262B ILE* 2.8 30.5 + - + +
263B LEU* 2.8 25.1 + - - +
305B ILE* 5.1 4.3 - - + -
306B CYS* 3.8 9.5 - - - -
309B VAL* 3.6 31.8 - - + +
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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
----------------------------------------------------------
256B THR* 2.8 22.6 + - + +
257B GLY* 3.7 11.2 - - - +
259B THR* 1.3 72.0 + - - +
261B ALA* 1.3 57.5 + - - +
263B LEU* 4.5 3.5 - - + +
264B LEU* 3.1 50.1 + - + +
302B ILE* 4.2 22.9 - - + -
306B CYS* 3.8 16.6 - - - -
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Residues in contact with ALA 261 (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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257B GLY 3.0 12.2 + - - +
258B LEU* 3.5 13.5 - - + +
259B THR 3.0 0.4 - - - -
260B LEU* 1.3 77.4 - - - +
262B ILE* 1.3 60.6 + - + +
264B LEU* 3.1 5.6 + - - +
265B ALA* 2.9 33.3 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.0 39.4 + - + +
259B THR* 2.8 17.7 + - + +
261B ALA* 1.3 72.3 - - + +
263B LEU* 1.3 63.4 + - + +
265B ALA* 4.0 5.2 + - - +
266B GLY* 3.3 16.5 + - - -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B THR* 2.8 19.5 + - - +
260B LEU* 4.5 3.4 - - - +
262B ILE* 1.3 80.2 - - + +
264B LEU* 1.3 53.9 + - + +
266B GLY* 3.0 3.8 + - - -
267B LEU* 2.6 36.3 + - - +
302B ILE* 4.3 32.1 - - + +
305B ILE* 3.7 48.7 - - + -
306B CYS* 4.7 10.1 - - - -
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Residues in contact with LEU 264 (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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260B LEU* 3.1 40.7 + - + +
261B ALA* 3.1 6.3 + - - +
263B LEU* 1.3 79.0 - - + +
265B ALA* 1.3 61.2 + - - +
267B LEU* 3.4 17.1 + - + +
268B ALA* 3.1 23.7 + - - +
302B ILE* 3.8 28.9 - - + -
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ALA 2.9 19.9 + - - +
262B ILE* 4.2 5.4 - - - +
264B LEU* 1.3 72.7 - - - +
266B GLY* 1.3 58.8 + - - +
268B ALA* 3.6 5.0 + - - +
269B LEU* 3.1 39.0 + - + +
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Residues in contact with GLY 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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262B ILE 3.3 10.8 + - - -
263B LEU* 3.0 8.1 + - - -
265B ALA* 1.3 76.7 - - - +
267B LEU* 1.3 66.3 + - - +
269B LEU* 3.4 19.9 + - - +
270B LEU* 3.4 17.5 + - - +
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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
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70A PHE* 5.6 3.8 - - + -
263B LEU 2.6 19.3 + - - +
264B LEU* 3.6 24.2 - - + +
265B ALA 3.3 0.2 - - - -
266B GLY* 1.3 72.9 - - - +
268B ALA* 1.3 57.8 + - - +
270B LEU* 2.9 33.1 + - + +
271B VAL* 3.2 13.7 + - + +
278B LEU* 6.0 1.8 - - + -
291B PHE* 4.0 29.6 - - + -
295B LEU* 6.1 0.7 - - + -
298B ILE* 3.8 39.3 - - + -
302B ILE* 4.3 7.4 - - + -
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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
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264B LEU 3.1 13.6 + - - +
265B ALA* 3.9 6.5 - - - +
267B LEU* 1.3 78.7 - - - +
269B LEU* 1.3 59.4 + - + +
271B VAL* 3.6 10.8 - - + -
272B LEU* 3.0 47.8 + - + +
273B PRO* 3.3 5.4 - - - +
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Residues in contact with LEU 269 (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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265B ALA* 3.1 29.9 + - + +
266B GLY* 3.4 16.2 - - - +
267B LEU 3.1 0.4 - - - -
268B ALA* 1.3 77.1 - - + +
270B LEU* 1.3 61.6 + - + +
273B PRO* 3.5 27.9 - - + +
276B ALA* 4.5 1.9 - - - +
277B PRO* 4.7 2.9 - - - +
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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
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66A LEU* 3.7 25.4 - - + -
70A PHE* 3.8 34.3 - - + -
266B GLY 3.5 16.6 - - - +
267B LEU* 2.9 15.3 + - + +
269B LEU* 1.3 79.6 - - + +
271B VAL* 1.3 57.8 + - - +
276B ALA* 3.1 10.0 - - - +
277B PRO* 3.4 23.9 - - + +
278B LEU* 2.9 46.3 + - + +
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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
----------------------------------------------------------
267B LEU* 3.2 18.2 - - + +
268B ALA* 3.3 11.9 + - + -
269B LEU 3.4 0.2 - - - -
270B LEU* 1.3 78.3 - - - +
272B LEU* 1.3 77.3 + - + +
273B PRO 3.5 2.2 - - - -
276B ALA* 3.1 12.5 - - - +
278B LEU* 4.5 4.3 - - + +
279B ARG* 2.7 32.4 + - + +
286B VAL* 4.1 22.0 - - + -
291B PHE* 3.7 46.7 - - + -
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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
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268B ALA* 3.0 37.0 + - + +
271B VAL* 1.3 83.4 - - + +
273B PRO* 1.3 68.8 - - + +
274B ASN* 5.2 0.7 - - - +
279B ARG* 3.4 10.4 + - - +
286B VAL* 5.6 2.7 - - + -
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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