Contacts of the helix formed by residues 251 - 270 (chain B) in PDB entry 3IEU
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 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B ILE* 3.4 27.0 - - - +
248B GLY 3.0 6.5 + - - -
249B ASN 2.9 1.4 + - - -
250B LYS* 1.3 76.1 - - - +
252B ALA* 1.3 61.9 + - - +
253B LYS 3.3 2.9 - - - -
254B ILE* 3.4 7.1 - - - +
255B LYS* 3.2 24.7 + - - +
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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
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249B ASN* 3.2 13.9 + - - +
250B LYS* 3.2 15.5 - - + -
251B GLY* 1.3 76.5 - - - +
253B LYS* 1.3 60.7 + - - +
255B LYS* 3.5 10.8 - - + +
256B THR* 2.9 35.9 + - - +
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Residues in contact with LYS 253 (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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205B PHE* 3.8 32.5 + - + +
206B LEU* 4.2 12.3 - - + -
209B GLU* 4.2 17.0 + - - -
245B MET 4.0 10.3 - - - +
246B VAL 3.4 12.6 - - - +
247B ILE 3.2 11.7 + - - +
248B GLY* 3.6 12.6 - - - -
249B ASN 4.6 1.1 + - - +
252B ALA* 1.3 80.3 - - - +
254B ILE* 1.3 58.0 + - - +
256B THR* 3.7 3.8 - - - -
257B ILE* 3.1 36.2 + - + +
306B SO4 5.4 4.4 + - - -
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Residues in contact with ILE 254 (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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235B ILE* 4.0 18.6 - - + -
246B VAL* 3.3 16.5 + - + +
247B ILE* 3.2 25.0 + - + +
251B GLY* 3.4 13.9 - - - +
253B LYS* 1.3 76.5 - - - +
255B LYS* 1.3 66.7 + - - +
257B ILE* 3.9 7.9 - - + -
258B GLY* 3.2 16.8 + - - -
277B LEU* 3.9 37.6 - - + +
279B VAL* 4.1 18.8 - - + -
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Residues in contact with LYS 255 (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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251B GLY 3.2 21.0 + - - +
252B ALA* 3.5 11.7 - - + +
253B LYS 3.1 0.2 - - - -
254B ILE* 1.3 81.2 - - - +
256B THR* 1.3 59.3 + - - +
258B GLY* 3.4 1.4 + - - -
259B ILE* 3.0 47.9 + - + +
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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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205B PHE* 3.5 39.5 - - + -
252B ALA* 2.9 18.9 + - - +
253B LYS* 3.7 5.4 - - - -
255B LYS* 1.3 75.2 - - - +
257B ILE* 1.3 65.6 + - - +
259B ILE* 3.0 12.1 + - + +
260B GLU* 2.8 29.5 + - + +
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Residues in contact with ILE 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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198B ILE* 5.0 3.6 - - + +
201B LYS* 4.1 19.3 - - + +
202B LEU* 3.5 37.0 - - + +
205B PHE* 4.1 30.1 - - + -
206B LEU* 4.7 5.6 - - + -
235B ILE* 5.0 1.3 - - + -
246B VAL* 4.7 4.5 - - + +
253B LYS* 3.1 29.3 + - + +
254B ILE* 4.0 12.8 - - + +
255B LYS 3.4 0.2 - - - -
256B THR* 1.3 77.3 - - - +
258B GLY* 1.3 59.5 + - - +
260B GLU* 3.9 3.0 - - - +
261B ALA* 3.0 30.9 + - + +
277B LEU* 3.9 16.4 - - + -
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Residues in contact with GLY 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 ILE 3.2 10.2 + - - -
255B LYS 3.7 3.8 - - - -
256B THR 3.2 0.6 - - - -
257B ILE* 1.3 78.0 - - - +
259B ILE* 1.3 64.4 + - - +
262B ARG* 2.9 28.1 + - - +
275B LEU* 3.7 9.2 - - - +
277B LEU* 3.6 20.4 - - - +
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Residues in contact with ILE 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 LYS* 3.0 44.2 + - + +
256B THR* 3.0 10.3 + - + +
258B GLY* 1.3 74.5 - - - +
260B GLU* 1.3 77.6 + - - +
262B ARG* 3.9 17.7 + - - +
263B LYS* 3.0 23.5 + - + +
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Residues in contact with GLU 260 (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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201B LYS* 3.7 28.1 - - + -
205B PHE* 3.7 26.9 - - + -
256B THR* 2.8 26.4 + - + +
259B ILE* 1.3 86.1 - - - +
261B ALA* 1.3 57.5 + - - +
263B LYS* 3.3 32.0 + - - +
264B ASP* 2.9 33.6 + - - +
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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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197B ILE* 3.8 17.9 - - + +
198B ILE* 4.5 11.0 - - + -
201B LYS* 4.3 10.8 - - + -
257B ILE* 3.0 20.9 + - + +
258B GLY* 4.6 0.2 - - - -
260B GLU* 1.3 75.2 - - - +
262B ARG* 1.3 61.1 + - - +
265B MET* 2.9 52.8 + - + +
275B LEU* 3.8 8.7 - - + -
277B LEU* 5.3 0.4 - - + -
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Residues in contact with ARG 262 (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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258B GLY 2.9 18.2 + - - +
259B ILE* 3.9 23.3 + - - +
261B ALA* 1.3 75.7 - - - +
263B LYS* 1.3 68.9 + - - +
265B MET* 3.5 6.5 - - - +
266B GLN* 3.1 43.2 + - - +
273B VAL* 3.3 32.2 + - + +
274B HIS* 4.9 0.7 - - - +
275B LEU* 3.6 28.6 - - + +
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Residues in contact with LYS 263 (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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259B ILE* 3.0 15.1 + - + +
260B GLU* 3.4 33.6 + - - +
261B ALA 3.1 0.2 - - - -
262B ARG* 1.3 77.5 - - - +
264B ASP* 1.3 80.1 + - - +
265B MET 2.8 5.1 + - - -
266B GLN* 2.9 21.7 + - - +
267B GLU* 3.1 21.7 + - + +
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.8 23.5 - - + +
200B GLU* 3.9 5.5 - - - +
201B LYS* 2.7 35.5 + - - -
260B GLU* 2.9 16.8 + - - +
263B LYS* 1.3 87.9 - - - +
265B MET* 1.3 56.6 + - - +
267B GLU* 3.7 12.7 + - - +
268B MET* 3.2 28.8 + - - +
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Residues in contact with MET 265 (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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194B ALA* 4.2 13.9 - - - +
197B ILE* 3.8 23.1 - - + -
198B ILE* 4.3 11.9 - - + -
231B ILE* 3.7 25.8 - - - -
261B ALA* 2.9 46.0 + - + +
262B ARG* 3.5 6.7 - - - +
263B LYS 2.8 1.2 + - - -
264B ASP* 1.3 75.9 - - - +
266B GLN* 1.3 59.8 + - - +
268B MET* 3.4 1.4 + - - -
269B PHE* 2.9 50.2 + - + -
273B VAL* 4.1 12.1 - - + -
275B LEU* 3.4 30.3 - - + -
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Residues in contact with GLN 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 ARG* 3.1 38.5 + - - +
263B LYS* 2.9 11.5 + - - +
265B MET* 1.3 75.4 - - - +
267B GLU* 1.3 53.7 + - - +
269B PHE* 4.9 0.2 - - - -
270B GLU* 2.7 35.9 + - - -
271B ALA 2.9 25.0 + - - +
272B PRO* 3.8 5.2 - - + +
273B VAL* 2.9 40.8 + - + +
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Residues in contact with GLU 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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263B LYS* 3.1 20.5 + - + +
264B ASP* 3.8 20.3 - - - +
266B GLN* 1.3 79.5 - - - +
268B MET* 1.3 61.4 + - - +
270B GLU* 3.5 19.3 + - - +
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Residues in contact with MET 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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193B MET* 3.6 46.9 - - + +
197B ILE* 4.6 10.8 - - + -
264B ASP 3.2 15.7 + - - +
265B MET 4.1 2.0 - - - +
266B GLN 3.4 0.2 - - - -
267B GLU* 1.3 79.8 - - - +
269B PHE* 1.3 75.7 + - + +
270B GLU* 3.7 7.2 + - - +
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Residues in contact with PHE 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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190B GLN* 3.5 54.7 - - + +
193B MET* 4.2 4.7 - - + -
194B ALA* 4.3 9.4 - - + -
197B ILE* 5.5 0.4 - - + -
221B PHE* 3.8 22.9 - + - -
229B TYR* 4.1 30.5 - + + -
231B ILE* 4.2 4.5 - - + -
265B MET* 2.9 37.3 + - + +
266B GLN* 4.3 2.0 - - - +
268B MET* 1.3 103.9 - - + +
270B GLU* 1.3 73.0 + - - +
271B ALA* 3.1 7.1 + - - +
273B VAL* 4.5 8.1 - - + -
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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
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266B GLN 2.7 11.9 + - - -
267B GLU* 3.8 14.7 - - - +
268B MET 3.3 7.3 - - - +
269B PHE* 1.3 78.4 - - - +
271B ALA* 1.3 57.8 + - - +
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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