Contacts of the helix formed by residues 250 - 268 (chain B) in PDB entry 3SF4
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 GLU 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY* 3.5 23.6 - - - +
163A PHE* 3.7 19.1 + - - +
212B ARG* 2.7 45.7 + - - -
245B TYR* 3.0 36.9 + - + +
248B LEU* 3.9 13.3 - - - +
249B GLY* 1.3 77.9 - - - +
251B PHE* 1.3 58.6 + - - +
252B GLU* 3.4 2.7 - - - +
253B THR* 3.5 7.0 + - - +
254B ALA* 3.0 26.3 + - - +
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Residues in contact with PHE 251 (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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246B ILE* 3.5 40.2 - - + -
249B GLY* 3.3 21.6 + - - -
250B GLU* 1.3 70.4 - - - +
252B GLU* 1.3 68.7 + - - +
254B ALA* 4.2 4.5 - - - -
255B SER* 2.9 21.8 + - - -
284B THR* 3.5 12.5 - - + +
287B LEU* 3.6 45.8 - - + -
288B LEU* 3.6 27.1 - - + -
20E LEU* 3.8 29.4 - - + -
32E MET* 5.2 0.9 - - + -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLY* 4.6 22.4 - - - +
250B GLU* 3.4 0.8 - - - +
251B PHE* 1.3 75.6 - - - +
253B THR* 1.3 63.4 - - - +
255B SER* 2.6 28.2 + - - -
256B GLU* 3.3 33.1 + - + +
259B LYS* 5.6 0.5 + - - -
285B TYR* 5.3 3.6 + - - -
288B LEU* 4.1 21.7 - - + +
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Residues in contact with THR 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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161A GLY 4.2 1.7 + - - -
162A GLU* 4.1 26.2 + - + +
163A PHE 5.1 0.2 + - - -
245B TYR* 3.5 43.9 - - + -
250B GLU* 3.5 16.2 + - - +
251B PHE 3.2 0.4 - - - -
252B GLU* 1.3 79.3 - - - +
254B ALA* 1.3 63.5 + - - +
256B GLU* 3.1 24.2 + - + +
257B TYR* 3.3 16.0 + - + -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLY* 3.4 28.6 - - - +
245B TYR* 3.8 10.0 - - + +
246B ILE* 3.8 23.8 - - + +
250B GLU 3.0 17.1 + - - +
251B PHE 3.2 4.7 + - - +
253B THR* 1.3 75.7 - - - +
255B SER* 1.3 56.9 + - - +
257B TYR* 3.0 5.0 + - - +
258B TYR* 2.9 34.4 + - + -
284B THR* 4.6 0.4 - - + -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE 2.9 12.3 + - - -
252B GLU* 2.6 30.0 + - - -
254B ALA* 1.3 76.6 - - - +
256B GLU* 1.3 63.5 + - - +
258B TYR* 4.3 1.3 - - - -
259B LYS* 2.9 34.9 + - - +
281B LEU* 3.6 13.4 - - - +
284B THR* 3.9 16.0 - - - +
285B TYR* 3.9 27.4 + - - -
288B LEU* 4.5 1.5 - - - +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLU* 3.5 31.1 - - + +
253B THR* 3.1 14.4 + - + +
255B SER* 1.3 80.3 + - - +
257B TYR* 1.3 67.5 + - + +
259B LYS* 3.5 25.8 + - - +
260B LYS* 3.2 37.8 + - - +
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Residues in contact with TYR 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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219B GLU* 4.5 13.0 + - - +
222B LEU* 4.9 4.8 - - + +
238B TYR* 3.4 40.2 - + - +
241B LEU* 3.7 30.5 - - + +
242B GLY 3.8 6.7 - - - +
245B TYR* 3.4 38.9 + + - -
253B THR* 3.3 27.7 + - + -
254B ALA 3.0 7.6 + - - +
256B GLU* 1.3 80.1 - - + +
258B TYR* 1.3 64.5 + - - +
260B LYS* 3.2 21.8 + - + +
261B THR* 3.0 28.2 + - - +
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Residues in contact with TYR 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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239B SER* 4.1 13.2 - - - -
242B GLY* 3.4 18.4 + - - -
243B ASN* 2.5 40.0 + - - -
246B ILE* 3.5 16.7 - - + +
254B ALA* 2.9 24.3 + - + +
255B SER* 4.3 2.0 - - - -
256B GLU 3.4 0.2 - - - -
257B TYR* 1.3 77.6 - - - +
259B LYS* 1.3 57.6 + - - +
261B THR* 2.8 25.4 + - - +
262B LEU* 2.9 16.1 + - - +
277B SER* 4.2 5.9 - - - +
280B SER* 3.9 31.4 - - - -
281B LEU* 3.5 23.3 - - + -
284B THR* 3.3 27.8 - - - -
31E TRP* 3.9 8.2 - + - -
35E LEU* 4.0 0.5 - - - +
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Residues in contact with LYS 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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252B GLU* 5.6 0.6 + - - -
255B SER 2.9 22.6 + - - +
256B GLU* 3.6 28.9 + - - +
258B TYR* 1.3 77.9 - - - +
260B LYS* 1.3 55.5 - - + +
262B LEU* 3.2 11.8 - - + +
263B LEU* 3.0 34.7 + - + +
281B LEU* 4.2 13.5 - - + -
285B TYR* 3.0 29.5 + - - -
293B LYS* 4.8 8.7 - - - +
297B TYR* 3.8 17.9 - - - +
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 3.7 43.5 + - + +
256B GLU* 3.2 24.8 + - - +
257B TYR* 3.6 25.8 + - + +
258B TYR 3.2 0.4 - - - -
259B LYS* 1.3 75.3 - - + +
261B THR* 1.3 65.7 + - - +
262B LEU 3.0 1.6 - - - -
263B LEU* 3.4 12.1 + - + +
264B LEU* 3.0 24.8 + - - +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 4.0 13.2 - - - +
238B TYR* 3.0 34.3 - - + -
239B SER* 3.2 32.0 + - - +
257B TYR 3.0 11.7 + - - +
258B TYR* 2.8 23.7 + - + -
260B LYS* 1.3 75.9 - - - +
262B LEU* 1.3 51.5 + - - +
264B LEU* 3.9 3.4 - - - +
265B ALA* 2.8 37.1 + - - +
277B SER* 3.0 17.9 + - - -
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Residues in contact with LEU 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 TYR 2.9 14.1 + - - +
259B LYS* 3.2 13.0 - - + +
260B LYS 3.0 0.2 - - - -
261B THR* 1.3 74.2 + - - +
263B LEU* 1.3 68.2 + - + +
265B ALA* 3.1 4.2 + - - +
266B ARG* 3.0 57.5 + - - +
274B GLU* 3.7 39.0 - - + +
277B SER* 3.9 10.8 - - - -
278B CYS* 3.9 7.9 - - - -
281B LEU* 3.9 20.2 - - + -
297B TYR* 4.1 13.5 - - + +
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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
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259B LYS* 3.0 20.0 + - + +
260B LYS* 3.4 11.6 + - + +
262B LEU* 1.3 82.8 - - + +
264B LEU* 1.3 61.8 + - - +
266B ARG* 3.4 23.6 + - - +
267B GLN* 3.2 34.0 + - - +
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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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231B LYS* 3.6 50.7 - - + +
234B GLU* 3.9 19.5 - - + +
235B ARG* 3.6 28.0 - - + +
238B TYR* 4.3 6.5 - - + -
260B LYS 3.0 17.6 + - - +
261B THR 3.9 3.4 - - - +
263B LEU* 1.3 76.6 - - - +
265B ALA* 1.3 64.6 + - - +
266B ARG 3.1 0.2 - - - -
267B GLN* 3.4 25.4 + - - +
268B LEU* 3.0 30.4 + - + +
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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
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235B ARG* 4.9 4.0 - - - -
261B THR 2.8 23.9 + - - +
262B LEU* 3.1 5.6 + - - +
264B LEU* 1.3 72.5 - - - +
266B ARG* 1.3 58.9 + - - +
268B LEU* 3.7 4.9 + - - -
269B LYS 3.3 1.7 + - - -
270B ASP* 2.8 36.8 + - - +
273B VAL* 3.8 17.7 - - + +
274B GLU* 3.7 31.9 - - - +
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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
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262B LEU* 3.0 49.8 + - - +
263B LEU* 3.6 22.0 - - - +
265B ALA* 1.3 74.5 - - - +
267B GLN* 1.3 57.8 + - + +
269B LYS* 2.6 27.9 + - - +
270B ASP 4.9 0.2 - - - +
271B ARG* 5.8 0.7 - - - +
274B GLU* 2.7 38.4 + - - +
278B CYS* 4.5 1.6 - - - -
300B LYS* 4.1 24.5 - - - +
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Residues in contact with GLN 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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231B LYS* 4.5 9.9 - - - +
263B LEU* 3.2 20.4 + - - +
264B LEU* 3.4 28.9 + - + +
266B ARG* 1.3 76.6 - - + +
268B LEU* 1.3 57.3 + - + +
269B LYS* 2.7 14.6 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS* 3.6 50.0 - - + +
232B ALA* 4.6 6.3 - - + +
235B ARG* 4.6 11.7 - - + +
264B LEU* 3.0 28.7 + - + +
265B ALA* 3.9 5.8 - - - +
267B GLN* 1.3 76.3 - - + +
269B LYS* 1.3 69.6 + - - +
270B ASP* 3.1 12.5 + - + +
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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