Contacts of the helix formed by residues 264 - 284 (chain A) in PDB entry 2FK8
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 SER 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ILE* 3.3 15.8 + - - -
263A THR* 1.3 82.9 + - - +
265A GLU* 1.3 64.3 + - - +
266A GLU* 3.3 12.8 + - - +
267A VAL* 3.2 24.8 + - - +
268A TYR* 3.2 22.3 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ILE* 4.0 26.8 - - + +
264A SER* 1.3 74.7 - - - +
266A GLU* 1.3 56.8 + - - +
268A TYR* 3.4 1.1 + - - +
269A ASN* 2.9 45.7 + - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A HIS* 5.8 3.1 - - - +
264A SER* 3.3 11.7 - - - +
265A GLU* 1.3 80.4 - - - +
267A VAL* 1.3 58.5 + - + +
269A ASN* 3.8 5.7 - - - +
270A ARG* 2.8 52.7 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.9 24.2 - - + -
31A PHE* 3.8 16.6 - - + -
263A THR* 3.4 32.3 - - + +
264A SER* 3.2 14.6 + - - +
266A GLU* 1.3 72.0 - - + +
268A TYR* 1.3 67.4 + - - +
270A ARG* 3.3 21.3 + - - +
271A TYR* 3.0 36.2 + - + +
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.3 8.6 - - - -
252A LEU* 3.6 28.9 - - + +
253A GLN* 3.5 27.5 + - - +
256A LYS* 3.5 42.9 - - + +
259A ALA* 4.0 22.7 - - + -
260A ILE* 4.0 15.7 - - + -
264A SER 3.2 17.7 + - - +
265A GLU* 3.7 3.4 - - - +
266A GLU 3.3 0.2 - - - -
267A VAL* 1.3 78.6 - - - +
269A ASN* 1.3 76.9 + - - +
271A TYR* 3.4 2.1 + - - +
272A MET* 3.0 53.4 + - + +
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 6.0 0.4 - - - +
265A GLU* 2.9 30.8 + - - +
266A GLU* 3.9 4.8 - - - +
268A TYR* 1.3 94.3 - - - +
270A ARG* 1.3 66.2 + - - +
272A MET* 3.3 5.3 + - - +
273A LYS* 2.9 26.6 + - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A HIS* 4.5 14.6 + - - -
25A TYR* 3.6 29.8 - - - +
27A VAL* 5.8 2.0 - - - +
203A PHE* 3.5 15.3 - - + -
207A GLU* 3.0 49.0 + - - +
208A ILE* 3.6 15.3 - - + -
266A GLU* 2.8 44.9 + - - +
267A VAL* 3.5 31.8 - - - +
269A ASN* 1.3 77.1 - - - +
271A TYR* 1.3 66.4 + - + +
273A LYS* 3.5 2.0 + - - -
274A TYR* 3.2 21.8 + - - +
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR 4.7 4.7 + - - -
27A VAL* 4.2 17.3 - - + +
31A PHE* 3.5 18.6 - + + -
32A PHE* 4.1 21.9 - + - -
35A PHE* 4.3 11.0 - + - -
42A TYR* 3.5 23.6 + - - -
207A GLU 4.6 1.7 + - - -
208A ILE* 4.0 39.4 + - + +
252A LEU* 3.7 22.4 - - + -
267A VAL* 3.0 35.2 + - + +
268A TYR 4.1 0.2 - - - +
270A ARG* 1.3 86.4 - - + +
272A MET* 1.3 60.0 + - - +
274A TYR* 3.6 9.2 - + - +
275A LEU* 2.9 37.1 + - + +
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Residues in contact with MET 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLY* 3.8 25.1 - - - +
252A LEU* 3.9 22.2 - - + -
253A GLN* 3.8 22.2 - - + +
268A TYR* 3.0 49.4 + - + +
269A ASN* 3.3 6.5 + - - +
271A TYR* 1.3 72.5 - - - +
273A LYS* 1.3 61.4 + - - +
275A LEU* 4.6 1.6 - - + -
276A ARG* 2.9 71.0 + - + +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.5 12.3 - - + +
203A PHE* 3.7 47.4 - - + +
269A ASN 2.9 17.6 + - - +
270A ARG* 3.7 4.7 - - - +
272A MET* 1.3 78.3 - - - +
274A TYR* 1.3 57.2 + - - +
276A ARG* 5.0 1.8 - - - -
277A GLY* 2.8 29.0 + - - +
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 4.3 13.7 - + - -
178A SER* 5.8 0.7 + - - -
200A PHE* 3.7 2.0 - + - -
203A PHE* 3.8 8.7 - + + -
204A ILE* 3.8 30.6 - - + +
208A ILE* 3.7 38.6 - - + -
209A PHE* 3.4 22.9 - + - -
241A TYR* 4.7 10.7 + - - -
245A LEU* 4.8 5.8 - - + +
248A TRP* 5.4 2.5 - + - -
270A ARG 3.2 15.0 + - - +
271A TYR* 3.6 14.1 - + - +
272A MET 3.3 0.2 - - - -
273A LYS* 1.3 76.8 - - - +
275A LEU* 1.3 80.9 + - + +
278A CYS* 2.9 55.7 + - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.4 15.5 - - + -
245A LEU* 4.0 16.1 - - + +
248A TRP* 3.6 42.2 - - + +
249A GLY* 3.8 32.1 - - - +
252A LEU* 3.9 23.1 - - + -
271A TYR* 2.9 27.1 + - + +
272A MET* 4.2 4.0 - - - +
274A TYR* 1.3 95.3 - - + +
276A ARG* 1.3 58.7 + - - +
278A CYS* 3.9 1.6 - - - +
279A GLU* 3.1 28.6 + - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU 4.6 0.4 + - - -
246A ARG* 3.8 18.4 + - - +
249A GLY* 3.6 29.5 + - - -
250A ASP* 3.0 30.9 + - - +
253A GLN* 3.4 27.9 + - - +
272A MET* 2.9 39.7 + - + +
273A LYS* 4.6 1.8 - - - +
275A LEU* 1.3 76.3 - - - +
277A GLY* 1.3 57.9 + - - +
279A GLU* 3.4 16.3 + - - +
280A HIS* 3.0 28.0 + - - +
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.5 18.4 - - - -
273A LYS 2.8 24.4 + - - -
276A ARG* 1.3 71.3 - - - +
278A CYS* 1.3 64.5 + - - +
280A HIS* 3.2 6.6 + - - +
281A TYR* 3.0 32.5 + - - -
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Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.4 14.5 - - - -
204A ILE* 4.0 7.6 - - - -
245A LEU* 3.7 26.0 - - + -
274A TYR* 2.9 59.6 + - - +
277A GLY* 1.3 72.0 - - - +
279A GLU* 1.3 63.9 + - - +
280A HIS 3.2 0.2 + - - -
281A TYR* 3.2 1.3 + - - +
282A PHE* 2.9 36.8 + - + -
287A LEU* 4.6 9.0 - - - -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ILE* 3.7 33.2 - - + +
245A LEU* 3.7 12.6 - - + +
246A ARG* 2.6 67.8 + - - +
275A LEU 3.1 17.8 + - - +
276A ARG* 3.6 18.0 + - - +
277A GLY 3.3 0.2 - - - -
278A CYS* 1.3 75.6 - - - +
280A HIS* 1.3 52.8 + - - +
282A PHE* 3.9 2.9 - - - +
283A THR* 2.7 41.0 + - - +
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 5.1 2.4 - - - +
196A GLU* 4.2 7.5 + - - -
276A ARG 3.0 14.1 + - - +
277A GLY* 3.5 9.2 - - - +
278A CYS 3.1 0.2 - - - -
279A GLU* 1.3 77.6 - - - +
281A TYR* 1.3 90.4 + + - +
283A THR* 3.3 7.3 + - - -
284A ASP* 2.9 54.7 + - - +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.9 7.4 - - + -
196A GLU* 2.7 44.9 + - + +
197A THR* 3.7 30.5 - - + -
200A PHE* 3.5 44.8 - + + +
277A GLY* 3.0 29.6 + - - +
280A HIS* 1.3 91.2 - + - +
282A PHE* 1.3 64.1 + - - +
284A ASP* 3.6 3.0 - - + +
285A GLU 3.1 2.8 + - - -
286A MET* 2.9 38.9 + - + -
287A LEU* 3.4 26.1 + - + -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A SER* 4.0 11.0 - - - -
238A ARG* 3.4 37.5 - - + -
241A TYR* 3.5 33.7 - + + -
242A ILE* 3.7 19.4 - - + +
245A LEU* 3.8 15.5 - - + -
278A CYS* 2.9 33.7 + - + +
279A GLU* 3.9 1.8 - - - +
281A TYR* 1.3 75.6 - - - +
283A THR* 1.3 65.1 + - - +
285A GLU* 3.0 10.4 + - - -
287A LEU* 3.6 32.5 - - + -
288A ASP* 3.3 37.2 - - - -
289A CYS* 3.8 7.4 - - + -
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ILE* 3.7 27.4 - - + +
279A GLU* 2.7 28.3 + - - +
280A HIS* 3.4 8.2 - - - -
282A PHE* 1.3 77.3 - - - +
284A ASP* 1.3 62.2 + - - +
285A GLU* 3.4 10.9 + - - +
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG* 2.8 38.0 + - - +
193A LEU* 4.3 15.4 - - + +
280A HIS* 2.9 44.8 + - - +
281A TYR* 4.1 5.4 - - + +
282A PHE 3.2 0.2 - - - -
283A THR* 1.3 81.5 - - - +
285A GLU* 1.3 62.6 + - - +
286A MET* 3.2 12.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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