Contacts of the helix formed by residues 257 - 272 (chain W) in PDB entry 3FKS
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 ASN 257 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187W VAL* 3.0 25.8 + - - +
188W GLY 5.0 0.8 - - - -
189W GLU* 4.2 2.8 + - - +
256W ASP* 1.3 85.2 + - - +
258W ILE* 1.3 66.8 + - - +
259W PHE* 2.7 34.6 + - - +
260W ARG* 3.2 33.2 + - - +
261W PHE 3.6 3.1 + - - -
309W ALA* 3.5 9.0 - - - +
310W VAL 3.9 6.5 - - - +
311W TYR* 3.4 36.1 + - - +
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Residues in contact with ILE 258 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255W ILE* 4.1 18.6 - - + -
256W ASP* 4.0 2.8 - - - +
257W ASN* 1.3 75.9 + - - +
259W PHE* 1.3 66.9 + - - +
261W PHE* 3.2 23.5 + - + +
262W THR* 3.5 5.2 + - - -
289W MET* 4.2 31.0 - - + -
292W LEU* 5.0 5.4 - - + -
293W GLN* 4.3 2.7 - - - +
308W GLN* 3.5 32.1 - - + +
309W ALA 3.2 24.2 + - - +
310W VAL* 3.8 21.3 - - + -
325W THR* 4.0 15.5 - - + +
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Residues in contact with PHE 259 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257W ASN* 2.7 20.3 + - - +
258W ILE* 1.3 76.2 - - + +
260W ARG* 1.3 73.1 + - - +
262W THR* 2.9 10.0 + - - -
263W GLN* 2.8 56.7 + - + -
281W TYR* 4.1 10.3 - + - -
310W VAL* 5.6 0.7 - - + -
311W TYR* 3.3 55.9 - + + +
313W PRO* 3.8 19.3 - - + -
321W ALA* 3.9 24.0 - - + -
325W THR* 5.8 1.6 - - - -
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Residues in contact with ARG 260 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301S PHE* 4.2 18.6 - - + -
346S SER* 3.8 35.9 + - - -
187W VAL* 3.1 23.8 + - + +
188W GLY* 3.3 37.7 + - - -
189W GLU* 5.4 3.0 + - - +
190W ARG* 5.0 12.3 - - - +
222W MET* 5.1 3.1 - - - +
229W ARG* 5.1 6.2 - - - +
257W ASN* 3.2 20.8 + - - +
258W ILE 3.2 0.8 - - - -
259W PHE* 1.3 87.4 - - - +
261W PHE* 1.3 63.0 + - - +
263W GLN* 3.2 29.5 + - - +
264W ALA* 3.1 25.8 + - - +
311W TYR* 6.2 2.7 - - - +
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Residues in contact with PHE 261 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187W VAL* 3.7 17.6 - - + +
229W ARG 4.5 7.4 - - - -
230W ALA* 3.9 22.9 - - - -
233W ALA* 3.7 23.1 - - + -
234W LEU* 5.4 6.1 - - + -
255W ILE* 5.4 0.4 - - + -
257W ASN 3.6 3.0 + - - -
258W ILE* 3.2 26.4 + - + +
260W ARG* 1.3 80.3 - - - +
262W THR* 1.3 64.7 + - - +
264W ALA* 4.1 1.7 - - - +
265W GLY* 3.1 24.5 + - - -
288W ASP* 3.9 30.1 - - + -
289W MET* 4.5 13.2 - - + -
292W LEU* 3.7 33.4 - - + -
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Residues in contact with THR 262 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258W ILE 3.5 10.9 + - - -
259W PHE* 2.9 16.3 + - - -
261W PHE* 1.3 80.6 - - - +
263W GLN* 1.3 66.0 + - - +
265W GLY* 2.9 13.6 + - - +
266W SER* 3.0 12.7 + - - -
281W TYR* 4.1 22.7 - - + -
282W GLN* 4.0 4.8 + - - +
285W LEU* 3.8 28.9 - - + -
289W MET* 3.7 20.2 - - + +
321W ALA* 4.4 11.5 + - + +
325W THR* 4.5 4.3 + - - -
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Residues in contact with GLN 263 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301S PHE* 3.6 39.4 - - - +
343S ASN* 4.7 7.1 + - - +
229W ARG* 4.8 1.8 - - - +
259W PHE* 2.8 40.7 + - + +
260W ARG* 3.2 37.2 - - - +
261W PHE 3.5 0.2 - - - -
262W THR* 1.3 74.7 - - - +
264W ALA* 1.3 62.2 + - - +
266W SER* 3.0 19.1 + - - -
267W GLU* 3.0 24.5 + - + +
281W TYR* 5.6 3.4 - - - -
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Residues in contact with ALA 264 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226W PRO* 4.0 10.5 - - + +
229W ARG* 3.8 44.3 - - + +
230W ALA* 4.1 6.7 - - - +
260W ARG 3.1 14.9 + - - +
261W PHE 4.1 2.2 - - - +
263W GLN* 1.3 78.7 - - - +
265W GLY* 1.3 64.3 + - - +
267W GLU* 2.9 6.7 + - - +
268W VAL* 2.9 29.1 + - - +
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Residues in contact with GLY 265 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230W ALA* 4.5 10.4 - - - +
261W PHE* 3.1 15.1 + - - -
262W THR 2.9 9.5 + - - -
264W ALA* 1.3 74.7 - - - +
266W SER* 1.3 58.8 + - - +
268W VAL* 4.2 3.9 - - - +
269W SER* 3.5 17.3 + - - -
282W GLN* 3.3 22.9 + - - +
288W ASP* 4.4 5.9 - - - +
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Residues in contact with SER 266 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262W THR 3.0 5.9 + - - -
263W GLN* 3.0 12.2 + - - -
264W ALA 2.9 1.0 - - - -
265W GLY* 1.3 76.3 - - - +
267W GLU* 1.3 58.9 + - - +
268W VAL 3.2 0.2 - - - -
269W SER* 3.1 3.3 + - - -
270W ALA* 2.8 31.8 + - - +
280W GLY 3.0 25.1 + - - -
281W TYR* 3.8 10.4 - - - -
282W GLN* 3.3 23.2 + - - -
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Residues in contact with GLU 267 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298S GLY* 3.3 22.6 - - - +
299S ASP* 3.3 20.4 - - + +
301S PHE* 3.5 22.8 - - - +
302S TYR* 3.9 4.3 - - - +
226W PRO* 3.5 22.3 - - + +
229W ARG* 2.8 27.2 + - - -
263W GLN* 3.0 24.9 + - + +
264W ALA* 2.9 7.5 + - - +
266W SER* 1.3 76.2 - - - +
268W VAL* 1.3 61.3 + - - +
270W ALA* 3.2 9.6 + - - +
271W LEU* 3.0 28.5 + - - +
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Residues in contact with VAL 268 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62W ILE* 4.3 21.0 - - + +
226W PRO* 3.8 32.1 - - + +
227W GLY* 3.9 8.1 - - - +
230W ALA* 3.9 12.8 - - + -
231W ARG* 5.8 5.8 - - - +
264W ALA 2.9 18.2 + - - +
265W GLY* 4.2 5.2 - - - +
267W GLU* 1.3 75.6 - - - +
269W SER* 1.3 62.9 + - - +
271W LEU* 3.2 9.4 + - + +
272W LEU* 3.0 39.7 + - + +
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Residues in contact with SER 269 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265W GLY 3.5 6.9 + - - -
266W SER 3.1 7.9 + - - -
268W VAL* 1.3 81.4 - - - +
270W ALA* 1.3 61.3 + - - +
272W LEU* 3.6 4.4 + - - +
273W GLY 3.5 2.9 + - - -
274W ARG* 3.1 63.1 + - - +
282W GLN* 3.6 31.2 - - - +
283W PRO* 3.7 4.7 - - - +
288W ASP* 6.0 0.2 - - - -
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Residues in contact with ALA 270 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S PRO* 3.6 24.3 - - - +
291S PRO 5.4 7.2 - - - +
292S GLY* 5.6 3.8 - - - -
298S GLY* 4.0 24.7 - - - +
266W SER* 2.8 15.9 + - - +
267W GLU* 3.4 9.4 - - - +
268W VAL 3.1 0.2 - - - -
269W SER* 1.3 78.0 - - - +
271W LEU* 1.3 61.6 + - - +
273W GLY* 3.3 9.5 + - - -
274W ARG 4.5 5.7 + - - +
276W PRO* 6.3 1.3 - - + -
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Residues in contact with LEU 271 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S ARG* 6.1 5.4 - - - +
290S PRO* 4.7 7.9 - - - +
297S PRO* 6.0 0.9 - - + -
298S GLY 5.2 4.5 - - - +
299S ASP* 3.9 33.2 - - + +
18W GLY* 6.5 0.4 - - - -
19W ALA* 4.1 27.4 - - + +
20W ILE* 3.5 27.4 - - + +
62W ILE* 6.2 1.3 - - + -
226W PRO* 4.6 20.0 - - + -
267W GLU 3.0 19.3 + - - +
268W VAL* 3.2 9.2 + - + +
270W ALA* 1.3 73.4 - - - +
272W LEU* 1.3 62.5 + - - +
273W GLY* 3.0 7.4 + - - -
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Residues in contact with LEU 272 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288T ARG* 5.5 0.7 + - - -
20W ILE* 4.8 5.8 - - + +
51W ALA* 4.3 18.2 - - + -
52W GLN* 3.9 25.7 + - - +
60W ARG* 4.2 29.1 + - + +
62W ILE* 4.1 22.9 - - + -
268W VAL* 3.0 33.2 + - + +
269W SER* 3.8 6.7 - - - +
270W ALA 3.3 0.4 - - - -
271W LEU* 1.3 76.3 - - - +
273W GLY* 1.3 59.7 + - - +
274W ARG* 3.4 36.9 - - + +
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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