Contacts of the helix formed by residues 257 - 273 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163V LYS* 5.1 4.6 - - - +
187V VAL* 2.7 33.5 + - - +
189V GLU* 3.7 10.4 + - - +
256V ASP* 1.3 83.4 + - - +
258V ILE* 1.3 80.0 + - - +
259V PHE* 2.9 14.5 + - - -
260V ARG* 3.3 27.2 + - + +
309V ALA* 2.7 18.5 + - - +
310V VAL 3.9 1.4 - - - -
311V TYR* 3.2 42.6 + - - +
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Residues in contact with ILE 258 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233V ALA* 5.9 0.2 - - + -
255V ILE* 3.9 22.4 - - + +
257V ASN* 1.3 75.8 + - - +
259V PHE* 1.3 66.6 + - - +
261V PHE* 3.1 28.0 + - + +
262V THR* 3.6 5.5 + - - -
289V MET* 4.5 14.1 - - + -
292V LEU* 3.7 29.6 - - + -
293V GLN* 3.9 8.3 - - - +
308V GLN* 3.6 25.6 - - + +
309V ALA 3.5 17.7 + - - +
310V VAL* 3.6 29.2 - - + -
325V THR* 4.2 8.5 - - + +
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Residues in contact with PHE 259 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342U THR* 5.8 4.5 - - + -
346U SER* 5.2 3.1 - - - -
257V ASN* 2.9 14.0 + - - +
258V ILE* 1.3 81.1 - - - +
260V ARG* 1.3 78.6 + - - +
262V THR* 3.2 15.8 + - - -
263V GLN* 3.2 40.9 + - + +
281V TYR* 3.7 7.4 - - - -
310V VAL* 4.8 3.4 - - + -
311V TYR* 3.6 52.5 - + + +
313V PRO* 3.3 30.1 - - + -
321V ALA* 3.6 26.9 - - + -
325V THR* 6.0 1.3 - - - -
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Residues in contact with ARG 260 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301U PHE* 4.0 16.3 - - - -
346U SER* 3.2 52.1 + - - +
187V VAL* 3.3 24.5 - - + +
188V GLY* 3.2 31.1 + - - +
189V GLU* 5.4 2.8 + - - +
190V ARG* 4.3 12.5 - - - +
222V MET* 3.9 20.9 - - - +
229V ARG* 4.6 7.8 + - + +
257V ASN* 3.5 18.9 - - + +
258V ILE 3.2 0.2 - - - -
259V PHE* 1.3 89.7 - - - +
261V PHE* 1.3 57.5 + - - +
263V GLN* 3.6 16.8 + - - +
264V ALA* 2.8 33.3 + - - +
311V TYR* 4.8 11.3 - - - -
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Residues in contact with PHE 261 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187V VAL* 4.0 14.5 - - + +
229V ARG 4.5 4.3 - - - -
230V ALA* 3.6 29.3 - - + +
231V ARG* 5.7 2.0 - - - -
233V ALA* 4.0 18.8 - - + -
234V LEU* 5.4 4.9 - - + -
257V ASN 3.8 1.2 + - - -
258V ILE* 3.1 23.4 + - + +
259V PHE 3.1 0.4 - - - -
260V ARG* 1.3 80.4 - - - +
262V THR* 1.3 68.9 + - - +
264V ALA* 3.5 1.9 + - - +
265V GLY* 2.9 26.2 + - - -
282V GLN* 6.1 0.9 - - - -
288V ASP* 3.8 37.2 - - + -
289V MET* 4.4 10.5 - - + -
292V LEU* 3.8 31.4 - - + -
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Residues in contact with THR 262 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258V ILE 3.8 7.1 + - - -
259V PHE* 3.2 9.2 + - - -
261V PHE* 1.3 82.9 - - + +
263V GLN* 1.3 57.2 + - - +
265V GLY 3.3 0.5 + - - -
266V SER* 2.9 24.6 + - - -
281V TYR* 3.6 27.3 - - + -
282V GLN* 3.3 24.4 + - - +
285V LEU* 4.2 14.6 - - + -
289V MET* 3.6 25.4 - - + +
321V ALA* 4.7 13.9 + - - +
325V THR* 5.0 0.9 + - - -
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Residues in contact with GLN 263 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301U PHE* 3.4 51.6 - - + +
339U TYR* 5.9 1.2 - - - -
343U ASN* 3.9 15.2 + - - +
346U SER* 5.1 0.2 + - - -
229V ARG* 4.6 5.8 + - - +
259V PHE* 3.2 42.9 + - + +
260V ARG* 3.6 16.1 + - - +
261V PHE 3.2 0.2 - - - -
262V THR* 1.3 73.6 - - - +
264V ALA* 1.3 59.7 + - - +
265V GLY 3.0 1.3 - - - -
266V SER* 3.0 9.0 + - - -
267V GLU* 2.8 33.2 + - + +
281V TYR* 5.6 3.4 - - - +
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Residues in contact with ALA 264 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226V PRO* 3.9 4.4 - - - +
229V ARG* 3.7 22.8 - - + +
230V ALA* 3.5 31.8 - - + +
260V ARG 2.8 21.0 + - - +
261V PHE 3.8 1.1 - - - +
263V GLN* 1.3 72.8 - - - +
265V GLY* 1.3 61.9 + - - +
267V GLU* 3.3 14.1 + - - +
268V VAL* 3.2 27.9 + - - +
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Residues in contact with GLY 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230V ALA* 4.1 6.5 - - - +
261V PHE* 2.9 17.2 + - - -
262V THR 3.5 4.9 - - - -
263V GLN 3.0 0.4 - - - -
264V ALA* 1.3 75.3 - - - +
266V SER* 1.3 65.4 + - - +
268V VAL* 3.1 24.2 - - - +
269V SER* 3.1 10.2 + - - -
274V ARG* 5.4 0.9 + - - -
282V GLN* 4.0 12.8 - - - +
288V ASP* 5.3 5.6 - - - +
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Residues in contact with SER 266 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262V THR 2.9 10.6 + - - -
263V GLN* 3.0 11.6 + - - -
265V GLY* 1.3 74.2 - - - +
267V GLU* 1.3 64.7 + - - +
269V SER* 3.3 12.6 - - - -
270V ALA* 3.4 9.2 + - - +
280V GLY 3.2 24.4 + - - +
281V TYR* 3.6 12.0 - - - -
282V GLN* 3.2 28.1 + - - -
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Residues in contact with GLU 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298U GLY* 3.5 27.2 - - - +
299U ASP* 4.0 0.2 - - - -
301U PHE* 3.5 12.6 - - + +
302U TYR* 3.4 28.6 + - - +
226V PRO* 3.3 19.3 - - + +
229V ARG* 2.9 40.9 + - - -
263V GLN* 2.8 19.0 + - + +
264V ALA* 3.4 9.0 - - - +
265V GLY 3.2 0.2 - - - -
266V SER* 1.3 76.2 - - - +
268V VAL* 1.3 63.4 + - - +
270V ALA* 3.0 17.3 + - - +
271V LEU* 3.2 16.3 + - + +
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Residues in contact with VAL 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62V ILE* 3.8 32.8 - - + -
226V PRO* 3.7 21.8 - - + +
227V GLY* 3.8 14.4 - - - +
230V ALA* 4.9 6.5 - - + -
264V ALA 3.2 13.0 + - - +
265V GLY* 3.1 21.1 - - - +
267V GLU* 1.3 75.7 - - - +
269V SER* 1.3 62.8 + - - +
271V LEU* 3.2 11.5 + - + +
272V LEU* 3.0 31.0 + - + +
274V ARG* 5.7 3.1 - - - +
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Residues in contact with SER 269 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265V GLY 3.1 9.0 + - - -
266V SER 3.3 11.7 - - - -
267V GLU 3.1 0.6 - - - -
268V VAL* 1.3 79.8 - - - +
270V ALA* 1.3 57.5 + - - +
272V LEU* 3.9 0.8 + - - -
273V GLY 3.5 1.6 + - - -
274V ARG* 2.9 71.1 + - - +
281V TYR 4.9 0.7 + - - -
282V GLN* 3.4 22.3 - - - +
283V PRO* 3.3 14.7 - - - +
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Residues in contact with ALA 270 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290U PRO* 3.2 32.1 - - + +
291U PRO 5.4 0.7 - - - +
292U GLY* 4.7 13.2 - - - -
298U GLY* 4.1 19.7 - - - -
266V SER 3.4 6.8 + - - +
267V GLU 3.0 10.3 + - - +
269V SER* 1.3 77.0 - - - +
271V LEU* 1.3 63.9 + - - +
272V LEU 3.1 2.0 - - - -
273V GLY* 3.2 11.1 + - - +
274V ARG 4.6 7.0 - - - -
276V PRO* 6.5 0.9 - - + -
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Residues in contact with LEU 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289U ARG* 6.0 5.4 - - - +
290U PRO* 4.7 10.6 - - + +
298U GLY* 5.0 4.7 - - - +
299U ASP* 4.3 33.7 - - + +
17V ILE 5.4 1.8 - - - +
18V GLY* 5.9 1.8 - - - -
19V ALA* 4.6 23.6 - - + +
20V ILE* 3.5 37.6 - - + +
60V ARG* 5.4 0.9 + - - -
62V ILE* 5.7 1.3 - - + -
226V PRO* 4.3 22.4 - - + -
267V GLU* 3.2 13.6 + - + +
268V VAL* 3.2 17.6 + - + +
270V ALA* 1.3 76.1 - - - +
272V LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 272 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S ASP* 5.1 2.2 - - - +
290U PRO* 5.2 0.4 - - - -
20V ILE* 4.0 9.2 - - + -
51V ALA* 4.1 17.5 - - + -
52V GLN* 5.0 14.3 + - - +
60V ARG* 3.2 43.7 + - + +
62V ILE* 3.7 36.3 - - + -
268V VAL* 3.0 25.0 + - + +
269V SER 4.1 3.8 - - - +
271V LEU* 1.3 80.6 - - - +
273V GLY* 1.3 57.5 + - - +
274V ARG* 3.8 32.3 - - + +
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Residues in contact with GLY 273 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288S ARG* 2.7 30.3 + - - -
290U PRO* 4.4 14.8 - - - -
269V SER 3.5 0.2 + - - -
270V ALA 3.2 12.8 + - - -
272V LEU* 1.3 79.5 - - - +
274V ARG* 1.3 65.1 + - - +
275V ILE* 3.5 2.6 + - - +
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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