Contacts of the helix formed by residues 257 - 273 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187N VAL* 2.9 18.5 + - - +
255N ILE* 4.5 0.2 - - - -
256N ASP* 1.3 77.2 + - - +
258N ILE* 1.3 80.8 + - - +
259N PHE* 2.9 14.8 + - - +
260N ARG* 3.1 42.9 + - + +
261N PHE 3.5 6.4 + - - -
309N ALA* 2.7 27.4 + - - +
310N VAL 3.9 2.4 + - - -
311N TYR* 3.6 25.8 + - - +
610N PO4 2.9 22.2 + - - -
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Residues in contact with ILE 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255N ILE* 4.3 18.8 + - + +
256N ASP* 4.3 2.2 - - - +
257N ASN* 1.3 79.8 + - - +
259N PHE* 1.3 60.5 + - + +
261N PHE* 3.0 38.9 + - + +
262N THR* 3.1 15.4 + - - +
289N MET* 4.9 1.6 - - - -
292N LEU* 4.1 9.0 - - + -
293N GLN* 3.9 22.0 - - - +
308N GLN* 4.2 18.4 - - + +
309N ALA 3.2 20.5 + - - +
310N VAL* 3.8 25.6 - - + -
325N THR* 4.1 22.4 - - + +
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Residues in contact with PHE 259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J THR* 5.4 11.2 - - + -
257N ASN* 2.9 5.6 + - - +
258N ILE* 1.3 80.7 - - + +
260N ARG* 1.3 59.3 + - + +
261N PHE 3.1 0.2 - - - -
262N THR* 3.1 8.5 + - - -
263N GLN* 2.7 64.4 + - + -
281N TYR* 3.6 18.4 - + - -
311N TYR* 3.6 57.4 - + + +
313N PRO* 3.5 28.9 - - + -
321N ALA* 3.7 17.9 - - + -
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Residues in contact with ARG 260 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J PHE* 5.0 4.0 - - + -
346J SER* 4.3 23.5 + - - +
187N VAL* 3.2 16.7 + - - +
188N GLY* 3.0 24.7 + - - -
189N GLU* 5.0 3.2 + - - +
190N ARG* 4.7 4.6 - - - +
222N MET* 3.6 26.5 - - - -
229N ARG* 4.7 6.1 + - - +
256N ASP* 3.9 3.0 + - - -
257N ASN* 3.1 39.5 + - + +
259N PHE* 1.3 80.9 - - + +
261N PHE* 1.3 58.4 + - - +
263N GLN* 4.3 20.0 - - - +
264N ALA* 3.2 26.1 + - - +
311N TYR* 6.1 2.8 - - - +
610N PO4 2.8 41.8 + - - -
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Residues in contact with PHE 261 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N VAL* 3.8 17.7 - - + +
229N ARG 4.4 0.7 - - - -
230N ALA* 3.2 31.5 - - + -
233N ALA* 3.7 22.2 - - + -
234N LEU* 5.4 5.4 - - + -
257N ASN 3.5 3.2 + - - +
258N ILE* 3.0 31.5 + - + +
260N ARG* 1.3 78.6 - - - +
262N THR* 1.3 64.7 + - - +
264N ALA* 3.6 3.9 + - - +
265N GLY* 3.0 24.3 + - - -
288N ASP* 3.8 28.7 - - + -
289N MET* 4.3 15.3 - - + -
292N LEU* 4.0 23.3 - - + -
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Residues in contact with THR 262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258N ILE* 3.1 12.6 + - - +
259N PHE* 3.1 16.3 + - - -
261N PHE* 1.3 79.2 - - - +
263N GLN* 1.3 65.7 + - - +
265N GLY* 3.0 13.6 + - - -
266N SER* 3.1 9.2 + - - -
281N TYR* 4.5 4.7 - - + -
282N GLN* 3.7 7.9 + - - +
285N LEU* 3.5 30.5 - - + -
289N MET* 3.4 26.2 - - + +
321N ALA* 4.4 21.5 + - + +
325N THR* 4.7 3.6 + - - -
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Residues in contact with GLN 263 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J PHE* 3.5 20.9 - - - -
339J TYR* 4.3 15.0 + - + +
342J THR* 5.7 3.3 - - - +
343J ASN* 3.1 25.1 - - - +
346J SER* 5.2 2.8 + - - -
229N ARG* 5.5 1.2 - - - +
259N PHE* 2.7 48.6 + - + +
260N ARG* 4.3 14.7 - - - +
262N THR* 1.3 73.8 - - - +
264N ALA* 1.3 57.2 + - - +
266N SER* 2.8 25.7 + - - -
267N GLU* 2.9 32.0 + - + +
281N TYR* 5.3 5.2 - - + -
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Residues in contact with ALA 264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226N PRO 4.2 4.7 - - - +
229N ARG* 4.0 17.7 - - + +
230N ALA* 4.0 26.9 - - + +
260N ARG 3.2 20.7 + - - +
261N PHE 3.7 5.2 - - - +
262N THR 3.2 0.2 - - - -
263N GLN* 1.3 78.2 - - - +
265N GLY* 1.3 56.9 + - - +
267N GLU* 2.9 27.8 + - - +
268N VAL* 2.9 20.1 + - - +
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Residues in contact with GLY 265 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230N ALA* 4.3 8.4 - - - +
261N PHE* 3.0 13.1 + - - -
262N THR* 3.0 10.3 + - - -
264N ALA* 1.3 76.8 - - - +
266N SER* 1.3 56.5 + - - +
268N VAL* 4.3 4.1 - - - +
269N SER* 3.4 23.4 + - - -
282N GLN* 3.6 18.7 - - - +
288N ASP* 4.9 7.4 - - - +
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Residues in contact with SER 266 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262N THR 3.1 6.0 + - - -
263N GLN* 2.8 17.1 + - - -
265N GLY* 1.3 78.4 - - - +
267N GLU* 1.3 63.4 + - - +
268N VAL 3.5 0.2 - - - -
269N SER* 4.0 1.5 - - - -
270N ALA* 3.2 22.9 + - - +
280N GLY 3.1 24.4 + - - -
281N TYR* 3.7 9.5 - - - -
282N GLN* 3.5 24.3 + - - +
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Residues in contact with GLU 267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298J GLY* 3.2 26.6 - - - +
301J PHE* 3.2 27.9 - - - +
302J TYR 4.3 2.1 + - - -
339J TYR* 4.3 12.8 - - - +
226N PRO* 3.7 19.8 - - + +
229N ARG* 2.7 34.5 + - - -
263N GLN* 2.9 33.8 + - + +
264N ALA* 2.9 5.6 + - - +
266N SER* 1.3 77.0 - - - +
268N VAL* 1.3 65.0 + - - +
270N ALA* 3.5 3.7 + - - +
271N LEU* 3.2 26.5 + - - +
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Residues in contact with VAL 268 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N ILE* 4.1 27.6 - - + -
226N PRO* 3.5 37.2 - - + +
227N GLY* 3.8 9.4 - - - +
230N ALA* 4.3 9.2 - - + -
231N ARG* 5.4 10.5 - - - +
264N ALA 2.9 14.6 + - - +
265N GLY* 4.6 4.5 - - - +
267N GLU* 1.3 74.3 - - - +
269N SER* 1.3 61.7 + - - +
271N LEU* 2.9 9.7 + - + +
272N LEU* 2.8 40.0 + - + +
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Residues in contact with SER 269 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265N GLY 3.4 19.8 + - - -
266N SER 4.0 2.2 - - - -
267N GLU 3.4 0.2 - - - -
268N VAL* 1.3 80.5 - - - +
270N ALA* 1.3 63.1 + - - +
272N LEU* 3.3 9.8 + - - +
273N GLY 3.2 16.6 + - - -
274N ARG* 3.2 43.4 + - - +
282N GLN* 3.4 23.9 - - - +
283N PRO* 3.6 6.1 - - - +
284N THR* 5.4 0.7 - - - -
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Residues in contact with ALA 270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J PRO* 3.0 29.2 - - - +
291J PRO 4.9 4.1 - - - +
292J GLY* 4.6 19.1 - - - +
298J GLY* 4.1 17.0 - - - +
266N SER 3.2 17.3 + - - +
267N GLU* 3.7 5.8 - - - +
268N VAL 3.2 0.4 - - - -
269N SER* 1.3 77.7 - - - +
271N LEU* 1.3 60.8 + - - +
273N GLY* 3.5 4.7 + - - -
274N ARG 4.7 7.5 - - - +
276N PRO* 6.2 1.8 - - + -
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Residues in contact with LEU 271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289J ARG* 6.4 3.4 - - + -
290J PRO* 3.7 18.9 - - + +
297J PRO* 5.9 0.7 - - + -
298J GLY* 4.1 11.2 - - - +
299J ASP* 4.2 29.6 - - + +
17N ILE 5.6 0.9 - - - +
19N ALA* 4.3 17.7 - - + +
20N ILE* 3.6 35.7 - - + +
60N ARG* 5.7 1.4 + - - -
62N ILE* 5.5 5.6 - - + -
226N PRO* 3.8 28.3 - - + -
267N GLU 3.2 18.1 + - - +
268N VAL* 2.9 10.1 + - + +
270N ALA* 1.3 76.6 - - - +
272N LEU* 1.3 64.9 + - - +
273N GLY 3.2 0.7 + - - -
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Residues in contact with LEU 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J PRO* 5.1 0.7 - - - +
20N ILE* 5.1 2.9 - - + -
51N ALA* 4.2 22.7 - - + -
52N GLN* 4.4 18.6 + - - +
60N ARG* 4.5 33.3 + - + +
62N ILE* 3.7 23.3 - - + +
268N VAL* 2.8 33.4 + - + +
269N SER* 3.3 9.8 + - - +
271N LEU* 1.3 74.9 - - - +
273N GLY* 1.3 58.5 + - - +
274N ARG* 3.7 39.7 - - + +
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Residues in contact with GLY 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J PRO* 4.1 15.9 - - - -
38K ASP* 5.5 1.5 - - - +
288K ARG* 2.8 32.0 + - - -
269N SER 3.2 2.0 + - - -
270N ALA 3.5 8.5 + - - -
271N LEU 3.1 3.0 - - - -
272N LEU* 1.3 80.3 - - - +
274N ARG* 1.3 66.4 + - - +
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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
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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