Contacts of the helix formed by residues 258 - 279 (chain B) in PDB entry 2FQ6
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 THR 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B HIS* 4.6 9.4 - - + -
254B ARG 4.8 1.7 + - - +
255B GLY* 3.5 7.1 + - - -
257B ARG* 1.3 82.0 - - + +
259B LEU* 1.3 64.4 + - - +
260B GLY 3.3 2.9 - - - -
261B VAL* 3.3 19.5 - - + +
262B ARG* 2.8 50.8 + - - +
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Residues in contact with LEU 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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10B LEU* 4.1 17.0 - - + -
190B ALA* 4.1 9.6 - - + +
192B VAL* 4.2 17.5 - - + -
211B TYR* 3.4 43.7 - - + +
212B LEU* 3.6 24.0 - - + -
255B GLY 3.4 3.5 + - - +
256B LEU* 3.0 19.9 + - + +
257B ARG 3.5 0.2 - - - -
258B THR* 1.3 77.7 - - - +
260B GLY* 1.3 57.7 + - - +
262B ARG* 3.5 14.8 - - - +
263B LEU* 2.9 45.8 + - + +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 5.8 3.4 - - - -
7B ASP* 3.9 13.7 - - - -
10B LEU* 3.4 21.3 - - - +
257B ARG 5.1 1.0 + - - -
258B THR 3.3 0.8 - - - -
259B LEU* 1.3 76.0 - - - +
261B VAL* 1.3 65.3 + - - +
263B LEU* 4.0 4.3 - - - +
264B ARG* 3.0 39.0 + - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 4.8 0.6 + - - -
258B THR* 3.3 30.7 - - + +
260B GLY* 1.3 75.4 - - - +
262B ARG* 1.3 67.6 + - + +
264B ARG* 3.5 23.8 - - - +
265B GLN* 3.4 21.7 + - - +
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.0 39.2 + - - -
212B LEU 3.5 5.9 + - - -
213B VAL 4.8 0.7 - - - -
214B GLY* 3.6 25.5 + - - -
215B HIS* 4.6 10.0 - - - -
255B GLY* 2.9 27.9 + - - -
258B THR* 2.8 35.2 + - - +
259B LEU* 3.5 20.9 - - - +
261B VAL* 1.3 78.2 - - + +
263B LEU* 1.3 61.3 + - - +
265B GLN* 3.0 5.5 + - - +
266B HIS* 2.8 42.0 + - - +
341B GLY 4.4 0.6 + - - -
342B GLY 6.1 0.4 - - - -
343B TYR* 6.0 0.4 - - - -
377B LEU* 4.3 27.8 - - + -
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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
----------------------------------------------------------
6B LEU* 6.1 1.6 - - + -
190B ALA* 4.4 4.9 - - + -
192B VAL* 4.0 22.7 - - + -
193B LEU* 4.2 21.3 - - + -
211B TYR* 4.0 26.2 - - + -
259B LEU* 2.9 41.7 + - + +
260B GLY* 4.0 4.7 - - - +
262B ARG* 1.3 77.2 - - - +
264B ARG* 1.3 54.1 + - + +
266B HIS* 3.7 4.2 - - + +
267B HIS* 2.8 36.1 + - - +
307B SER 3.7 4.9 - - - +
308B SER* 3.9 30.7 - - - -
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 6.3 0.8 - - - +
7B ASP* 2.9 41.1 + - - -
260B GLY* 3.0 24.3 + - - +
261B VAL* 3.5 35.2 - - - +
263B LEU* 1.3 75.7 - - + +
265B GLN* 1.3 58.9 + - - +
267B HIS* 3.5 6.6 - - - +
268B GLU* 2.9 31.2 + - - +
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL 3.4 11.0 + - - +
262B ARG 3.0 9.2 + - - +
264B ARG* 1.3 78.3 - - - +
266B HIS* 1.3 59.3 + - - +
268B GLU* 3.9 15.3 + - - +
269B SER* 2.9 49.9 + - - +
376B GLY 4.8 0.9 - - - +
377B LEU* 3.6 32.8 + - + -
378B GLU 4.4 12.3 + - - -
379B ASP* 5.9 0.4 - - - +
380B VAL* 5.7 1.2 - - - +
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Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.4 26.3 - + - -
262B ARG* 2.8 46.5 + - + +
263B LEU* 3.7 8.1 - - - +
265B GLN* 1.3 72.9 - - - +
267B HIS* 1.3 56.2 + - - +
269B SER* 4.9 0.9 - - - -
270B SER* 2.9 36.5 + - - +
308B SER* 4.0 2.9 - - - -
309B GLY* 3.7 18.3 - - - +
342B GLY 3.3 25.8 + - - -
374B HIS* 3.9 5.3 - + - -
375B ILE 2.9 26.2 + - - +
376B GLY* 3.9 8.2 + - - -
377B LEU* 3.7 22.1 - - + +
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU 2.8 17.6 + - - +
264B ARG* 3.5 8.3 - - - +
266B HIS* 1.3 70.9 - - - +
268B GLU* 1.3 70.0 + - - +
270B SER* 3.4 4.9 + - - -
271B LEU* 3.1 46.7 + - + +
290B ALA* 5.0 4.5 - - + -
300B TRP* 4.5 8.1 - + - -
306B GLY* 3.9 9.8 - - - -
307B SER* 3.1 53.8 + - - +
308B SER 4.1 1.1 - - - -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG 2.9 20.7 + - - +
265B GLN* 3.9 16.2 + - - +
267B HIS* 1.3 78.7 + - - +
269B SER* 1.3 64.8 + - - +
271B LEU* 3.9 3.8 - - - +
272B LYS* 3.2 21.4 + - + +
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN* 2.9 42.6 + - - -
266B HIS 4.4 0.2 - - - -
268B GLU* 1.3 73.2 + - - +
270B SER* 1.3 65.5 + - - +
272B LYS* 3.3 1.9 + - - -
273B VAL* 3.0 27.4 + - - +
375B ILE* 3.7 19.5 - - - -
376B GLY 4.6 5.1 + - - -
378B GLU 4.6 3.9 + - - -
380B VAL* 3.6 29.2 - - - +
383B LEU* 5.5 0.2 - - - -
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS 2.9 24.1 + - - -
267B HIS* 3.4 4.0 + - - -
269B SER* 1.3 77.4 - - - +
271B LEU* 1.3 59.4 + - - +
273B VAL* 3.3 2.4 + - - +
274B ALA* 3.0 29.8 + - - +
288B HIS* 3.0 24.4 - - - -
308B SER 3.2 8.8 + - - -
309B GLY* 3.8 17.9 - - - -
311B PHE* 3.8 5.0 - - - -
375B ILE* 3.9 22.8 - - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B HIS* 3.1 37.7 + - + +
268B GLU* 3.9 3.8 - - - +
270B SER* 1.3 80.0 + - - +
272B LYS* 1.3 58.0 + - - +
274B ALA* 3.2 3.1 + - + -
275B GLU* 2.9 58.3 + - - +
288B HIS* 4.2 7.2 - - + +
290B ALA* 4.3 25.1 - - + +
291B LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 272 (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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268B GLU* 3.2 14.4 + - + +
269B SER* 3.3 7.2 + - - +
271B LEU* 1.3 77.2 - - - +
273B VAL* 1.3 62.2 + - - +
275B GLU* 3.8 11.3 - - + +
276B TRP* 3.1 23.2 + - + +
380B VAL* 3.8 26.9 - - + +
381B ASP* 2.9 32.1 + - - -
384B ILE* 4.4 10.1 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER 3.0 22.6 + - - +
270B SER 3.8 4.0 - - - +
272B LYS* 1.3 75.9 - - - +
274B ALA* 1.3 52.2 + - - +
276B TRP* 3.3 4.2 + - + +
277B LEU* 2.7 46.5 + - + +
311B PHE* 3.9 8.3 - - + -
373B LEU* 4.1 3.8 - - + -
375B ILE* 4.1 20.0 - - + -
380B VAL* 3.7 18.8 - - + +
383B LEU* 4.9 5.6 - - + -
384B ILE* 3.9 16.8 - - + -
387B LEU* 3.5 30.3 - - + -
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Residues in contact with ALA 274 (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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270B SER 3.0 16.9 + - - +
271B LEU* 3.7 4.9 - - - +
273B VAL* 1.3 74.4 - - - +
275B GLU* 1.3 60.0 + - - +
277B LEU* 3.7 3.0 - - - +
278B ALA* 2.8 31.0 + - - +
286B VAL* 3.8 14.5 - - + +
288B HIS* 3.7 24.0 - - + +
291B LEU* 3.9 9.3 - - + +
311B PHE* 3.8 18.4 - - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 2.9 41.5 + - - +
272B LYS* 3.8 8.8 - - - +
274B ALA* 1.3 76.6 - - - +
276B TRP* 1.3 60.5 + - - +
278B ALA* 3.2 16.4 + - - +
279B GLU* 3.3 24.9 + - - +
291B LEU* 3.8 19.6 - - + +
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Residues in contact with TRP 276 (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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272B LYS* 3.1 18.1 + - + +
273B VAL 3.6 3.6 - - - +
275B GLU* 1.3 72.1 - - - +
277B LEU* 1.3 104.6 + - + +
279B GLU* 3.2 19.6 + - + +
280B HIS* 3.3 22.4 + - - +
384B ILE* 3.5 42.4 - - + +
387B LEU* 3.8 16.8 - - + -
388B ASP* 3.7 35.2 - - + -
391B PHE* 3.5 24.2 - + - -
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Residues in contact with LEU 277 (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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273B VAL* 2.7 30.0 + - + +
274B ALA 3.7 3.8 - - - +
276B TRP* 1.3 92.0 - - + +
278B ALA* 1.3 56.7 + - - +
280B HIS* 2.9 25.0 + - - +
283B VAL* 3.4 19.3 - - + +
286B VAL* 3.9 9.9 - - + -
311B PHE* 3.6 35.4 - - + -
313B PHE* 3.6 30.1 - - + -
373B LEU* 4.1 1.3 - - + -
387B LEU* 4.5 5.4 - - + -
391B PHE* 3.5 32.1 - - + -
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Residues in contact with ALA 278 (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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274B ALA 2.8 20.8 + - - +
275B GLU* 3.2 9.4 + - - +
277B LEU* 1.3 73.4 - - - +
279B GLU* 1.3 60.1 + - + +
280B HIS 3.3 2.7 + - - +
283B VAL* 4.9 4.8 - - - +
286B VAL* 3.6 16.1 - - + +
291B LEU* 4.2 12.8 - - + -
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Residues in contact with GLU 279 (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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275B GLU* 3.3 18.6 + - - +
276B TRP* 3.2 12.6 + - + +
277B LEU 3.1 0.8 - - - -
278B ALA* 1.3 76.4 - - + +
280B HIS* 1.3 62.0 + - - +
281B PRO* 3.7 6.1 - - - +
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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