Contacts of the helix formed by residues 266 - 280 (chain B) in PDB entry 2FYU
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B ALA* 3.7 8.8 - - - +
263B ALA* 2.8 24.7 + - - -
264B ILE 3.3 4.6 + - - -
265B GLY* 1.3 77.6 - - - +
267B ALA* 1.3 62.8 + - - +
268B GLU* 3.8 7.2 + - - +
269B ALA* 3.3 26.7 + - - +
270B ASN* 3.8 7.1 - - - +
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Residues in contact with ALA 267 (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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265B GLY 3.8 2.0 + - - -
266B SER* 1.3 71.8 - - - +
268B GLU* 1.3 60.3 + - - +
270B ASN* 3.2 29.8 + - - +
271B ALA* 3.4 5.9 + - - +
405B VAL* 4.8 2.8 - - - +
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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
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262B ALA* 3.7 19.7 - - + +
266B SER* 3.2 7.4 + - - +
267B ALA* 1.3 74.6 - - - +
269B ALA* 1.3 64.2 + - - +
271B ALA* 3.1 20.6 + - + +
272B PHE* 3.1 29.0 + - + -
413B ALA* 5.6 2.8 - - + -
416B LYS* 3.0 42.5 + - - +
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Residues in contact with ALA 269 (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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262B ALA* 3.5 8.4 - - + +
263B ALA 3.5 20.6 - - - +
264B ILE* 4.4 2.7 - - - -
265B GLY 4.5 0.4 - - - +
266B SER* 3.3 17.3 + - - +
268B GLU* 1.3 76.1 - - - +
270B ASN* 1.3 58.0 - - - +
272B PHE* 3.3 7.2 + - - +
273B SER* 3.0 30.7 + - - -
313B ASN* 4.8 0.7 - - - +
315B SER* 4.0 15.5 - - - +
7I ARG* 3.4 18.1 + - - +
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Residues in contact with ASN 270 (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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265B GLY 5.5 0.7 - - - +
266B SER 3.8 5.3 - - - +
267B ALA* 3.2 25.0 + - - +
269B ALA* 1.3 73.6 - - - +
271B ALA* 1.3 63.2 + - - +
273B SER* 3.4 3.4 + - - -
274B VAL* 3.1 28.6 + - - +
364B LEU* 4.7 1.0 - - - +
401B GLN* 4.3 31.1 + - - +
402B ILE* 5.0 6.6 - - + +
405B VAL* 3.7 18.4 - - + -
1I MET* 3.9 21.8 - - - +
7I ARG* 3.2 20.6 - - - +
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Residues in contact with ALA 271 (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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267B ALA 3.4 6.3 + - - +
268B GLU* 3.1 17.5 + - + +
270B ASN* 1.3 74.2 - - - +
272B PHE* 1.3 57.8 + - - +
274B VAL* 3.4 3.3 + - - +
275B LEU* 2.9 29.3 + - - +
405B VAL* 3.8 13.1 - - + +
409B ASP* 3.7 42.0 - - + +
410B VAL* 4.3 4.2 - - - +
413B ALA* 4.2 7.2 - - + +
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Residues in contact with PHE 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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260B GLU 4.8 1.3 - - - -
261B SER* 3.6 37.0 - - - +
262B ALA* 4.1 7.6 - - + +
268B GLU* 3.1 45.9 + - + -
269B ALA* 3.5 10.1 - - - +
270B ASN 3.3 0.2 - - - -
271B ALA* 1.3 75.3 - - - +
273B SER* 1.3 56.3 + - - +
275B LEU* 3.3 6.2 + - + +
276B GLN* 3.0 29.1 + - - +
313B ASN* 3.6 16.4 - - - +
322B PHE* 3.4 40.9 - + + -
413B ALA* 3.3 44.2 - - + -
416B LYS* 4.2 12.1 - - + -
417B PHE* 5.0 4.0 - - + -
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Residues in contact with SER 273 (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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269B ALA 3.0 8.4 + - - -
270B ASN 3.6 5.8 - - - -
271B ALA 3.4 0.2 - - - -
272B PHE* 1.3 73.1 - - - +
274B VAL* 1.3 62.0 + - - +
276B GLN* 3.4 12.3 + - - +
277B HIS* 3.1 26.2 + - - -
313B ASN* 3.5 12.9 + - - -
364B LEU* 3.8 24.5 - - - +
1I MET* 4.5 1.1 - - - -
7I ARG* 2.8 41.3 + - - +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASN 3.1 18.1 + - - +
271B ALA 3.8 4.5 - - - +
272B PHE 3.4 0.2 - - - -
273B SER* 1.3 71.7 - - - +
275B LEU* 1.3 60.8 + - - +
277B HIS* 3.0 7.4 + - - +
278B VAL* 3.0 27.4 + - + +
357B VAL* 4.0 17.5 - - + -
360B ALA* 3.7 12.4 - - + +
361B LYS* 4.0 24.7 - - + +
364B LEU* 3.8 18.4 - - + -
402B ILE* 4.6 3.6 - - + -
405B VAL* 4.3 14.8 - - + -
410B VAL* 3.7 24.2 - - + -
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Residues in contact with LEU 275 (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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271B ALA 2.9 17.0 + - - +
272B PHE* 3.3 7.2 + - + +
274B VAL* 1.3 77.4 - - - +
276B GLN* 1.3 55.2 + - - +
278B VAL* 3.4 6.1 + - + +
279B LEU* 3.0 42.6 + - + +
322B PHE* 3.6 33.9 - - + -
344B VAL* 5.3 0.4 - - + -
347B ILE* 3.9 15.9 - - + -
410B VAL* 3.9 21.5 - - + +
413B ALA* 3.8 10.1 - - + -
414B ALA* 3.5 46.7 - - + +
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Residues in contact with GLN 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 PHE 3.0 13.4 + - - +
273B SER* 3.4 17.9 + - - +
275B LEU* 1.3 73.6 - - - +
277B HIS* 1.3 77.4 + - - +
279B LEU 3.5 0.2 + - - -
280B GLY 2.7 37.8 + - - -
281B ALA* 4.4 14.2 - - + +
311B ALA* 3.5 24.2 - - + +
313B ASN* 3.4 21.4 + - + +
322B PHE* 3.7 14.4 - - + -
364B LEU* 4.9 1.8 - - - +
7I ARG 3.7 11.4 + - - +
8I SER* 3.0 26.4 - - - +
26I LEU* 5.3 0.5 - - - +
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Residues in contact with HIS 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 SER 3.1 18.3 + - - +
274B VAL 3.0 7.9 + - - +
276B GLN* 1.3 97.8 + - - +
278B VAL* 1.3 66.8 + - - +
280B GLY* 4.0 7.5 + - - +
281B ALA* 4.2 17.9 - - + +
284B HIS* 5.4 5.2 - + - -
292B THR 4.8 0.2 - - - +
360B ALA* 3.4 31.2 - - + +
363B LYS* 3.6 50.2 + - + +
364B LEU* 3.7 26.9 + - + +
367B GLY* 6.0 1.4 - - - -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.0 19.0 + - + +
275B LEU* 3.4 8.9 + - + +
277B HIS* 1.3 77.7 - - - +
279B LEU* 1.3 62.0 + - - +
280B GLY* 4.4 0.2 - - - -
292B THR 4.0 6.9 - - - +
294B SER* 3.4 21.8 + - - +
347B ILE* 4.0 22.0 - - + -
352B LEU* 3.6 28.0 - - + -
356B ASP* 4.5 14.8 - - + +
357B VAL* 4.6 5.6 - - - -
360B ALA* 3.5 15.0 - - + +
410B VAL* 4.0 21.5 - - + -
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Residues in contact with LEU 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 LEU* 3.0 28.4 + - + +
276B GLN 4.0 2.5 - - - +
278B VAL* 1.3 74.0 - - - +
280B GLY* 1.3 59.8 + - - +
293B SER* 3.2 2.6 + - - -
294B SER* 3.1 9.3 + - - -
295B LEU* 2.9 58.2 + - + +
311B ALA* 4.1 3.6 - - + -
322B PHE* 3.7 32.5 - - + -
323B GLY 5.2 1.8 - - - +
324B PHE* 6.3 0.2 - - + -
343B GLN* 4.3 6.1 - - + -
344B VAL* 3.8 35.2 - - + +
347B ILE* 3.7 26.2 - - + -
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Residues in contact with GLY 280 (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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276B GLN 2.7 14.9 + - - -
277B HIS 4.3 8.1 - - - -
278B VAL 3.4 1.4 - - - -
279B LEU* 1.3 75.9 - - - +
281B ALA* 1.3 61.3 + - - +
293B SER* 3.4 19.5 - - - -
295B LEU* 4.4 0.9 - - - +
309B VAL 4.8 0.4 - - - +
310B SER* 3.6 3.5 - - - -
311B ALA* 2.8 32.1 + - - +
363B LYS* 5.9 1.8 - - - -
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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
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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