Contacts of the helix formed by residues 254 - 275 (chain B) in PDB entry 5F2R
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 GLY 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 4.0 13.0 - - - -
226B GLY 3.5 8.7 - - - -
227B GLY 3.1 13.8 + - - -
228B GLY 4.2 0.2 - - - -
229B THR 4.4 0.2 - - - -
253B LEU* 1.3 78.0 - - - +
255B GLY* 1.3 61.8 + - - -
256B GLU 3.2 0.4 - - - -
257B ASP* 2.9 28.8 + - - +
258B PHE* 3.5 15.8 + - - -
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLY 2.9 8.5 + - - -
227B GLY 2.8 8.1 + - - -
254B GLY* 1.3 71.0 - - - -
256B GLU* 1.3 54.1 + - - -
258B PHE* 3.1 14.5 + - - +
259B ASP* 2.9 32.2 + - - +
296B LYS* 3.2 11.7 + - - -
365B SER* 3.4 17.7 + - - -
501B ACP 3.5 11.2 - - - -
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 4.0 17.4 - - - +
65B TYR* 4.8 9.2 + - - -
81B LYS* 5.9 1.4 + - - -
93B PHE* 6.0 1.9 - - - -
94B ASP* 5.0 10.1 - - - +
97B ARG* 5.2 0.7 + - - -
227B GLY* 2.8 22.3 + - - +
228B GLY* 3.4 17.7 - - - -
255B GLY* 1.3 75.6 - - - +
257B ASP* 1.3 60.9 + - - +
259B ASP* 3.4 16.0 + - - +
260B GLN* 3.0 33.3 + - + +
501B ACP 3.9 3.3 + - - +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY 5.1 0.2 - - - +
228B GLY* 5.0 2.1 - - - +
252B HIS 3.8 6.7 - - - +
253B LEU* 3.2 20.2 + - + -
254B GLY 2.9 31.3 + - - +
256B GLU* 1.3 80.2 - - - +
258B PHE* 1.3 63.8 + - - +
260B GLN* 3.4 9.1 + - - +
261B ARG* 3.1 27.0 + - - +
334B LEU* 4.0 18.8 - - + -
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 4.0 27.8 - - + -
253B LEU* 4.7 6.5 - - + -
254B GLY* 3.8 20.6 - - - -
255B GLY* 3.1 20.8 + - - +
257B ASP* 1.3 76.8 - - - +
259B ASP* 1.3 64.5 + - - +
261B ARG 3.4 0.9 + - - -
262B VAL* 3.3 26.0 + - - +
296B LYS* 4.4 2.7 - - + -
327B PHE* 4.0 12.6 - - + -
331B ASN* 3.1 32.5 + - - +
334B LEU* 3.7 31.0 - - + -
335B PHE* 3.6 26.9 - + - -
338B THR* 5.6 0.9 - - + -
365B SER* 4.2 1.6 - - - -
368B ILE* 3.9 23.1 - - + -
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B GLY 2.9 10.3 + - - +
256B GLU* 3.4 19.1 - - - +
258B PHE* 1.3 75.3 - - - +
260B GLN* 1.3 60.3 + - + +
262B VAL* 2.9 7.2 + - - +
263B MET* 2.8 32.3 + - + +
289B ARG* 5.2 13.5 - - + +
292B VAL* 3.8 14.6 - - + +
293B GLU* 3.7 27.3 - - - +
296B LYS* 2.6 38.4 + - - +
501B ACP 4.8 0.5 + - - -
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 3.0 14.7 + - + +
257B ASP* 3.7 11.0 - - - +
258B PHE 3.3 0.2 - - - -
259B ASP* 1.3 81.8 - - - +
261B ARG* 1.3 57.1 + - + +
263B MET* 3.3 18.4 + - - +
264B GLU* 3.0 45.6 + - - +
289B ARG* 3.2 35.8 - - - +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP 3.1 15.7 + - - +
258B PHE 3.7 0.7 - - - +
259B ASP 3.3 0.4 - - - -
260B GLN* 1.3 76.4 - - + +
262B VAL* 1.3 63.1 + - - +
264B GLU* 3.5 26.4 + - - +
265B HIS* 3.2 20.4 + - - +
330B LEU* 2.9 32.6 + - + +
331B ASN* 3.3 32.1 - - - +
333B ASP* 2.7 43.6 + - - -
334B LEU* 3.7 26.4 - - + +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE 3.3 13.7 + - - +
259B ASP* 2.9 9.2 + - - +
261B ARG* 1.3 75.0 - - - +
263B MET* 1.3 65.0 + - - +
265B HIS* 3.1 8.0 + - - +
266B PHE* 3.0 49.4 + - + -
292B VAL* 3.5 22.9 - - + -
296B LYS* 6.1 1.6 - - + -
307B ILE* 5.0 0.2 - - + -
322B LEU* 3.9 18.4 - - + -
327B PHE* 3.8 26.9 - - + -
330B LEU* 4.3 10.8 - - + -
331B ASN* 4.3 1.8 - - - +
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP 2.8 23.2 + - - +
260B GLN* 3.4 32.3 - - - +
262B VAL* 1.3 73.3 - - - +
264B GLU* 1.3 64.7 + - - +
266B PHE* 3.1 1.2 + - - +
267B ILE* 2.9 38.1 + - + +
285B VAL* 3.4 42.4 - - + +
288B LEU* 3.7 30.1 - - + +
289B ARG* 3.4 34.3 - - + +
292B VAL* 4.0 8.3 - - - -
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLN* 3.0 34.6 + - - +
261B ARG* 3.7 28.6 + - - +
263B MET* 1.3 75.9 - - + +
265B HIS* 1.3 63.2 + - - +
267B ILE* 4.0 7.8 - - - +
268B LYS* 3.0 44.4 + - - +
279B ARG* 6.2 3.8 - - - +
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Residues in contact with HIS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG 3.2 4.1 + - - +
262B VAL* 3.1 7.7 + - + +
264B GLU* 1.3 81.0 - - - +
266B PHE* 1.3 92.7 + + - +
268B LYS* 3.9 9.6 - - - +
269B LEU* 3.1 40.5 + - + +
321B THR 5.7 0.6 + - - -
322B LEU* 4.5 3.5 - - + +
326B LYS* 3.3 36.6 + - - +
330B LEU* 3.7 35.9 - - + +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 3.0 40.3 + - + +
263B MET 4.0 1.3 - - - +
265B HIS* 1.3 96.0 - + - +
267B ILE* 1.3 61.8 + - - +
269B LEU* 3.3 14.8 + - + +
270B TYR* 2.9 32.3 + - - +
288B LEU* 4.3 11.4 - - + -
292B VAL* 4.3 4.9 - - + -
307B ILE* 3.3 32.1 - - + -
318B PHE* 3.9 27.8 - + + -
320B GLU* 3.5 22.0 - - + -
321B THR 3.6 20.9 - - - -
322B LEU* 3.9 13.2 - - + -
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Residues in contact with ILE 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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263B MET* 2.9 39.0 + - + +
264B GLU* 4.0 5.8 - - - +
266B PHE* 1.3 78.1 - - - +
268B LYS* 1.3 63.0 + - + +
270B TYR* 3.4 3.1 + - - +
271B LYS* 3.1 23.7 + - + +
276B LYS 4.9 0.7 - - - +
277B ASP* 4.4 5.8 - - - +
278B VAL* 3.6 31.8 - - + +
279B ARG* 4.0 51.1 - - + +
285B VAL* 4.9 7.0 - - + -
288B LEU* 3.8 16.6 - - + -
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLU* 3.0 36.8 + - - +
265B HIS* 3.9 8.1 - - - +
267B ILE* 1.3 76.4 - - + +
269B LEU* 1.3 57.9 + - - +
271B LYS* 3.3 10.0 + - + +
272B LYS* 2.9 28.4 + - - +
279B ARG* 6.2 2.2 - - - +
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Residues in contact with LEU 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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265B HIS* 3.1 30.9 + - + +
266B PHE* 3.5 22.9 - - + +
267B ILE 3.3 0.2 - - - -
268B LYS* 1.3 77.1 - - - +
270B TYR* 1.3 57.2 + - - +
272B LYS* 3.0 15.7 + - + +
273B LYS* 2.8 50.7 + - + +
318B PHE* 6.2 0.4 - - + -
320B GLU* 3.6 32.3 - - + +
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Residues in contact with TYR 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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266B PHE 2.9 20.8 + - - +
267B ILE* 3.8 6.3 - - - +
269B LEU* 1.3 73.0 - - - +
271B LYS* 1.3 52.2 - - - +
273B LYS* 3.2 6.3 + - + +
274B THR* 2.8 77.5 + - + +
276B LYS* 3.9 19.6 - - + +
278B VAL* 4.7 8.5 - - + -
312B PHE* 3.8 35.0 - + + -
313B TYR* 4.1 18.6 + + + -
316B GLU* 3.6 26.7 + - - +
317B ASP 4.2 10.9 + - - -
318B PHE* 3.7 25.5 - + + -
320B GLU* 5.8 2.9 - - - -
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.1 18.2 + - + +
268B LYS* 3.6 9.6 - - + +
270B TYR* 1.3 77.4 - - - +
272B LYS* 1.3 56.8 + - - +
275B GLY* 2.7 37.3 + - - +
276B LYS 3.3 22.8 + - - +
277B ASP* 3.8 34.3 - - + +
279B ARG* 5.1 4.2 - - - +
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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
----------------------------------------------------------
268B LYS 2.9 13.5 + - - +
269B LEU* 3.0 18.6 + - + +
271B LYS* 1.3 78.7 - - - +
273B LYS* 1.3 61.9 + - + +
275B GLY 4.4 1.6 + - - -
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 2.8 38.1 + - + +
270B TYR* 3.8 7.0 - - + +
272B LYS* 1.3 80.9 - - + +
274B THR* 1.3 67.7 + - + +
320B GLU* 3.1 40.4 + - - +
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TYR* 2.8 55.4 + - + +
273B LYS* 1.3 84.2 - - + +
275B GLY* 1.3 57.7 + - - +
276B LYS* 3.1 37.8 + - - +
316B GLU* 6.4 2.0 - - + -
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Residues in contact with GLY 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 LYS* 2.7 31.9 + - - +
272B LYS 4.4 1.2 + - - -
273B LYS 3.8 0.4 - - - -
274B THR* 1.3 71.8 - - - +
276B LYS* 1.3 64.9 + - - +
277B ASP 4.0 1.2 + - - -
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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