Contacts of the helix formed by residues 258 - 276 (chain B) in PDB entry 5YWB
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 ARG 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B LYS* 4.5 21.4 - - - +
253B LEU* 3.4 30.9 + - + +
254B PRO 3.2 17.1 + - - +
255B ILE* 4.1 11.3 + - - +
256B ALA 3.8 1.0 - - - -
257B MET* 1.3 79.4 - - - +
259B ALA* 1.3 65.8 + - - +
260B LEU* 3.1 11.0 + - + +
261B THR* 3.2 22.8 + - - +
262B ASN* 3.4 11.7 + - - -
1232B ASP* 4.3 19.5 + - - +
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Residues in contact with ALA 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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257B MET 3.6 2.4 + - - -
258B ARG* 1.3 72.2 - - - +
260B LEU* 1.3 56.9 + - - +
261B THR 3.3 0.2 - - - -
262B ASN* 3.8 10.8 - - - +
263B TYR* 2.9 31.5 + - - +
389B GLY* 4.6 15.0 - - - +
393B THR* 4.2 4.2 - - + +
1228B LEU* 4.7 7.2 - - + -
1231B THR* 4.1 20.2 - - + -
1232B ASP* 3.2 22.9 + - - +
1235B ASN* 4.5 13.6 - - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 3.1 9.3 - - + +
259B ALA* 1.3 78.7 - - - +
261B THR* 1.3 58.5 + - - +
263B TYR* 3.4 17.9 + - + +
264B GLN* 2.9 34.3 + - - +
1225B GLN* 5.5 4.5 - - - +
1228B LEU* 3.8 36.1 - - + +
1232B ASP* 4.9 1.2 + - - -
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Residues in contact with THR 261 (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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255B ILE 4.0 16.8 + - - +
256B ALA* 5.7 5.8 - - - -
258B ARG* 3.2 15.8 + - - +
260B LEU* 1.3 78.3 - - - +
262B ASN* 1.3 60.0 + - - +
264B GLN* 3.4 9.2 - - + +
265B ARG* 2.9 43.0 + - + +
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Residues in contact with ASN 262 (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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256B ALA 5.2 4.1 + - - +
257B MET* 4.2 6.3 + - - +
258B ARG 3.4 14.4 + - - -
259B ALA* 3.8 10.4 - - - +
260B LEU 3.3 0.6 - - - -
261B THR* 1.3 76.2 - - - +
263B TYR* 1.3 60.5 + - - +
265B ARG* 3.4 13.0 + - - +
266B LEU* 2.9 31.0 + - - +
386B ASN* 2.6 53.5 + - - +
389B GLY* 5.9 0.6 - - - -
390B ALA* 3.9 19.5 - - + +
1235B ASN* 5.9 1.4 - - - +
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Residues in contact with TYR 263 (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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259B ALA 2.9 17.9 + - - +
260B LEU* 3.7 20.2 - - + +
262B ASN* 1.3 75.8 - - - +
264B GLN* 1.3 65.4 + - + +
266B LEU* 3.4 5.9 + - + +
267B CYS* 2.9 57.2 + - + +
390B ALA* 4.1 4.6 - - - +
393B THR* 3.4 37.0 - - + +
394B LYS* 3.9 26.2 - - + -
397B ASN* 3.6 29.9 + - + -
1224B GLN* 4.7 9.1 + - - -
1228B LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 264 (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 LEU* 2.9 23.3 + - - +
261B THR* 3.4 12.3 - - + +
262B ASN 3.2 0.2 - - - -
263B TYR* 1.3 84.9 - - + +
265B ARG* 1.3 63.7 + - - +
267B CYS* 3.3 5.0 + - - +
268B VAL* 2.9 43.3 + - + +
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Residues in contact with ARG 265 (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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261B THR* 2.9 32.5 + - + +
262B ASN* 3.8 13.2 + - - +
264B GLN* 1.3 73.4 - - - +
266B LEU* 1.3 58.0 + - - +
268B VAL* 3.3 7.1 + - - +
269B ALA* 2.9 29.3 + - + +
293B HIS* 6.3 1.6 - - + +
294B ALA* 3.8 34.6 + - + +
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Residues in contact with LEU 266 (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 ASN 2.9 18.6 + - - +
263B TYR* 3.7 4.9 - - + +
265B ARG* 1.3 78.3 - - - +
267B CYS* 1.3 57.7 + - - +
269B ALA* 3.3 3.9 + - - +
270B PHE* 2.8 28.9 + - - +
290B ALA* 4.8 11.9 - - + +
291B LEU* 3.8 26.7 - - + +
294B ALA* 4.7 16.2 - - + -
295B PHE* 6.4 0.4 - - + -
390B ALA* 3.8 33.0 - - + +
391B ILE* 4.3 10.5 - - + +
394B LYS* 3.6 34.3 - - + +
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Residues in contact with CYS 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 TYR* 2.9 53.0 + - + +
264B GLN* 3.9 5.8 - - - +
266B LEU* 1.3 73.6 - - - +
268B VAL* 1.3 61.9 + - + +
270B PHE* 3.6 9.4 - - - +
271B ASP* 2.9 30.0 + - - +
394B LYS* 4.3 19.5 - - - -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLN* 2.9 38.7 + - + +
265B ARG* 3.7 6.7 - - - +
267B CYS* 1.3 77.1 - - - +
269B ALA* 1.3 57.5 + - - +
271B ASP* 3.3 6.6 + - - +
272B ALA* 3.0 29.5 + - + +
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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
----------------------------------------------------------
265B ARG* 2.9 17.6 + - + +
266B LEU* 3.8 6.1 - - - +
268B VAL* 1.3 78.0 - - - +
270B PHE* 1.3 58.9 + - - +
272B ALA* 3.3 7.2 + - - +
273B GLN* 2.9 29.8 + - - +
290B ALA* 4.4 19.7 - - + +
293B HIS* 4.1 28.3 - - + +
294B ALA* 4.9 3.8 - - + -
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Residues in contact with PHE 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 LEU 2.8 18.8 + - - +
267B CYS* 3.6 8.1 - - - +
269B ALA* 1.3 76.8 - - - +
271B ASP* 1.3 60.0 + - - +
273B GLN* 3.3 8.1 + - + +
274B ALA* 2.9 37.6 + - + +
283B GLY 6.0 2.9 - - - -
286B ALA* 5.6 5.4 - - + -
287B ILE* 3.6 35.0 - - + -
290B ALA* 4.4 8.2 - - + +
394B LYS* 3.3 30.5 - - - +
614B LEU* 4.0 24.5 - - + -
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Residues in contact with ASP 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 CYS 2.9 16.5 + - - +
268B VAL* 3.6 7.0 - - - +
270B PHE* 1.3 81.4 - - + +
272B ALA* 1.3 61.9 + - - +
274B ALA* 3.1 7.2 + - - +
275B ARG* 2.9 30.2 + - - +
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Residues in contact with ALA 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 VAL* 3.0 17.9 + - + +
269B ALA* 3.3 7.6 + - - +
271B ASP* 1.3 77.3 - - - +
273B GLN* 1.3 61.4 + - - +
275B ARG* 3.6 27.5 + - - +
276B LYS* 3.4 20.4 + - - +
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Residues in contact with GLN 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 2.9 17.2 + - - +
270B PHE* 3.6 9.0 - - + +
272B ALA* 1.3 75.5 - - - +
274B ALA* 1.3 64.5 + - - +
276B LYS* 3.4 25.2 + - - +
286B ALA* 3.7 36.1 - - + +
289B ARG* 3.6 25.3 - - - +
290B ALA* 4.4 7.3 + - + -
293B HIS* 6.0 0.5 - - - +
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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 PHE* 2.9 29.1 + - + +
271B ASP* 3.1 9.4 + - - +
273B GLN* 1.3 76.9 - - - +
275B ARG* 1.3 64.8 + - - +
276B LYS 3.3 4.5 + - - -
286B ALA* 6.2 1.6 - - - -
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Residues in contact with ARG 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 ASP* 2.9 21.8 + - - +
272B ALA* 4.0 28.5 + - - +
273B GLN 3.4 0.2 - - - -
274B ALA* 1.3 76.2 - - - +
276B LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 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 ALA 3.4 11.3 + - - +
273B GLN* 3.7 25.1 - - - +
274B ALA 3.2 5.8 - - - +
275B ARG* 1.3 87.2 - - - +
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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
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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