Contacts of the helix formed by residues 258 - 277 (chain B) in PDB entry 2WO6
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 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B VAL* 1.3 75.8 - - - +
259B LEU* 1.3 56.0 + - - +
260B ASN* 3.5 9.8 + - - +
261B LEU* 3.1 23.0 + - - +
262B THR* 2.8 35.3 + - - -
355B HIS* 3.7 0.7 - - - -
438B ARG* 3.4 28.8 - - - +
441B GLU* 4.6 4.5 - - - -
444B HIS* 4.1 7.6 - - - -
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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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258B SER* 1.3 71.5 - - - +
260B ASN* 1.3 57.0 + - - +
262B THR* 3.5 6.0 - - - -
263B ARG* 2.7 39.3 + - - +
355B HIS* 3.6 17.8 - - + -
443B GLY 3.7 20.6 - - - +
444B HIS* 3.1 24.6 + - + +
448B ASP* 4.2 16.8 - - + -
449B TYR* 4.1 28.9 - - + +
452B PHE* 3.7 36.6 - - + -
478B PHE* 4.3 15.7 - - + -
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B SER* 3.5 8.0 + - - +
259B LEU* 1.3 78.7 - - - +
261B LEU* 1.3 60.9 + - - +
263B ARG* 3.0 28.1 + - - +
264B LYS* 3.2 31.0 + - - +
441B GLU* 5.9 0.8 + - - -
442B SER* 4.7 12.9 + - - -
443B GLY* 4.2 17.0 - - - +
444B HIS* 4.5 6.1 - - - -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.2 8.5 - - + -
257B VAL* 3.9 25.8 - - + -
258B SER* 3.1 17.7 + - - +
260B ASN* 1.3 75.6 - - - +
262B THR* 1.3 66.6 + - - +
264B LYS* 3.1 12.1 + - + +
265B PHE* 2.9 51.1 + - + -
301B SER* 3.6 30.5 - - - -
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.6 13.0 - - - +
258B SER 2.8 24.7 + - - -
259B LEU* 3.2 11.6 + - + -
261B LEU* 1.3 76.8 - - - +
263B ARG* 1.3 57.3 + - - +
265B PHE* 3.3 11.3 + - - +
266B ALA* 2.9 26.5 + - - +
351B LEU* 3.8 32.2 - - + +
354B MET* 4.3 3.0 - - + -
355B HIS* 3.7 16.1 + - + +
452B PHE* 3.8 25.8 - - + -
478B PHE* 5.1 0.2 - - + -
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 2.7 20.0 + - - +
260B ASN* 3.0 37.1 + - - +
262B THR* 1.3 74.7 - - - +
264B LYS* 1.3 62.0 + - + +
266B ALA* 3.3 0.6 + - - -
267B GLN* 3.0 24.6 + - - +
443B GLY* 4.4 13.1 + - - -
448B ASP* 4.6 14.3 + - - +
478B PHE* 2.9 65.0 + - + -
479B PHE* 3.5 23.0 - - + +
480B LYS 5.8 1.0 + - - -
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Residues in contact with LYS 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 ASN* 3.2 20.0 + - - +
261B LEU* 3.1 18.4 + - + +
263B ARG* 1.3 72.6 - - + +
265B PHE* 1.3 66.2 + - - +
267B GLN* 3.5 9.4 + - - +
268B GLN* 3.2 37.9 + - - +
301B SER* 4.0 26.3 + - - +
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.6 22.4 - - + -
248B LEU* 3.4 35.2 - - + -
257B VAL* 4.3 2.9 - - + -
261B LEU* 2.9 44.7 + - + -
262B THR* 3.6 10.8 - - - +
264B LYS* 1.3 75.7 - - - +
266B ALA* 1.3 62.2 + - - +
268B GLN* 3.2 4.8 + - - +
269B MET* 2.9 29.0 + - + +
295B LEU* 4.1 8.3 - - + -
301B SER* 3.6 23.6 - - - -
303B ILE* 3.7 35.9 - - + -
351B LEU* 4.5 8.5 - - + -
354B MET* 4.2 13.9 - - + -
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR* 2.9 17.6 + - + +
263B ARG* 3.6 9.2 - - - +
264B LYS 3.3 0.2 - - - -
265B PHE* 1.3 75.3 - - - +
267B GLN* 1.3 57.8 + - - +
269B MET* 4.0 3.0 - - - +
270B CYS* 2.9 35.7 + - - -
351B LEU* 3.6 33.1 - - + +
455B LEU* 5.1 1.8 - - + -
478B PHE* 4.4 7.6 - - + -
479B PHE* 3.7 16.6 - - + -
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Residues in contact with GLN 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 ARG 3.0 12.0 + - - +
264B LYS* 3.8 9.6 + - - +
265B PHE 3.3 0.2 - - - -
266B ALA* 1.3 76.2 - - - +
268B GLN* 1.3 57.2 + - + +
270B CYS 3.6 0.2 + - - -
271B THR* 2.8 38.1 + - - +
474B LEU* 3.6 19.5 - - + +
479B PHE* 3.5 41.0 - - + +
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Residues in contact with GLN 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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220B TYR* 3.4 42.4 - - + +
264B LYS* 3.2 26.7 + - - +
265B PHE* 3.2 7.6 + - - +
267B GLN* 1.3 78.8 - - + +
269B MET* 1.3 59.2 + - - +
271B THR* 3.3 5.8 + - - -
272B ALA* 2.9 27.0 + - - +
301B SER* 2.9 26.8 + - - -
302B ALA* 3.3 8.3 - - - +
303B ILE* 2.8 39.0 + - + +
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 6.3 0.7 - - - -
265B PHE* 2.9 20.3 + - + +
266B ALA 4.0 1.3 - - - +
268B GLN* 1.3 74.2 - - - +
270B CYS* 1.3 59.2 + - - +
272B ALA* 3.2 3.3 + - - +
273B LEU* 2.8 37.2 + - + +
288B LEU* 3.8 22.4 - - + -
293B ILE* 3.6 32.5 - - + -
303B ILE* 3.8 20.0 - - + -
304B LYS* 5.6 0.7 - - - -
305B ILE* 3.4 40.2 - - + -
347B LEU* 3.5 30.7 - - + -
350B ILE* 6.3 0.2 - - + -
351B LEU* 5.7 0.7 - - + -
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Residues in contact with CYS 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 ALA 2.9 26.9 + - - +
269B MET* 1.3 76.0 - - - +
271B THR* 1.3 56.7 + - - +
273B LEU* 3.4 5.7 + - - -
274B LEU* 2.9 23.4 + - - +
344B MET* 5.0 3.4 - - - -
347B LEU* 4.0 8.5 - - - -
459B MET* 4.0 21.3 - - - -
470B PRO* 3.4 13.7 - - + +
473B ALA* 3.7 27.1 - - + -
474B LEU* 3.5 25.0 - - + +
479B PHE* 4.4 9.2 - - - -
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Residues in contact with THR 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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217B MET* 3.6 30.1 - - + +
220B TYR* 3.6 25.3 + - + -
267B GLN* 2.8 25.7 + - - +
268B GLN* 3.6 5.6 - - - -
269B MET 3.2 0.2 - - - -
270B CYS* 1.3 73.3 - - - +
272B ALA* 1.3 59.8 + - - +
273B LEU 3.2 0.2 - - - -
274B LEU* 3.2 6.5 + - - +
275B PHE* 2.9 27.4 + - - +
474B LEU* 3.8 18.0 - - + +
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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
----------------------------------------------------------
217B MET 4.8 0.4 - - - -
220B TYR* 3.7 22.5 - - + +
221B ILE* 4.1 7.8 - - + +
268B GLN 2.9 14.2 + - - +
269B MET* 3.5 9.2 - - - +
271B THR* 1.3 74.3 - - - +
273B LEU* 1.3 64.3 + - - +
275B PHE* 3.2 9.9 + - - +
276B LEU* 3.0 26.8 + - - +
305B ILE* 3.6 27.8 - - + -
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Residues in contact with LEU 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 MET* 2.8 23.6 + - + +
270B CYS* 3.7 4.9 - - - +
271B THR 3.2 0.2 - - - -
272B ALA* 1.3 70.7 - - - +
274B LEU* 1.3 63.7 + - - +
276B LEU* 3.4 21.1 + - + +
277B ALA* 3.0 23.6 + - - +
288B LEU* 4.0 13.9 - - + -
305B ILE* 4.7 7.4 - - + -
340B LEU* 5.3 0.7 - - - +
343B ASP* 4.0 25.6 - - + +
344B MET* 4.0 33.4 - - + +
347B LEU* 3.9 27.4 - - + -
470B PRO* 3.7 14.4 - - + +
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Residues in contact with LEU 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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217B MET* 3.6 26.1 - - + +
270B CYS 2.9 14.0 + - - +
271B THR* 3.2 10.3 + - + +
273B LEU* 1.3 76.5 - - - +
275B PHE* 1.3 63.8 + - - +
277B ALA* 3.1 16.1 + - + +
278B THR* 3.3 9.7 + - - -
470B PRO* 3.5 9.3 - - + +
471B TYR* 3.9 39.7 - - + +
474B LEU* 3.9 21.1 - - + -
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 3.7 38.4 - - + -
213B HIS* 3.8 12.1 - + + -
215B THR* 3.4 34.8 - - + -
217B MET* 3.8 20.5 - - + +
218B LYS* 3.2 28.3 - - + -
221B ILE* 3.7 24.0 - - + -
271B THR 2.9 13.0 + - - +
272B ALA 3.3 8.1 - - - +
274B LEU* 1.3 76.0 - - - +
276B LEU* 1.3 63.2 + - + +
278B THR* 2.4 38.6 + - - -
281B LEU* 3.6 20.0 - - + +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 3.8 29.4 - - + -
221B ILE* 4.2 7.0 - - + -
272B ALA 3.0 19.0 + - - +
273B LEU* 3.7 26.2 - - + +
274B LEU 3.4 0.2 - - - -
275B PHE* 1.3 82.2 - - + +
277B ALA* 1.3 57.6 + - - +
278B THR 3.2 0.2 - - - -
281B LEU* 3.9 4.0 - - - +
282B SER 3.1 9.5 + - - -
283B ILE* 3.0 56.0 + - + +
285B HIS* 4.4 14.1 - - + +
305B ILE* 5.2 3.8 - - + -
308B PHE* 4.0 24.5 - - + -
340B LEU* 3.8 2.4 - - + +
343B ASP* 4.4 2.0 - - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU 3.0 16.4 + - - +
274B LEU* 3.1 13.8 + - + +
276B LEU* 1.3 73.6 - - - +
278B THR* 1.3 67.3 + - - +
279B PRO* 3.0 9.2 - - - +
282B SER* 4.5 3.3 + - - -
340B LEU* 3.5 22.6 - - + +
470B PRO* 4.9 10.5 - - + -
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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