Contacts of the helix formed by residues 275 - 291 (chain A) in PDB entry 1WR6
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.8 18.1 + - - -
274A ASN* 1.3 78.8 - - - +
276A LEU* 1.3 67.1 + - - +
277A GLY 3.1 3.6 - - - +
278A ASP* 3.1 17.3 + - - +
279A ILE* 3.0 34.7 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA* 4.2 19.3 - - + -
269A THR* 3.9 28.7 - - + +
273A ASP* 3.4 18.1 + - + +
274A ASN 3.8 0.2 - - - -
275A SER* 1.3 76.7 - - - +
277A GLY* 1.3 64.0 + - - +
279A ILE* 3.4 8.5 + - + +
280A LEU* 3.1 48.7 + - + +
259B ARG* 3.7 37.5 - - - +
263B PHE* 4.7 4.7 - - + -
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP 5.4 0.4 + - - -
274A ASN 5.3 0.6 - - - -
275A SER* 3.1 1.4 - - - +
276A LEU* 1.3 81.3 - - - +
278A ASP* 1.3 62.7 + - - +
280A LEU* 3.8 5.4 - - - +
281A GLN* 2.9 23.3 + - - +
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.2 28.0 - - + +
274A ASN 4.2 5.5 - - - +
275A SER* 3.1 23.0 + - - +
277A GLY* 1.3 76.3 - - - +
279A ILE* 1.3 63.8 + - + +
281A GLN* 3.0 7.9 + - - +
282A ALA* 2.8 25.3 + - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.9 5.1 - - + +
262A LEU* 3.2 43.2 - - + +
263A PHE* 5.9 0.2 - - + -
265A LEU* 3.8 31.6 - - + +
266A ALA* 4.2 18.8 - - + +
269A THR* 5.6 2.2 - - - +
273A ASP* 5.3 1.6 - - - +
275A SER* 3.0 29.3 + - - +
276A LEU* 3.6 11.0 - - + +
277A GLY 3.3 0.2 - - - -
278A ASP* 1.3 77.2 - - + +
280A LEU* 1.3 60.0 + - + +
282A ALA* 3.4 6.6 + - - +
283A SER* 3.0 26.3 + - - -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PHE* 4.8 4.9 - - + -
266A ALA* 4.4 9.4 - - + -
276A LEU* 3.1 37.3 + - + +
277A GLY* 3.8 5.6 - - - +
279A ILE* 1.3 79.9 - - + +
281A GLN* 1.3 60.8 + - - +
283A SER* 2.5 25.8 + - - +
284A ASP* 2.9 22.5 + - - +
259B ARG* 5.3 1.3 - - - +
263B PHE* 3.7 38.4 - - + -
284B ASP* 5.8 4.7 - - - +
287B SER* 4.9 10.1 - - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLY 2.9 13.9 + - - +
278A ASP* 3.4 11.7 - - - +
280A LEU* 1.3 75.5 - - - +
282A ALA* 1.3 64.9 + - - +
284A ASP* 3.0 22.6 + - - +
285A ASN* 3.0 38.7 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.0 19.7 - - + -
221A VAL* 4.0 15.4 - - + +
222A ASN* 5.5 3.8 - - - +
262A LEU* 3.5 21.1 - - + -
278A ASP 2.8 11.7 + - - +
279A ILE 3.6 4.5 - - - +
281A GLN* 1.3 78.6 - - - +
283A SER* 1.3 62.1 + - - +
285A ASN* 3.1 13.0 + - - +
286A LEU* 2.9 23.6 + - - +
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 4.2 6.1 - - - -
262A LEU* 3.6 15.6 - - - +
263A PHE* 3.8 31.9 - - - -
279A ILE 3.0 13.8 + - - -
280A LEU* 2.5 28.4 + - - +
282A ALA* 1.3 75.7 - - - +
284A ASP* 1.3 54.7 + - - +
286A LEU* 3.1 9.7 + - - +
287A SER* 2.8 38.8 + - - -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LEU* 2.9 22.6 + - - +
281A GLN* 3.0 20.4 + - - +
283A SER* 1.3 80.4 + - - +
285A ASN* 1.3 54.1 + - - +
287A SER* 3.0 10.3 + - - -
288A ARG* 2.7 35.1 + - - +
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL* 5.7 0.4 - - + -
222A ASN* 4.2 13.4 - - - +
225A VAL* 4.4 18.8 - - + +
281A GLN* 3.0 40.3 + - - +
282A ALA* 3.3 11.2 - - - +
284A ASP* 1.3 77.5 - - - +
286A LEU* 1.3 64.2 + - - +
288A ARG* 3.1 17.0 + - - +
289A VAL* 3.0 25.6 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL* 3.7 30.5 - - + +
224A ASN* 5.1 0.4 - - + -
225A VAL* 3.9 16.2 - - + -
255A CYS* 3.7 36.6 - - + +
258A LYS* 3.9 12.1 - - + -
259A ARG* 3.5 39.0 - - + +
262A LEU* 3.8 15.5 - - + -
282A ALA 2.9 7.7 + - - +
283A SER* 3.4 7.9 - - - +
285A ASN* 1.3 76.4 - - - +
287A SER* 1.3 57.5 + - - +
289A VAL* 3.1 5.3 - - - +
290A ILE* 2.9 37.2 + - + +
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 3.1 35.0 + - - +
263A PHE* 5.3 0.9 - - - -
283A SER* 2.8 16.5 + - - -
284A ASP* 3.2 12.2 + - - -
286A LEU* 1.3 77.7 - - - +
288A ARG* 1.3 61.5 + - - +
290A ILE* 3.3 3.5 + - - +
291A ASN* 3.1 32.8 + - - -
280B LEU* 5.1 6.2 - - - +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ASP 2.7 18.2 + - - +
285A ASN* 3.1 17.8 + - - +
287A SER* 1.3 73.7 - - - +
289A VAL* 1.3 61.1 + - - +
291A ASN* 3.6 7.6 + - - +
292A SER* 3.5 17.0 + - - -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 4.0 31.0 - - + +
228A LEU* 3.8 29.4 - - + +
229A SER* 4.3 9.9 - - - +
232A LEU* 4.2 7.6 - - + +
255A CYS* 4.2 16.2 - - - -
285A ASN 3.0 14.7 + - - +
286A LEU* 3.1 21.8 - - - +
288A ARG* 1.3 76.3 - - - +
290A ILE* 1.3 64.3 + - - +
291A ASN 3.3 0.2 - - - -
292A SER* 3.3 16.6 + - - -
293A TYR* 3.4 8.8 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PHE* 3.1 34.3 - - + -
255A CYS* 3.7 22.7 - - + +
256A GLU* 3.1 47.1 - - - +
259A ARG* 3.8 28.7 - - - +
286A LEU 2.9 26.3 + - - +
287A SER* 3.6 5.6 - - - +
288A ARG 3.3 0.2 - - - -
289A VAL* 1.3 77.6 - - - +
291A ASN* 1.3 65.8 + - - +
292A SER 3.1 2.8 + - - -
293A TYR 3.4 3.8 + - - -
294A LYS* 3.1 22.1 - - - +
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A SER* 3.1 21.0 + - - +
288A ARG* 4.0 8.1 - - - +
289A VAL 3.3 0.2 - - - -
290A ILE* 1.3 78.5 - - - +
292A SER* 1.3 59.3 - - - +
294A LYS* 3.3 29.1 - - + +
295A THR* 3.0 31.3 + - - +
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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