Contacts of the helix formed by residues 268 - 279 (chain A) in PDB entry 1W31
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 TYR 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PHE* 3.5 49.1 - + + +
212A SER 4.2 4.0 + - - -
213A GLY* 5.1 3.6 - - - -
215A LEU* 4.9 3.9 - - + +
239A PRO* 3.8 32.9 - - + +
262A VAL* 4.2 7.2 - - + +
264A PRO* 3.5 54.5 - - + +
265A SER 2.8 7.3 + - - -
267A PHE* 1.3 98.0 - - + +
269A LEU* 1.3 58.5 + - - +
270A ASP* 3.1 9.4 - - - -
271A ILE* 2.9 34.6 + - + +
272A MET* 3.3 4.5 + - - +
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Residues in contact with LEU 269 (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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265A SER 3.0 7.3 + - - +
266A THR* 3.2 30.0 + - + +
267A PHE 3.7 0.6 - - - -
268A TYR* 1.3 77.4 - - - +
270A ASP* 1.3 62.8 + - - +
272A MET* 3.1 19.4 + - + +
273A ARG* 3.2 10.6 + - - +
314A SER 5.2 0.9 - - - +
317A GLY* 3.6 32.3 - - - +
318A PHE* 3.9 19.5 - - + +
320A ARG* 4.1 18.6 - - - +
321A ALA* 3.6 16.6 - - + +
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Residues in contact with ASP 270 (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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242A ARG* 5.3 5.4 - - - +
267A PHE 4.4 3.6 - - - +
268A TYR* 3.6 15.2 - - - -
269A LEU* 1.3 75.1 + - - +
271A ILE* 1.3 78.8 + - - +
273A ARG* 3.2 10.9 + - - +
274A ASP* 3.0 28.0 + - - +
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Residues in contact with ILE 271 (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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209A ALA* 3.8 29.2 - - + -
211A PHE* 3.7 30.1 - - + -
242A ARG* 4.3 16.4 - - + -
245A ALA* 4.3 13.2 - - + -
246A ARG* 6.1 0.2 - - + -
249A LEU* 4.7 7.6 - - + -
262A VAL* 4.0 9.6 - - + -
268A TYR* 2.9 21.6 + - + +
270A ASP* 1.3 92.8 - - - +
272A MET* 1.3 59.6 - - - +
274A ASP* 3.2 16.2 + - + +
275A ALA* 3.0 26.3 + - - +
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Residues in contact with MET 272 (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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262A VAL* 3.8 31.0 - - + -
265A SER* 3.2 54.5 - - - +
268A TYR 3.3 1.2 + - - +
269A LEU* 3.1 16.9 + - + +
271A ILE* 1.3 78.5 - - - +
273A ARG* 1.3 58.5 + - - +
275A ALA* 3.3 3.1 + - - +
276A SER* 2.9 25.6 + - - -
284A ILE* 4.2 12.5 - - + +
286A ALA* 3.7 23.3 - - + -
318A PHE* 4.0 26.5 - - + +
321A ALA* 3.4 17.6 - - + +
322A GLY* 4.9 0.5 - - - -
323A ALA* 4.3 4.7 - - - +
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Residues in contact with ARG 273 (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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33A GLU* 4.3 12.7 + - - -
269A LEU 3.2 8.5 + - - +
270A ASP* 3.2 15.0 - - - +
272A MET* 1.3 80.3 - - - +
274A ASP* 1.3 61.4 + - - +
276A SER* 2.7 45.0 + - - -
277A GLU* 3.5 23.7 + - - +
320A ARG 2.7 29.9 + - - -
321A ALA* 3.3 24.9 + - + +
322A GLY* 3.6 3.6 - - - +
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Residues in contact with ASP 274 (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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242A ARG* 3.1 40.9 + - - +
246A ARG* 2.8 39.5 + - + +
249A LEU* 4.9 2.7 - - + -
270A ASP* 3.0 18.4 + - - +
271A ILE* 3.2 17.3 + - + +
273A ARG* 1.3 74.5 - - - +
275A ALA* 1.3 65.0 + - - +
277A GLU* 3.1 8.5 + - - +
278A ILE* 3.0 29.7 + - + +
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Residues in contact with ALA 275 (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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249A LEU* 3.8 33.3 - - + +
260A ILE* 4.2 11.2 - - + -
262A VAL* 4.5 2.5 - - + -
271A ILE 3.0 15.7 + - - +
272A MET* 3.6 8.7 - - - +
274A ASP* 1.3 76.2 - - - +
276A SER* 1.3 56.2 + - - +
278A ILE* 4.6 0.9 - - - -
279A CYS* 2.7 39.0 + - - +
284A ILE* 3.3 12.9 - - + +
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Residues in contact with SER 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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272A MET 2.9 16.1 + - - -
273A ARG* 2.7 42.8 + - - -
274A ASP 3.2 0.4 - - - -
275A ALA* 1.3 76.2 - - - +
277A GLU* 1.3 61.5 + - - +
280A LYS* 3.1 25.5 - - - +
284A ILE* 3.3 15.0 - - - +
321A ALA 4.1 5.4 - - - -
322A GLY* 4.2 9.6 - - - -
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Residues in contact with GLU 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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246A ARG* 5.9 2.0 - - - +
273A ARG* 3.7 26.4 + - - +
274A ASP* 3.1 8.2 + - - +
275A ALA 3.1 0.6 - - - -
276A SER* 1.3 88.0 + - - +
278A ILE* 1.3 68.2 + - + +
280A LYS* 3.5 29.8 + - - +
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Residues in contact with ILE 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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246A ARG* 3.8 61.7 - - + +
249A LEU* 4.1 6.3 - - + -
250A GLU* 4.0 38.6 - - + +
253A MET* 3.4 15.7 - - + +
274A ASP 3.0 19.4 + - - +
275A ALA* 4.3 1.8 - - - +
277A GLU* 1.3 80.8 - - + +
279A CYS* 1.3 67.4 + - - +
280A LYS* 3.4 5.8 + - - +
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Residues in contact with CYS 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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249A LEU* 4.0 31.4 - - - -
253A MET* 3.9 25.4 - - - -
260A ILE* 4.2 19.3 - - + -
275A ALA 2.7 23.8 + - - +
278A ILE* 1.3 81.4 - - - +
280A LYS* 1.3 58.4 + - - +
281A ASP 3.1 3.4 - - - -
282A LEU* 2.9 37.2 + - + +
284A ILE* 4.3 10.4 - - + +
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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