Contacts of the helix formed by residues 266 - 278 (chain C) in PDB entry 1WLZ
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 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C ILE* 1.3 76.6 - - - +
267C ARG* 1.3 58.7 + - - +
268C GLU* 3.5 14.1 + - - +
269C GLU* 2.9 44.7 + - - +
270C PHE* 2.9 28.1 + - - +
290C TRP* 4.8 0.9 - - - -
300C ARG* 3.6 25.5 - - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP* 3.9 20.5 + - - -
261B LYS* 3.7 36.0 - - - +
265C ILE 4.0 0.2 + - - -
266C SER* 1.3 74.4 - - - +
268C GLU* 1.3 66.6 + - + +
270C PHE* 3.3 1.9 + - - +
271C ARG* 3.0 25.4 + - - +
286C PHE* 3.5 31.1 - - + -
287C ASP* 2.8 43.2 + - - +
290C TRP* 3.1 65.1 - - + +
299C GLY 4.1 9.8 + - - +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 3.5 26.0 - - - +
275A ASN* 5.1 1.2 - - - +
280A ILE* 3.9 13.5 - - + +
281A LEU 3.5 15.0 - - - +
282A THR* 3.4 15.9 - - - +
283A ASP* 3.0 32.1 + - - +
266C SER* 3.3 12.4 + - - +
267C ARG* 1.3 83.0 + - + +
269C GLU* 1.3 66.2 + - - +
271C ARG* 3.3 9.2 + - - +
272C ALA* 3.0 21.5 + - - +
286C PHE* 5.9 0.2 - - - -
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 4.1 17.3 - - + -
257C PHE* 3.6 48.7 - - + +
265C ILE* 3.5 14.9 - - + +
266C SER* 2.9 45.9 + - - +
268C GLU* 1.3 73.2 - - - +
270C PHE* 1.3 66.6 + - - +
272C ALA* 3.1 17.9 + - - +
273C ILE* 3.1 17.0 + - - +
300C ARG* 4.7 3.0 + - - -
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Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LEU* 4.6 5.2 - - + -
254C PHE* 4.4 10.1 - + - -
265C ILE* 3.7 10.7 - - + +
266C SER 2.9 12.9 + - - +
267C ARG 3.3 7.4 + - - +
269C GLU* 1.3 77.8 - - - +
271C ARG* 1.3 56.2 + - - +
273C ILE* 3.1 10.6 + - + +
274C CYS* 2.9 50.8 + - - -
286C PHE* 3.8 12.6 - + - -
289C LEU* 4.3 5.6 - - + -
290C TRP* 3.6 27.4 - + + -
293C MET* 3.7 36.3 - - + -
301C LEU* 3.4 24.5 - - + -
306C PHE* 3.8 26.7 - + - -
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Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 3.6 10.1 - - - +
271A ARG* 4.0 31.2 - - - +
275A ASN* 5.9 0.4 - - - +
283A ASP* 5.0 4.0 + - - -
267C ARG* 3.0 11.2 + - - +
268C GLU* 3.5 12.6 - - - +
269C GLU 3.2 0.2 - - - -
270C PHE* 1.3 77.7 - - - +
272C ALA* 1.3 57.3 + - - +
274C CYS* 3.2 4.4 + - + +
275C ASN* 2.8 47.2 + - - +
281C LEU* 3.1 27.5 + - + +
282C THR 3.5 0.8 - - - -
283C ASP* 2.7 43.2 + - - +
286C PHE* 3.6 55.6 - - + +
287C ASP* 5.7 1.0 + - - -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASN* 3.8 27.1 + - + +
280A ILE* 3.9 22.9 - - + -
257C PHE* 4.7 4.0 - - + -
268C GLU 3.0 13.6 + - - +
269C GLU 3.3 9.9 - - - +
271C ARG* 1.3 77.4 - - - +
273C ILE* 1.3 61.7 + - - +
275C ASN* 3.4 17.4 + - - +
276C ARG* 3.5 8.8 + - - +
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Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ILE* 4.8 12.6 - - + +
253C GLU* 3.7 35.2 - - + +
254C PHE* 3.3 39.5 - - + -
257C PHE* 3.8 21.8 - - + -
265C ILE* 4.0 7.4 - - + -
269C GLU 3.1 8.0 + - - +
270C PHE* 3.1 12.7 + - + +
272C ALA* 1.3 74.3 - - - +
274C CYS* 1.3 59.6 + - - +
276C ARG* 3.1 4.0 + - - +
277C ARG* 2.9 46.2 + - + +
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Residues in contact with CYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LEU* 4.7 11.0 - - - -
270C PHE* 2.9 53.5 + - - +
271C ARG* 3.2 11.0 + - + +
273C ILE* 1.3 77.9 - - - +
275C ASN* 1.3 62.7 + - - +
277C ARG* 4.5 1.1 - - - +
278C VAL* 2.9 31.3 + - + +
279C GLN 3.1 10.6 + - - +
281C LEU* 4.4 16.8 - - + -
286C PHE* 4.8 1.8 - - + -
289C LEU* 4.0 15.7 - - - -
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Residues in contact with ASN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU 4.9 1.2 + - - -
271A ARG* 5.3 1.8 - - - +
272A ALA* 3.9 21.0 - - + +
275A ASN* 3.6 21.8 + - - -
271C ARG* 2.8 35.1 + - - +
272C ALA* 3.5 8.8 - - - +
273C ILE 3.2 0.2 - - - -
274C CYS* 1.3 78.2 - - - +
276C ARG* 1.3 59.4 + - + +
278C VAL 4.8 0.2 - - - -
279C GLN* 3.4 19.8 - - - +
280C ILE* 3.5 37.9 - - + +
281C LEU* 3.9 6.1 + - - +
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Residues in contact with ARG 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C GLU* 5.5 4.0 - - - +
272C ALA 3.5 7.8 + - - +
273C ILE* 3.1 8.3 + - - +
275C ASN* 1.3 81.2 - - + +
277C ARG* 1.3 69.0 + - + +
278C VAL 5.3 0.6 - - - -
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Residues in contact with ARG 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ARG 5.1 0.5 - - - +
239C LEU* 5.8 1.8 - - + -
242C ALA* 3.7 22.8 - - + +
246C HIS* 3.9 32.7 + - - +
249C ALA* 3.4 27.1 + - - +
250C ILE* 3.8 20.3 - - + +
253C GLU* 2.7 31.6 + - - +
273C ILE* 2.9 34.0 + - + +
274C CYS* 4.9 0.4 - - - -
276C ARG* 1.3 84.3 - - + +
278C VAL* 1.3 66.7 + - + +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ILE* 4.2 22.9 - - + +
238C ARG* 3.7 33.7 + - + +
239C LEU* 3.6 41.1 - - + +
242C ALA* 4.3 4.0 - - + -
274C CYS* 2.9 17.7 + - + +
275C ASN 4.8 0.7 - - - -
276C ARG 5.3 0.2 - - - -
277C ARG* 1.3 87.1 - - + +
279C GLN* 1.3 74.3 + - + +
281C LEU* 5.5 2.0 - - + -
289C LEU* 6.5 0.4 - - + -
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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