Contacts of the helix formed by residues 274 - 285 (chain C) in PDB entry 2WZJ
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 274 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLU* 2.6 34.3 + - - -
272C TYR 3.2 5.8 + - - -
273C MET* 1.3 82.8 - - - +
275C THR* 1.3 62.5 + - - +
276C ASP* 3.1 10.2 + - - +
277C CYS* 2.8 20.1 + - - +
278C GLU* 3.2 20.0 + - - +
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Residues in contact with THR 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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273C MET 3.8 0.4 + - - -
274C SER* 1.3 73.4 - - - +
276C ASP* 1.3 65.5 + - - +
278C GLU* 3.6 15.7 + - - +
279C ASN* 3.2 35.2 + - - +
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Residues in contact with ASP 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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149C GLU* 4.8 0.2 - - - +
274C SER* 3.1 10.7 + - - +
275C THR* 1.3 76.6 - - - +
277C CYS* 1.3 60.1 + - - +
279C ASN* 2.9 30.0 + - - +
280C LEU* 3.1 12.1 + - - +
301C ASP* 5.1 0.9 - - - +
302C ARG* 3.0 36.5 - - - +
303C TRP* 3.9 22.3 - - + +
306C VAL* 4.2 13.2 - - - +
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Residues in contact with CYS 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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149C GLU* 4.0 3.8 - - - +
240C LEU* 4.6 12.1 - - - -
244C VAL* 3.8 29.4 - - - -
273C MET* 3.8 25.4 - - + -
274C SER* 2.8 22.9 + - - +
276C ASP* 1.3 71.3 - - - +
278C GLU* 1.3 62.7 + - - +
280C LEU* 3.0 15.5 + - - +
281C LEU* 3.0 22.1 + - - +
303C TRP* 3.5 23.6 - - + +
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Residues in contact with GLU 278 (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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267C TYR* 5.0 2.3 + - + -
269C ILE* 4.0 38.7 - - + +
273C MET* 4.1 13.3 - - - +
274C SER 3.2 14.4 + - - +
275C THR* 3.7 16.8 + - - +
276C ASP 3.3 0.2 - - - -
277C CYS* 1.3 78.5 - - - +
279C ASN* 1.3 60.8 + - - +
281C LEU* 4.1 6.1 + - - +
282C LYS* 3.6 42.3 + - + +
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Residues in contact with ASN 279 (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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275C THR* 3.2 29.4 + - - +
276C ASP* 2.9 18.6 + - - +
278C GLU* 1.3 77.0 - - - +
280C LEU* 1.3 62.9 + - - +
282C LYS* 3.1 35.3 + - - +
283C LYS* 3.2 19.9 - - - +
301C ASP* 5.0 4.9 - - - +
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Residues in contact with LEU 280 (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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156C PHE* 4.2 2.7 - - + -
240C LEU* 3.6 20.2 - - + -
276C ASP 3.1 8.1 + - - +
277C CYS* 3.0 10.4 + - - +
279C ASN* 1.3 75.1 - - - +
281C LEU* 1.3 54.5 + - - +
283C LYS* 2.8 40.5 + - + +
284C PHE* 3.2 30.8 + - + -
298C ILE* 3.9 16.2 - - + -
301C ASP* 3.3 29.2 + - + +
303C TRP* 3.5 33.9 - - + -
304C MET* 3.6 15.0 - - + -
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Residues in contact with LEU 281 (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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237C GLY* 3.3 31.2 - - - +
240C LEU* 3.2 28.3 - - + -
241C TYR* 3.6 33.2 - - + +
267C TYR* 3.6 27.8 + - + +
269C ILE* 6.2 0.2 - - + -
273C MET* 4.2 23.1 - - + -
277C CYS* 3.0 16.1 + - - +
278C GLU* 4.2 5.4 - - - +
280C LEU* 1.3 78.5 - - - +
282C LYS* 1.3 57.2 + - - +
283C LYS 3.0 0.2 - - - -
284C PHE* 3.2 3.0 + - + -
285C LEU* 2.9 33.2 + - + +
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Residues in contact with LYS 282 (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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267C TYR* 4.3 10.3 - - - +
278C GLU* 3.6 37.5 + - + +
279C ASN* 3.1 28.6 + - - +
280C LEU 3.1 1.6 - - - -
281C LEU* 1.3 77.2 - - - +
283C LYS* 1.3 58.2 + - + +
285C LEU 4.5 2.9 - - - -
286C ILE* 3.2 23.6 - - - +
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Residues in contact with LYS 283 (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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233C VAL* 4.6 1.6 - - - +
279C ASN* 3.2 26.7 - - - +
280C LEU* 2.8 16.8 + - + +
282C LYS* 1.3 80.6 - - + +
284C PHE* 1.3 57.8 + - - +
286C ILE* 3.1 17.7 - - - +
292C ARG* 4.8 0.5 - - - -
293C GLY 4.3 9.9 + - - -
297C GLN 5.1 6.1 + - - -
298C ILE* 4.0 29.0 - - + +
301C ASP* 3.1 40.3 + - + +
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Residues in contact with PHE 284 (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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156C PHE* 3.8 29.2 - + - -
160C VAL* 4.9 3.1 - - + -
233C VAL* 3.2 29.2 - - + +
234C TRP* 3.9 9.0 + - - -
236C LEU* 3.9 15.7 - - + -
237C GLY* 3.3 29.6 - - - +
240C LEU* 4.4 2.7 - - + -
280C LEU* 3.2 43.2 + - + -
281C LEU* 3.2 6.4 + - - +
283C LYS* 1.3 78.0 - - - +
285C LEU* 1.3 61.3 + - - +
286C ILE 3.1 8.2 + - - -
292C ARG* 3.2 21.0 - - - -
295C LEU* 4.2 12.3 - - + -
298C ILE* 3.3 30.5 - - + -
304C MET* 5.5 0.2 - - - -
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Residues in contact with LEU 285 (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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234C TRP* 3.5 39.6 - - + +
237C GLY* 3.6 32.8 - - - +
238C VAL* 3.7 10.3 - - + +
241C TYR* 5.3 0.9 - - + -
249C PRO* 5.0 6.1 - - + -
250C PHE* 4.4 8.3 - - + -
265C GLY* 5.1 4.2 - - - +
267C TYR* 3.4 49.1 + - + +
281C LEU* 2.9 27.1 + - + +
282C LYS* 4.8 2.1 - - - +
284C PHE* 1.3 75.5 - - - +
286C ILE* 1.3 62.2 + - - +
287C LEU* 3.9 2.3 + - - +
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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