Contacts of the helix formed by residues 274 - 285 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D GLU* 2.6 38.4 + - - -
272D TYR 3.4 2.8 + - - -
273D MET* 1.3 82.5 - - - +
275D THR* 1.3 62.1 + - - +
276D ASP* 3.3 8.3 + - - +
277D CYS* 2.8 18.7 + - - +
278D GLU* 3.2 16.8 + - - +
303D TRP* 3.7 2.9 - - - -
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Residues in contact with THR 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MET 3.7 1.0 + - - -
274D SER* 1.3 71.7 - - - +
276D ASP* 1.3 73.8 + - - +
278D GLU* 3.1 15.1 + - - +
279D ASN* 3.0 43.7 + - - +
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Residues in contact with ASP 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D SER* 3.3 6.3 + - - +
275D THR* 1.3 82.1 + - - +
277D CYS* 1.3 61.6 + - - +
279D ASN* 3.3 13.0 + - - +
280D LEU* 3.1 16.8 + - - +
301D ASP* 4.8 1.6 - - - +
302D ARG* 3.2 40.7 + - + +
303D TRP* 3.7 35.4 + - + +
306D VAL* 5.1 6.2 - - + +
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Residues in contact with CYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.9 3.4 - - - +
240D LEU* 4.4 13.2 - - - -
244D VAL* 4.0 28.9 - - - -
273D MET* 3.8 24.0 - - + -
274D SER* 2.8 23.3 + - - +
276D ASP* 1.3 78.0 - - - +
278D GLU* 1.3 64.0 + - - +
280D LEU* 2.9 15.3 + - - +
281D LEU* 3.0 17.8 + - - +
303D TRP* 3.4 23.3 - - - +
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D TYR* 4.9 2.1 + - + -
269D ILE* 3.6 42.1 - - + +
273D MET* 4.0 13.8 - - - -
274D SER 3.2 9.9 + - - +
275D THR* 3.1 18.5 + - - +
277D CYS* 1.3 77.9 - - - +
279D ASN* 1.3 63.4 + - - +
281D LEU* 3.5 7.1 + - - +
282D LYS* 3.2 43.7 + - + +
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Residues in contact with ASN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D THR* 3.0 36.4 + - - +
276D ASP* 3.7 11.8 + - - +
278D GLU* 1.3 76.2 - - - +
280D LEU* 1.3 64.7 + - - +
282D LYS* 3.3 40.9 + - - +
283D LYS* 3.5 20.9 - - - +
301D ASP* 5.3 1.8 - - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PHE* 4.2 1.8 - - + -
240D LEU* 3.5 21.5 - - + -
276D ASP 3.1 11.6 + - - +
277D CYS* 2.9 10.3 + - - +
279D ASN* 1.3 74.3 - - - +
281D LEU* 1.3 67.0 + - - +
283D LYS* 3.0 18.6 + - + +
284D PHE* 3.1 32.1 + - + -
298D ILE* 4.2 12.8 - - + -
301D ASP* 3.3 29.3 + - + +
303D TRP* 3.5 29.6 - - + -
304D MET* 3.8 15.3 - - - -
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Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D GLY* 3.3 29.8 - - - +
240D LEU* 3.6 24.4 - - + +
241D TYR* 3.7 30.5 - - + -
267D TYR* 3.9 20.9 - - + +
273D MET* 3.7 31.9 - - + -
277D CYS* 3.0 17.1 + - - +
278D GLU* 3.8 9.2 - - + +
279D ASN 3.4 0.2 - - - -
280D LEU* 1.3 75.0 - - - +
282D LYS* 1.3 54.3 + - - +
284D PHE* 3.0 7.7 + - - +
285D LEU* 2.8 39.8 + - + +
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Residues in contact with LYS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D TYR* 4.2 12.6 - - - +
278D GLU* 3.2 37.8 + - + +
279D ASN* 3.3 35.8 + - - +
280D LEU 3.1 1.0 - - - -
281D LEU* 1.3 76.3 - - - +
283D LYS* 1.3 56.5 + - + +
284D PHE 3.4 0.2 - - - -
285D LEU* 4.4 3.4 - - - +
286D ILE* 3.4 22.9 + - - +
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 4.5 0.3 - - - +
279D ASN* 3.5 21.3 - - - +
280D LEU* 3.0 11.1 + - + +
282D LYS* 1.3 78.7 - - + +
284D PHE* 1.3 63.1 + - - +
286D ILE* 3.9 11.2 - - - +
292D ARG* 4.4 0.9 - - - -
293D GLY* 3.7 22.4 + - - +
298D ILE* 3.8 29.2 - - + +
301D ASP* 2.9 43.6 + - + +
302D ARG 4.9 0.4 - - - +
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PHE* 3.8 27.4 - + - -
160D VAL* 4.7 1.8 - - + -
233D VAL* 2.9 29.4 - - + +
234D TRP* 4.1 6.1 - - - -
236D LEU* 3.5 18.4 - - + -
237D GLY* 3.4 25.6 - - - -
240D LEU* 4.4 4.7 - - + -
280D LEU* 3.1 46.6 + - + -
281D LEU* 3.0 4.3 + - - +
283D LYS* 1.3 80.3 - - - +
285D LEU* 1.3 59.6 + - - +
286D ILE 2.9 12.0 + - - -
292D ARG* 3.3 21.1 - - - -
295D LEU* 3.8 15.5 - - + -
298D ILE* 3.4 31.2 - - + -
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D TRP* 3.5 60.5 - - + +
237D GLY* 3.7 24.2 - - - +
238D VAL* 3.8 6.1 - - + +
241D TYR* 5.2 0.4 - - + -
249D PRO* 4.7 7.2 - - + -
250D PHE* 4.3 10.3 - - + -
265D GLY* 5.0 4.0 - - - +
267D TYR* 3.7 48.7 + - + +
281D LEU* 2.8 28.7 + - + +
282D LYS* 4.8 3.1 - - - +
284D PHE* 1.3 67.9 - - - +
286D ILE* 1.3 60.0 + - - +
287D 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