Contacts of the helix formed by residues 272 - 282 (chain D) in PDB entry 4PEI
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 ASP 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D CYS* 3.3 40.4 + - + +
120D ASN* 2.9 31.4 + - - +
125D ARG* 2.9 38.8 + - - -
168D LEU* 4.1 0.3 - - - +
270D GLU 3.5 2.6 + - - -
271D TYR* 1.3 70.3 - - - +
273D LYS* 1.3 61.7 + - - +
274D ASP* 3.3 4.2 + - - +
275D TRP* 3.1 24.0 + - + +
276D VAL* 3.0 30.0 + - - +
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Residues in contact with LYS 273 (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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120D ASN* 4.3 11.7 - - - +
270D GLU* 4.4 15.0 + - - -
271D TYR 4.6 2.4 + - - +
272D ASP* 1.3 77.0 + - - +
274D ASP* 1.3 65.6 - - - +
276D VAL* 3.2 2.7 + - - -
277D CYS* 3.0 28.0 + - - -
315D ILE* 3.6 41.5 - - + +
324D LEU* 4.5 24.8 - - + +
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Residues in contact with ASP 274 (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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125D ARG* 3.6 13.4 + - - +
167D ASN* 5.5 2.9 - - - +
168D LEU* 3.9 18.6 - - + +
171D SER* 3.5 31.3 + - - -
272D ASP* 3.3 10.4 + - - +
273D LYS* 1.3 80.2 - - - +
275D TRP* 1.3 63.9 + - - +
277D CYS* 3.0 5.0 + - - +
278D ASN* 3.0 24.1 + - - +
306D ARG* 3.0 31.2 + - - +
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Residues in contact with TRP 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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102D ASN* 5.4 4.4 + - - -
116D CYS* 3.1 31.6 - - - -
117D SER* 3.3 25.4 - - - -
118D CYS* 3.7 26.0 - - + +
164D MET* 3.5 52.0 - - + -
165D LEU* 3.9 16.6 - - + -
168D LEU* 3.7 9.7 - - + +
271D TYR* 5.6 7.6 - + + -
272D ASP* 3.1 21.3 + - - +
273D LYS 3.3 0.2 - - - -
274D ASP* 1.3 75.6 - - - +
276D VAL* 1.3 72.8 + - + +
278D ASN* 3.1 8.1 + - + +
279D LEU* 2.8 52.0 + - + +
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Residues in contact with VAL 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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271D TYR* 3.6 25.8 - - + -
272D ASP 3.0 18.9 + - - +
273D LYS* 3.6 7.6 - - - +
274D ASP 3.2 0.2 - - - -
275D TRP* 1.3 79.9 - - + +
277D CYS* 1.3 64.7 + - - +
279D LEU* 3.0 8.4 + - - +
280D ILE* 3.0 22.4 + - + +
314D ILE* 3.9 11.9 - - + -
315D ILE* 3.9 19.7 - - + -
318D TRP* 3.4 46.9 - - + +
324D LEU* 5.6 2.2 - - + -
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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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273D LYS 3.0 19.5 + - - -
274D ASP* 3.0 6.2 + - - +
276D VAL* 1.3 77.8 - - - +
278D ASN* 1.3 57.6 + - - +
280D ILE* 3.9 0.5 - - - +
281D MET* 2.9 36.1 + - - +
306D ARG* 3.5 26.7 - - - +
311D ASP* 3.5 40.6 - - - +
314D ILE* 4.1 13.9 - - + -
315D ILE* 3.9 17.3 - - - -
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Residues in contact with ASN 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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164D MET* 3.0 30.6 + - + +
167D ASN* 2.9 31.5 + - - -
168D LEU* 3.8 13.5 - - - +
274D ASP 3.0 11.8 + - - +
275D TRP* 3.4 14.3 - - + +
277D CYS* 1.3 75.7 - - - +
279D LEU* 1.3 60.4 + - - +
282D THR* 2.8 32.9 + - - +
303D LEU* 3.2 23.2 - - + +
306D ARG* 3.1 22.5 + - - -
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Residues in contact with LEU 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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101D TYR* 6.0 0.2 - - + -
102D ASN* 3.4 33.2 - - + +
164D MET* 4.8 9.9 - - + -
271D TYR* 6.4 0.4 - - + -
275D TRP* 2.8 47.2 + - + +
276D VAL* 3.0 9.4 + - - +
278D ASN* 1.3 73.0 - - - +
280D ILE* 1.3 65.1 + - + +
282D THR* 3.3 14.4 + - - +
283D TRP* 3.6 5.9 + - - -
286D PHE* 5.7 5.0 - - + -
318D TRP* 3.9 25.6 - - + -
340D ARG* 5.3 1.6 - - - +
344D ILE* 3.7 33.8 - - + +
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Residues in contact with ILE 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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276D VAL* 3.0 20.1 + - + +
277D CYS 3.9 2.9 - - - +
279D LEU* 1.3 77.3 - - - +
281D MET* 1.3 64.3 + - - +
282D THR 3.1 0.2 - - - -
283D TRP* 3.0 21.1 + - - +
314D ILE* 3.7 23.3 - - + -
318D TRP* 4.6 5.4 - - + -
344D ILE* 3.5 40.2 - - + +
347D ILE* 3.7 26.5 - - + -
348D TYR* 3.3 28.4 - - + +
351D LEU* 4.1 16.4 - - + -
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Residues in contact with MET 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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277D CYS 2.9 22.3 + - - +
279D LEU 3.5 0.2 - - - -
280D ILE* 1.3 76.6 - - - +
282D THR* 1.3 61.5 + - - +
283D TRP 3.4 0.2 - - - -
284D PRO* 3.6 8.4 - - - +
302D LEU* 3.6 29.3 - - - +
303D LEU* 4.3 11.7 - - + -
305D LYS* 3.5 45.5 - - + +
306D ARG* 3.6 18.6 - - + +
310D LEU* 4.0 8.1 - - + -
314D ILE* 3.8 12.6 - - + -
348D TYR* 4.3 6.4 - - + -
351D LEU* 3.8 28.0 - - - -
353D ILE* 3.9 20.2 - - + -
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Residues in contact with THR 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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164D MET* 3.6 28.8 - - - +
278D ASN 2.8 21.3 + - - +
279D LEU* 3.3 7.8 + - - +
280D ILE 3.1 0.4 - - - -
281D MET* 1.3 75.8 - - - +
283D TRP* 1.3 66.8 + - - +
284D PRO* 3.1 5.4 - - - -
285D ALA* 2.8 16.1 + - - +
286D PHE* 3.4 24.4 - - - -
299D ILE* 4.1 11.4 - - + -
302D LEU* 4.1 12.6 - - + -
303D LEU* 3.8 26.9 - - + -
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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