Contacts of the helix formed by residues 272 - 282 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A CYS* 3.1 38.9 + - + +
119A ILE* 4.1 0.2 - - - +
120A ASN* 3.0 25.4 + - - +
125A ARG* 2.9 43.8 + - - -
168A LEU* 4.0 0.5 - - - +
270A GLU 3.6 1.6 + - - -
271A TYR* 1.3 71.6 - - - +
273A LYS* 1.3 61.3 + - - +
274A ASP* 3.3 4.0 + - - +
275A TRP* 3.0 27.9 + - + +
276A VAL* 2.9 29.6 + - - +
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Residues in contact with LYS 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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120A ASN* 4.6 12.7 - - - +
270A GLU* 5.2 7.7 + - - -
271A TYR 3.7 2.3 + - - +
272A ASP* 1.3 75.5 + - - +
274A ASP* 1.3 65.7 + - - +
276A VAL* 3.3 3.5 + - - +
277A CYS* 3.0 29.5 + - - -
315A ILE* 3.6 35.8 - - + +
319A GLU* 5.6 0.2 - - - -
324A LEU* 4.0 33.9 - - + +
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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
----------------------------------------------------------
125A ARG* 3.6 16.9 + - - +
167A ASN 5.8 1.1 - - - -
168A LEU* 3.8 21.3 - - + +
170A GLN* 6.6 0.2 - - - -
171A SER* 3.9 26.9 + - - -
272A ASP* 3.3 9.8 + - - +
273A LYS* 1.3 79.2 - - - +
275A TRP* 1.3 62.7 + - - +
277A CYS* 3.2 4.7 + - - +
278A ASN* 3.0 26.5 + - - +
306A ARG* 3.0 30.1 + - - +
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Residues in contact with TRP 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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102A ASN* 5.3 4.7 + - - -
116A CYS* 3.2 31.0 - - - -
117A SER* 3.4 24.9 - - - -
118A CYS* 3.7 23.8 - - + +
164A MET* 3.6 52.5 - - + -
165A LEU* 4.1 9.0 - - + -
168A LEU* 3.6 13.6 - - + +
271A TYR* 5.6 7.6 - + - -
272A ASP* 3.0 23.4 + - + +
274A ASP* 1.3 73.2 - - - +
276A VAL* 1.3 69.0 + - + +
278A ASN* 3.1 7.3 + - + +
279A LEU* 2.8 59.1 + - + +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TYR* 3.7 25.4 - - + -
272A ASP 2.9 22.8 + - - +
273A LYS* 3.6 4.7 - - - +
275A TRP* 1.3 76.8 - - + +
277A CYS* 1.3 57.9 + - - +
279A LEU* 3.2 8.4 + - + +
280A ILE* 2.9 29.3 + - + +
314A ILE* 3.8 18.4 - - + -
315A ILE* 3.9 12.8 - - + -
318A TRP* 3.5 49.8 - - + +
324A LEU* 5.2 1.6 - - + -
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Residues in contact with CYS 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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273A LYS* 3.0 18.3 + - - +
274A ASP 3.4 9.0 - - - +
276A VAL* 1.3 77.0 - - - +
278A ASN* 1.3 56.6 + - - +
280A ILE* 3.4 1.0 + - - +
281A MET* 2.9 37.7 + - - +
306A ARG* 3.6 22.2 - - - +
311A ASP* 3.4 46.9 - - - +
314A ILE* 4.1 13.9 - - + -
315A ILE* 3.9 10.3 - - - -
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Residues in contact with ASN 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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164A MET* 3.0 28.5 + - + +
167A ASN* 2.9 31.7 + - - +
168A LEU* 3.7 13.5 - - - +
274A ASP 3.0 10.5 + - - -
275A TRP* 3.4 14.1 - - + +
277A CYS* 1.3 71.3 - - - +
279A LEU* 1.3 59.9 + - - +
281A MET 3.4 0.3 + - - -
282A THR* 2.7 39.9 + - - +
303A LEU* 3.3 23.1 - - + +
306A ARG* 3.0 23.7 + - - -
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Residues in contact with LEU 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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102A ASN* 3.4 32.1 - - + +
164A MET* 4.8 8.7 - - + +
275A TRP* 2.8 46.1 + - + +
276A VAL* 3.4 9.6 - - - +
278A ASN* 1.3 77.5 - - - +
280A ILE* 1.3 63.8 + - + +
282A THR* 3.3 14.0 + - - +
283A TRP* 3.7 5.5 + - - -
286A PHE* 5.9 3.3 - - + -
318A TRP* 4.0 23.8 - - + -
340A ARG* 5.3 1.8 - - - +
344A ILE* 3.9 33.6 - - + +
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Residues in contact with ILE 280 (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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276A VAL* 2.9 19.5 + - + +
279A LEU* 1.3 76.2 - - - +
281A MET* 1.3 65.4 + - - +
283A TRP* 3.0 20.6 + - - +
314A ILE* 3.5 26.7 - - + -
318A TRP* 4.0 25.6 - - + -
344A ILE* 4.0 31.6 - - + -
347A ILE* 3.9 16.2 - - + -
348A TYR* 3.4 35.5 - - + +
351A LEU* 4.0 16.6 - - + -
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Residues in contact with MET 281 (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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277A CYS 2.9 22.0 + - - +
278A ASN 4.1 1.8 - - - +
280A ILE* 1.3 76.3 - - - +
282A THR* 1.3 60.7 + - - +
283A TRP 3.3 0.9 + - - -
284A PRO* 3.6 10.9 - - - +
302A LEU* 3.8 23.1 - - - +
303A LEU* 4.3 12.3 - - + -
305A LYS* 3.8 43.3 - - + +
306A ARG* 3.8 16.6 - - + +
310A LEU* 4.2 16.2 - - + -
314A ILE* 3.7 24.0 - - + -
348A TYR* 4.1 8.9 - - + -
351A LEU* 3.8 17.7 - - - -
353A ILE* 4.4 11.4 - - + -
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Residues in contact with THR 282 (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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164A MET* 3.6 19.3 - - - +
278A ASN 2.7 24.1 + - - +
279A LEU* 3.3 7.6 + - - +
281A MET* 1.3 75.0 - - - +
283A TRP* 1.3 66.5 + - - +
284A PRO* 3.2 4.3 - - - -
285A ALA* 2.9 15.1 + - - +
286A PHE* 3.4 25.3 - - - -
299A ILE* 3.9 26.2 - - + +
302A LEU* 4.2 9.0 - - + -
303A LEU* 3.6 27.6 - - + -
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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