Contacts of the helix formed by residues 270 - 277 (chain E) in PDB entry 1M1J
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 ALA 270 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269E ARG* 1.3 80.4 - - - +
271E TRP* 1.3 65.8 + - - +
272E ASP* 3.4 7.2 - - + +
273E GLU* 3.4 11.3 + - + +
274E TYR* 3.2 18.7 + - - -
381E THR* 3.9 2.2 - - - -
382E TYR* 3.5 24.4 + - + +
383E ASP* 3.5 20.4 - - - +
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Residues in contact with TRP 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ALA* 1.3 73.3 - - - +
272E ASP* 1.3 73.3 + - - +
274E TYR* 3.3 3.6 + - - +
275E LYS* 2.9 30.4 + - + +
300E ASN* 5.8 0.2 - - - -
338E GLU* 2.9 33.1 + - + -
341E LYS* 4.5 9.2 - - + -
342E TYR* 3.3 37.6 - + - -
379E PHE* 3.3 39.5 - + - -
381E THR* 3.3 28.9 + - + +
383E ASP* 2.9 18.7 + - - +
384E ARG* 3.3 60.5 - - + +
386E ASN* 4.3 6.5 - - - -
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Residues in contact with ASP 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ALA* 3.4 5.1 - - + +
271E TRP* 1.3 87.5 - - - +
273E GLU* 1.3 66.3 + - + +
275E LYS* 3.2 15.6 + - + +
276E ARG* 3.1 43.8 + - - +
383E ASP* 5.3 0.2 + - - -
384E ARG* 5.5 0.3 + - - -
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Residues in contact with GLU 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E ARG* 2.7 64.5 + - + -
270E ALA* 3.4 12.2 + - + +
271E TRP 3.2 0.6 - - - -
272E ASP* 1.3 78.7 - - + +
274E TYR* 1.3 55.6 + - - +
275E LYS 3.0 0.5 + - - -
276E ARG* 2.7 35.1 + - - +
277E GLY* 2.7 38.4 + - - +
278E PHE* 4.1 9.2 - - + +
136F GLN* 4.5 5.3 + - - +
137F GLU* 5.5 2.1 - - - +
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Residues in contact with TYR 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E PHE* 2.9 34.9 + - - -
269E ARG 3.4 25.4 - - - -
270E ALA 3.2 9.3 + - - +
271E TRP* 3.8 4.0 - - + +
273E GLU* 1.3 78.9 - - - +
275E LYS* 1.3 55.8 + - - +
277E GLY 4.2 0.2 - - - -
278E PHE* 3.8 22.0 - + - -
297E TRP* 3.2 36.0 + + - -
299E GLY* 3.7 0.2 - - - -
300E ASN* 2.9 29.0 + - - +
379E PHE* 3.6 26.0 - + + -
381E THR* 4.1 3.8 - - + -
405E GLY* 3.3 24.4 + - - -
417E ASN* 3.2 44.4 - - - +
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Residues in contact with LYS 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E TRP* 2.9 20.2 + - - +
272E ASP* 3.3 20.2 + - - +
273E GLU 3.0 0.2 - - - -
274E TYR* 1.3 79.5 - - - +
276E ARG* 1.3 67.1 + - + +
299E GLY 3.4 1.6 - - - -
300E ASN* 3.0 25.7 + - - +
301E ASP* 2.9 40.6 + - - +
302E LYS* 4.8 0.7 + - - +
338E GLU* 3.2 34.9 + - - +
342E TYR* 3.2 14.8 - - + +
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Residues in contact with ARG 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ASP* 3.1 29.6 + - - +
273E GLU* 2.7 29.3 + - - +
275E LYS* 1.3 87.6 - - + +
277E GLY* 1.3 69.8 + - - +
298E LEU 3.6 8.1 - - - +
299E GLY* 3.7 2.6 - - - -
301E ASP* 5.4 1.6 - - - +
302E LYS* 4.4 15.1 + - - +
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Residues in contact with GLY 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E GLU* 2.7 20.2 + - - +
276E ARG* 1.3 88.1 + - - +
278E PHE* 1.3 66.5 + - - +
297E TRP* 3.1 16.2 - - - -
298E LEU 3.5 3.4 - - - -
299E GLY* 3.5 13.1 - - - -
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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