Contacts of the helix formed by residues 358 - 367 (chain E) in PDB entry 4MNE
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 HIS 358 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333E GLU* 3.3 27.8 - - - -
336E ASP* 2.6 30.7 + - + -
337E PHE* 3.6 26.0 + + + -
340E LYS* 4.3 15.9 - - + -
354E GLN 3.4 6.8 + - - +
355E LEU* 3.3 24.3 + - + +
357E VAL* 1.3 81.0 - - - +
359E ALA* 1.3 88.0 + - + +
360E PHE* 3.0 20.9 + - + +
361E ILE* 3.0 4.5 + - - +
362E LYS* 3.0 17.4 + - - +
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Residues in contact with ALA 359 (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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333E GLU* 3.9 22.4 - - + -
357E VAL 3.7 2.1 + - - -
358E HIS* 1.3 79.0 + - + +
360E PHE* 1.3 63.9 + - - +
362E LYS* 2.9 14.4 + - - +
363E ARG* 2.9 25.5 + - - +
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Residues in contact with PHE 360 (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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163E GLU* 4.3 9.2 - - + -
167E GLY* 3.4 35.4 - - - -
170E SER* 3.9 10.5 - - - -
333E GLU* 3.5 21.4 - - - +
334E PHE* 3.4 46.0 - + + -
337E PHE* 3.6 28.0 - + + -
358E HIS* 3.0 15.4 + - + +
359E ALA* 1.3 77.6 - - - +
361E ILE* 1.3 71.2 + - + +
363E ARG* 3.6 20.9 + - - +
364E SER* 2.7 44.8 + - - -
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Residues in contact with ILE 361 (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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167E GLY 4.5 1.1 - - - +
170E SER* 4.0 12.8 - - - -
171E ILE* 4.2 22.2 - - + -
174E ILE* 4.2 8.7 - - + -
337E PHE* 3.5 23.3 - - + -
355E LEU 3.2 24.2 - - - +
356E MET* 3.4 35.4 - - - +
358E HIS 3.0 5.9 + - - +
360E PHE* 1.3 95.9 - - + +
362E LYS* 1.3 65.2 + - - +
364E SER* 3.3 1.8 + - - +
365E ASP* 3.0 28.6 + - + +
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Residues in contact with LYS 362 (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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356E MET 5.0 2.2 - - - +
357E VAL* 3.2 41.4 - - - +
358E HIS 3.0 10.4 + - - +
359E ALA* 2.9 13.8 + - - +
361E ILE* 1.3 76.6 - - - +
363E ARG* 1.3 62.5 + - - +
365E ASP* 3.6 5.8 + - - +
366E ALA* 3.5 18.4 + - - +
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Residues in contact with ARG 363 (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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163E GLU* 3.0 29.1 + - - +
164E GLN* 5.0 7.1 - - - +
331E SER* 3.2 16.8 + - - -
333E GLU* 3.6 23.9 + - + +
359E ALA 2.9 14.5 + - - +
360E PHE* 3.7 22.5 + - - +
362E LYS* 1.3 75.7 - - - +
364E SER* 1.3 68.1 + - - +
366E ALA* 3.2 13.7 + - - +
367E GLU* 2.9 51.9 + - + +
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Residues in contact with SER 364 (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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164E GLN* 5.3 2.3 + - - -
167E GLY* 3.7 29.8 - - - -
168E LYS* 3.1 21.6 + - - -
171E ILE* 4.0 11.9 - - - -
360E PHE* 2.7 34.8 + - - -
361E ILE* 3.3 5.1 + - - -
363E ARG* 1.3 79.2 + - - +
365E ASP* 1.3 64.5 + - - +
366E ALA 3.2 0.7 + - - -
367E GLU* 3.2 22.7 + - - +
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Residues in contact with ASP 365 (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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168E LYS* 4.0 7.8 + - - +
171E ILE* 3.6 29.9 - - + +
175E LYS* 5.5 6.7 + - - -
361E ILE* 3.0 21.1 + - + +
362E LYS* 3.9 6.5 - - - +
363E ARG 3.2 0.4 - - - -
364E SER* 1.3 77.1 - - - +
366E ALA* 1.3 59.7 + - - +
367E GLU 4.0 4.2 - - - +
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Residues in contact with ALA 366 (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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362E LYS 3.5 10.4 + - - +
363E ARG* 3.2 10.3 + - - +
364E SER 3.1 0.4 - - - -
365E ASP* 1.3 78.9 - - - +
367E GLU* 1.3 66.9 + - + +
368E GLU* 3.6 4.3 + - - +
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Residues in contact with GLU 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E GLN* 3.3 37.5 - - - +
168E LYS* 3.2 23.0 + - - -
363E ARG* 2.9 51.3 + - + +
364E SER* 3.2 15.6 + - - +
365E ASP 4.0 1.6 - - - +
366E ALA* 1.3 81.5 - - + +
368E GLU* 1.3 62.1 + - - +
369E VAL* 3.6 14.6 - - + +
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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