Contacts of the helix formed by residues 358 - 367 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333D GLU* 3.5 26.9 - - - -
336D ASP* 2.9 28.1 + - + -
337D PHE* 3.6 29.9 + + + -
340D LYS* 4.3 16.4 - - + -
354D GLN 3.4 12.2 + - - +
355D LEU* 3.0 21.5 + - + +
356D MET 3.5 0.2 - - - -
357D VAL* 1.3 81.8 - - - +
359D ALA* 1.3 80.4 + - + +
360D PHE* 2.9 18.6 + - - +
361D ILE 3.2 2.4 + - - +
362D LYS* 2.9 26.0 + - - +
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Residues in contact with ALA 359 (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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333D GLU* 3.9 22.6 - - + +
357D VAL 3.7 0.6 + - - -
358D HIS* 1.3 84.6 + - + +
360D PHE* 1.3 60.9 + - - +
362D LYS* 3.5 9.6 + - - +
363D ARG* 3.1 26.3 + - - +
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Residues in contact with PHE 360 (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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163D GLU* 3.5 13.7 - - + -
167D GLY* 3.6 36.8 - - - -
170D SER* 3.8 17.9 - - - -
333D GLU* 3.7 20.1 - - - +
334D PHE* 3.4 46.7 - + - -
337D PHE* 3.8 19.7 - + + -
358D HIS* 2.9 15.7 + - - +
359D ALA* 1.3 77.7 - - - +
361D ILE* 1.3 66.9 + - + +
363D ARG* 3.4 34.3 - - - +
364D SER* 3.2 25.3 + - - -
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Residues in contact with ILE 361 (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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167D GLY 4.4 2.5 - - - +
170D SER* 3.9 28.0 - - - -
171D ILE* 4.0 19.8 - - + +
174D ILE* 4.0 11.0 - - + -
337D PHE* 3.6 16.4 - - + -
355D LEU 3.3 21.1 - - - +
356D MET* 3.1 42.6 - - + +
358D HIS* 3.2 5.0 + - - +
359D ALA 3.1 0.8 - - - -
360D PHE* 1.3 84.8 - - + +
362D LYS* 1.3 65.8 + - - +
363D ARG 3.1 1.6 - - - -
364D SER* 3.3 1.7 + - - -
365D ASP* 3.0 26.2 + - + +
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Residues in contact with LYS 362 (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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356D MET 5.2 1.3 - - - +
357D VAL* 3.4 37.4 + - - +
358D HIS 2.9 15.9 + - - +
359D ALA* 3.9 7.6 - - - +
361D ILE* 1.3 76.3 - - - +
363D ARG* 1.3 63.7 + - - +
365D ASP* 3.7 6.3 + - - +
366D ALA* 3.4 17.7 + - - +
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Residues in contact with ARG 363 (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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163D GLU* 3.0 24.9 + - - +
164D GLN* 5.3 3.2 - - - +
331D SER* 3.1 30.5 + - - -
333D GLU* 3.7 20.4 + - - +
359D ALA 3.1 18.0 + - - +
360D PHE* 3.4 25.7 - - - +
362D LYS* 1.3 74.8 - - - +
364D SER* 1.3 68.3 + - - +
366D ALA* 2.8 25.2 + - - +
367D GLU* 2.9 41.1 + - + +
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Residues in contact with SER 364 (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 GLN* 4.7 1.6 + - - -
167D GLY* 3.5 36.3 - - - -
168D LYS* 2.7 33.7 + - - -
171D ILE* 4.2 3.6 - - - -
360D PHE* 3.2 19.1 + - - -
361D ILE* 3.3 3.3 + - - -
363D ARG* 1.3 92.3 + - - +
365D ASP* 1.3 56.1 + - - +
367D GLU* 3.2 25.5 + - - +
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Residues in contact with ASP 365 (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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168D LYS* 4.2 4.7 + - - +
171D ILE* 3.9 26.3 - - + +
175D LYS* 5.0 8.5 + - - -
356D MET* 4.8 11.9 - - - +
361D ILE* 3.0 20.0 + - + +
362D LYS* 3.8 7.4 - - - +
364D SER* 1.3 77.2 - - - +
366D ALA* 1.3 61.8 + - - +
367D GLU 3.8 4.2 - - - +
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Residues in contact with ALA 366 (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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362D LYS 3.4 9.9 + - - +
363D ARG* 2.8 11.9 + - - +
365D ASP* 1.3 78.6 - - - +
367D GLU* 1.3 64.8 + - - +
368D GLU* 3.5 8.0 + - - +
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Residues in contact with GLU 367 (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 GLN* 2.8 47.5 + - - +
168D LYS* 2.9 24.1 + - - -
363D ARG* 2.9 46.2 + - + +
364D SER* 3.2 25.5 + - - +
365D ASP 3.8 2.4 - - - +
366D ALA* 1.3 79.3 - - + +
368D GLU* 1.3 60.6 + - - +
369D VAL* 4.2 9.9 - - + +
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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