Contacts of the helix formed by residues 2413 - 2420 (chain E) in PDB entry 1MZN
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 GLY2413 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2411E GLN 3.3 0.6 - - - -
2412E PRO* 1.3 81.0 - - - +
2414E ARG* 1.3 62.4 + - - +
2415E PHE 3.3 3.1 - - - -
2416E ALA* 3.3 6.8 + - - +
2417E LYS* 3.0 24.3 + - - +
3397G TYR* 3.7 22.8 + - - -
3401G GLU* 5.6 2.0 - - - -
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Residues in contact with ARG2414 (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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2360E MET* 2.9 49.2 + - + +
2361E GLN* 3.1 16.8 + - - +
2362E MET* 3.6 2.6 - - - +
2366E GLU* 2.7 39.2 + - - +
2404E CYS* 4.8 7.9 - - + -
2408E TYR* 3.4 41.6 - - + +
2411E GLN* 2.8 60.0 + - + +
2412E PRO 3.3 0.4 - - - -
2413E GLY* 1.3 76.8 - - - +
2415E PHE* 1.3 63.5 + - - +
2417E LYS* 3.3 8.4 + - + +
2418E LEU* 3.0 29.9 + - + +
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Residues in contact with PHE2415 (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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2397E TYR* 3.4 32.5 - + + -
2400E LEU* 3.9 23.6 - - + -
2401E GLU* 3.7 49.8 - - + +
2404E CYS* 4.5 12.3 - - + +
2405E LYS* 5.1 11.2 - - - +
2412E PRO 4.5 2.1 + - - +
2413E GLY 3.3 0.4 - - - -
2414E ARG* 1.3 78.5 - - - +
2416E ALA* 1.3 64.5 + - - +
2418E LEU* 3.3 10.5 + - - +
2419E LEU* 3.2 37.8 + - + +
3401G GLU* 5.3 0.9 - - - -
3415G PHE* 4.7 15.5 - + - -
3416G ALA* 3.8 33.0 - - + -
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Residues in contact with ALA2416 (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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2413E GLY* 3.3 5.5 + - - +
2415E PHE* 1.3 77.2 - - - +
2417E LYS* 1.3 67.1 + - - +
2419E LEU* 3.2 2.2 + - - +
2420E LEU* 2.9 30.3 + - - +
3397G TYR* 3.5 35.9 - - + -
3401G GLU* 6.0 0.2 - - - +
3415G PHE* 3.9 22.4 - - + -
3419G LEU* 3.9 16.6 - - + -
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Residues in contact with LYS2417 (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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2356E LYS* 5.5 6.2 + - - -
2359E ASP* 5.6 4.4 - - - +
2360E MET* 4.0 42.7 - - + +
2413E GLY 3.0 18.8 + - - +
2414E ARG* 3.3 9.2 + - + +
2416E ALA* 1.3 77.8 - - - +
2418E LEU* 1.3 61.7 + - - +
2420E LEU* 3.4 11.6 + - - +
2421E ARG* 3.7 21.6 + - - +
3390G GLU* 4.7 15.6 + - - -
3394G GLU* 4.4 15.7 + - - +
3397G TYR* 3.8 15.6 + - - +
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Residues in contact with LEU2418 (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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2360E MET* 3.4 24.2 - - + -
2362E MET* 3.6 33.9 - - + -
2366E GLU* 3.8 22.2 - - + +
2370E LEU* 3.7 28.3 - - + +
2400E LEU* 4.1 14.1 - - + -
2404E CYS* 3.6 30.3 - - - -
2414E ARG* 3.0 17.9 + - + +
2415E PHE* 3.5 7.2 - - - +
2417E LYS* 1.3 76.3 - - - +
2419E LEU* 1.3 63.0 + - - +
2421E ARG* 3.2 21.9 + - - +
2422E LEU 4.3 1.0 + - - -
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Residues in contact with LEU2419 (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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2370E LEU* 4.1 11.4 - - + -
2373E ILE* 3.9 28.3 - - + -
2397E TYR* 4.9 1.1 - - + -
2400E LEU* 4.5 2.2 - - + -
2415E PHE* 3.2 46.2 + - + +
2416E ALA 3.7 5.4 - - - +
2418E LEU* 1.3 79.0 - - - +
2420E LEU* 1.3 59.1 + - - +
2421E ARG 3.1 0.7 - - - -
2422E LEU* 3.1 28.6 + - + +
2423E PRO* 3.8 2.6 - - - +
3416G ALA* 3.9 24.9 - - + +
3419G LEU* 4.1 27.9 - - + +
3420G LEU* 4.3 18.7 - - + +
3423G PRO* 5.5 0.3 - - - +
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Residues in contact with LEU2420 (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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2416E ALA* 2.9 21.6 + - + +
2417E LYS* 3.4 6.5 + - - +
2418E LEU 3.2 0.6 - - - -
2419E LEU* 1.3 75.5 - - - +
2421E ARG* 1.3 77.1 + - - +
2422E LEU 3.3 0.4 - - - -
2423E PRO* 3.5 15.6 - - + +
2424E ALA* 4.9 2.1 + - - +
3373G ILE* 4.1 11.9 - - + -
3393G ARG* 4.2 27.9 + - + +
3397G TYR* 3.4 43.5 - - + -
3419G LEU* 4.5 15.9 - - + +
3422G LEU* 3.7 30.3 - - + -
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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