Contacts of the helix formed by residues 373 - 381 (chain H) in PDB entry 3E20
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 LEU 373 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H VAL* 4.7 5.4 - - + -
306H MET* 4.1 17.3 - - + -
323H LEU* 5.0 1.3 - - + -
325H MET* 2.7 54.0 + - + +
326H ILE* 4.1 0.6 - - - +
327H ARG* 4.1 11.4 - - + +
341H TYR* 3.7 24.9 - - + -
371H MET 3.6 3.4 + - - -
372H LEU* 1.3 71.2 - - - +
374H SER* 1.3 63.7 + - - +
375H GLU 3.1 0.7 + - - -
376H TRP* 3.9 6.9 - - + +
377H LEU* 3.2 50.5 + - + +
408H ILE* 4.5 14.6 - - + -
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Residues in contact with SER 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TRP* 3.2 25.6 - - - -
16H ARG* 6.4 1.3 - - - -
319H CYS* 4.5 12.3 - - - -
321H ALA 3.4 15.3 + - - -
323H LEU* 4.3 23.9 - - - +
325H MET 4.1 1.8 + - - -
372H LEU* 4.6 8.7 - - - -
373H LEU* 1.3 81.0 - - - +
375H GLU* 1.3 58.9 + - - +
377H LEU* 4.0 2.4 + - - +
378H ALA* 3.8 6.8 + - - +
390H PHE* 3.7 25.6 - - - -
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Residues in contact with GLU 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TRP* 5.4 4.5 - - - +
13H LYS* 6.5 0.9 - - + -
16H ARG* 2.7 38.0 + - - +
371H MET* 4.1 22.2 - - + +
372H LEU* 2.7 25.0 + - + +
374H SER* 1.3 72.7 - - - +
376H TRP* 1.3 62.9 + - - +
377H LEU 3.2 1.6 - - - -
378H ALA* 3.3 8.8 + - + +
379H GLU* 3.3 26.8 + - + +
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Residues in contact with TRP 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H MET* 4.9 9.9 - - - -
309H LEU* 5.0 4.3 - - + -
327H ARG* 3.0 64.2 - - - +
371H MET* 3.8 27.3 - - + -
372H LEU 3.0 9.1 + - - +
373H LEU* 3.2 7.4 + - + +
375H GLU* 1.3 77.4 - - - +
377H LEU* 1.3 80.1 + - + +
379H GLU* 3.1 3.6 + - - +
380H HIS* 3.0 77.4 + + + +
384H TYR* 3.5 30.3 - + - -
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Residues in contact with LEU 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H MET* 3.5 24.9 - - + -
309H LEU* 4.0 15.7 - - + -
317H LEU* 4.2 16.6 - - + -
319H CYS* 4.4 20.0 - - + -
373H LEU* 3.2 34.5 + - + +
374H SER* 4.2 4.5 - - - +
376H TRP* 1.3 91.8 - - + +
378H ALA* 1.3 57.4 + - - +
381H TYR* 2.7 39.4 + - + +
388H LEU* 4.0 11.4 - - + -
390H PHE* 5.4 0.2 - - + -
408H ILE* 4.1 18.4 - - + -
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Residues in contact with ALA 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 4.9 4.8 - - + +
12H TRP* 4.1 16.2 - - + +
13H LYS* 5.0 17.3 + - + -
374H SER 3.8 4.0 + - - +
375H GLU* 3.3 11.1 + - + +
376H TRP 3.3 0.6 - - - -
377H LEU* 1.3 78.2 - - - +
379H GLU* 1.3 60.5 + - + +
380H HIS 3.5 0.2 - - - -
381H TYR* 3.3 25.7 - - - -
388H LEU* 3.9 5.1 - - + +
390H PHE* 4.0 22.4 - - + -
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Residues in contact with GLU 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LYS* 4.0 23.0 + - + +
371H MET* 5.6 4.3 - - - -
375H GLU* 3.3 21.4 + - + +
376H TRP* 3.1 6.8 + - - +
377H LEU 3.1 0.4 - - - -
378H ALA* 1.3 82.1 - - + +
380H HIS* 1.3 75.7 + - + +
381H TYR* 3.9 0.4 - - - -
383H ASP* 4.8 2.6 - - - +
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Residues in contact with HIS 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H MET* 5.8 3.8 - - + -
376H TRP* 3.0 69.8 + + + +
377H LEU* 5.1 0.2 - - - -
379H GLU* 1.3 100.1 + - + +
381H TYR* 1.3 68.6 + - - +
382H LYS 3.2 3.1 - - - -
383H ASP* 3.1 21.3 + - + +
384H TYR* 3.0 24.8 - + + -
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Residues in contact with TYR 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 3.5 38.9 - - + +
309H LEU* 5.3 5.4 - - - -
317H LEU* 4.9 10.5 - - + -
377H LEU* 2.7 34.7 + - - +
378H ALA* 3.3 24.7 - - - -
380H HIS* 1.3 72.0 - - - +
382H LYS* 1.3 96.9 + - + +
383H ASP 3.1 0.5 + - - -
384H TYR* 3.3 19.9 + - - +
386H ALA* 3.0 15.9 + - + +
387H ASN* 3.6 21.1 - - - -
388H LEU* 3.4 32.5 - - + -
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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
------------------------------------------------------------
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