Contacts of the helix formed by residues 372 - 380 (chain E) in PDB entry 5ZRV
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 MET 372 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369E ALA 5.4 0.2 + - - -
371E LEU* 1.3 77.3 - - - +
373E GLY* 1.3 53.5 + - - +
375E GLY* 4.4 0.7 - - - -
376E ILE* 2.5 35.2 + - - -
447E ALA* 5.9 2.4 + - - +
501E SER 5.9 1.1 - - - -
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Residues in contact with GLY 373 (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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366E ILE* 6.2 4.0 - - - -
368E GLY 3.6 22.2 + - - -
369E ALA* 4.7 2.4 + - - -
370E GLY 4.7 0.8 - - - -
371E LEU 3.6 2.2 - - - +
372E MET* 1.3 74.7 - - - +
374E ALA* 1.3 57.0 + - - +
376E ILE 3.3 0.7 + - - -
377E ALA* 2.9 25.1 + - - -
447E ALA* 5.3 10.3 + - - +
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Residues in contact with ALA 374 (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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369E ALA* 4.6 3.7 - - - +
370E GLY 4.3 18.7 + - - +
373E GLY* 1.3 72.1 - - - +
375E GLY* 1.3 57.7 + - - +
377E ALA* 3.4 2.4 + - - +
378E GLN* 3.0 24.6 + - - -
400E GLY* 4.9 17.5 - - - -
403E GLN* 5.6 2.1 - - - -
404E VAL* 5.0 8.1 + - - -
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Residues in contact with GLY 375 (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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370E GLY 4.8 0.8 + - - -
371E LEU* 3.4 20.6 + - - +
372E MET* 3.0 7.9 + - - -
374E ALA* 1.3 77.4 - - - +
376E ILE* 1.3 56.5 + - - +
378E GLN* 2.9 19.8 + - - -
379E VAL 3.7 3.5 + - - -
503E VAL* 5.3 13.6 - - - -
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Residues in contact with ILE 376 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372E MET 2.5 19.7 + - - -
373E GLY 3.8 0.9 - - - -
375E GLY* 1.3 72.5 - - - -
377E ALA* 1.3 57.0 + - - +
379E VAL* 3.4 2.7 + - - +
380E SER* 3.0 25.5 + - - -
503E VAL* 6.3 0.7 - - - +
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Residues in contact with ALA 377 (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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373E GLY 2.9 17.6 + - - -
374E ALA* 3.7 3.6 - - - +
375E GLY 3.1 0.4 - - - -
376E ILE* 1.3 77.9 - - - +
378E GLN* 1.3 60.3 + - - +
379E VAL 3.2 1.2 + - - -
380E SER* 3.4 9.3 + - - +
381E VAL* 3.5 13.7 + - - -
404E VAL* 5.9 0.7 - - - -
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Residues in contact with GLN 378 (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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374E ALA 3.0 10.4 + - - -
375E GLY* 2.9 11.6 + - - -
377E ALA* 1.3 76.6 - - - +
379E VAL* 1.3 56.2 + - - +
381E VAL* 4.8 1.2 + - - -
382E ASP 5.4 1.9 + - - -
404E VAL* 4.7 17.2 - - - +
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Residues in contact with VAL 379 (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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375E GLY 3.7 4.9 + - - -
376E ILE 3.4 4.7 + - - -
377E ALA 3.1 0.2 - - - -
378E GLN* 1.3 75.6 - - - +
380E SER* 1.3 58.0 + - - +
381E VAL 3.2 8.1 + - - -
382E ASP 4.1 5.6 + - - -
383E LYS 5.1 2.3 + - - -
532E GLN* 5.2 5.9 - - - +
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Residues in contact with SER 380 (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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376E ILE 3.0 16.0 + - - -
377E ALA* 3.4 4.9 + - - +
379E VAL* 1.3 74.4 - - - +
381E VAL* 1.3 57.5 + - - +
382E ASP 3.9 0.2 - - - -
383E LYS 5.3 1.6 - - - -
385E LEU* 3.7 19.3 - - - +
532E GLN* 6.2 3.8 - - - +
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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