Contacts of the helix formed by residues 420 - 426 (chain E) in PDB entry 3A13
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 PRO 420 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E GLN* 5.5 9.0 - - - +
418E GLY 3.3 11.0 - - - +
419E ILE* 1.3 92.1 - - + +
421E LEU* 1.3 64.7 + - - +
422E ASP* 3.5 3.4 - - + +
423E GLU* 3.4 11.5 + - + +
424E TYR 3.4 13.7 + - - -
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Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PRO 5.8 3.1 - - - +
373E GLY* 6.1 3.4 - - - -
376E GLN* 6.5 1.1 - - + -
411E ALA* 5.6 4.7 - - + -
414E ALA* 4.9 5.8 - - + -
415E ILE* 6.2 3.6 - - + +
419E ILE 3.3 5.0 + - - -
420E PRO* 1.3 70.4 - - - +
422E ASP* 1.3 60.0 + - - +
424E TYR* 2.9 10.4 + - - +
425E ALA* 2.8 28.9 + - - +
431E LEU* 4.2 12.8 - - + +
435E LEU* 4.1 18.4 - - + -
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Residues in contact with ASP 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E PRO* 3.5 2.3 - - + +
421E LEU* 1.3 79.2 - - - +
423E GLU* 1.3 63.5 + - - +
425E ALA* 3.2 20.1 - - - +
426E LYS* 3.7 4.5 + - - +
435E LEU* 3.9 17.6 - - - +
440E HIS* 5.8 4.5 + - - -
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Residues in contact with GLU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E ILE* 4.3 11.2 - - + -
420E PRO* 3.4 17.9 + - + +
421E LEU 3.2 0.2 - - - -
422E ASP* 1.3 77.6 - - - +
424E TYR* 1.3 61.7 + - - +
425E ALA 3.0 1.4 + - - -
426E LYS* 3.1 20.5 + - - +
427E THR* 3.8 5.8 + - - -
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Residues in contact with TYR 424 (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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410E GLN* 3.5 27.0 - - + +
413E ASP* 4.0 14.4 + - - +
414E ALA* 3.7 24.0 - - + -
417E GLN* 4.1 19.3 + - - -
419E ILE* 4.0 25.0 - - + +
420E PRO 3.4 6.3 + - - +
421E LEU 2.9 9.1 + - - +
423E GLU* 1.3 77.6 - - - +
425E ALA* 1.3 60.8 + - - +
426E LYS 3.3 0.2 - - - -
427E THR* 3.3 5.9 + - - -
428E HIS* 2.6 81.5 + + - +
431E LEU* 3.6 16.8 - - + -
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Residues in contact with ALA 425 (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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421E LEU 2.8 10.9 + - - +
422E ASP* 3.2 22.0 - - - +
423E GLU 3.0 0.4 - - - -
424E TYR* 1.3 73.3 - - - +
426E LYS* 1.3 54.7 + - - +
427E THR 3.1 5.2 - - - -
428E HIS 2.9 29.9 + - - +
429E LYS* 4.7 0.3 - - - -
431E LEU* 4.4 5.6 - - + -
432E ALA* 3.3 30.4 - - + +
435E LEU* 4.3 9.2 - - + -
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Residues in contact with LYS 426 (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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422E ASP 3.7 3.7 + - - +
423E GLU* 3.1 13.2 + - - +
425E ALA* 1.3 78.0 - - - +
427E THR* 1.3 59.9 + - - +
182I SER* 4.0 25.6 + - - +
183I ASN* 3.9 24.5 - - - +
219I GLU* 5.5 0.2 - - - +
220I THR* 4.4 13.3 - - - +
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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