Contacts of the helix formed by residues 441 - 446 (chain A) in PDB entry 2E3O
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 VAL 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A TYR* 3.5 44.4 - - + +
438A ASN* 3.3 27.6 - - + +
440A ASP* 1.3 83.7 - - + +
442A ARG* 1.3 66.6 + - - +
443A ASN 3.3 2.7 - - - -
444A ASP* 3.0 26.5 + - - +
445A TRP* 3.4 9.3 - - - +
586A TYR* 3.4 22.0 - - + +
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Residues in contact with ARG 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A PHE 3.0 22.7 + - - -
437A TRP* 3.4 19.8 + - - +
438A ASN 3.6 4.6 + - - -
439A VAL* 3.2 27.4 + - - +
440A ASP 3.6 0.2 - - - -
441A VAL* 1.3 75.6 - - - +
443A ASN* 1.3 60.5 + - - +
444A ASP 3.2 0.7 + - - -
445A TRP* 3.2 34.2 + - - +
446A GLU* 2.9 49.7 + - + +
449A ILE* 4.6 3.8 - - + -
452A PHE* 3.8 28.0 - - + -
465A ILE* 4.1 12.9 - - - +
467A GLN* 4.3 3.2 + - - -
482A TYR* 3.3 25.3 + - - -
484A SER* 5.1 3.8 + - - -
504A ASN* 5.7 1.8 + - - -
600A 16C 3.5 16.3 + - - -
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Residues in contact with ASN 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A VAL 4.8 0.8 + - - -
440A ASP 5.4 0.4 + - - -
441A VAL 3.3 1.0 - - - -
442A ARG* 1.3 76.2 - - - +
444A ASP* 1.3 63.4 + - - +
445A TRP 3.2 0.8 + - - -
446A GLU* 4.1 12.8 + - - +
449A ILE* 3.8 28.5 - - - +
451A ASN* 6.3 0.2 - - - +
452A PHE* 3.8 19.2 - - - -
582A ARG* 5.1 2.9 + - - -
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ASP 4.9 2.4 - - - +
441A VAL* 3.0 25.5 + - - +
443A ASN* 1.3 81.3 - - - +
445A TRP* 1.3 57.2 + - - +
582A ARG* 3.3 17.9 + - - -
586A TYR* 2.9 44.1 + - + +
590A LYS* 5.0 3.5 - - - -
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Residues in contact with TRP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A TYR 3.3 16.9 + - - -
436A PHE* 3.6 40.2 - + - -
441A VAL 3.4 25.7 + - - -
442A ARG* 3.4 35.8 - - - +
444A ASP* 1.3 79.7 - - - +
446A GLU* 1.3 99.3 + - + +
447A THR* 3.5 1.7 + - - +
579A PHE* 3.5 35.1 - + - -
582A ARG* 2.9 32.9 + - + +
583A PHE* 3.6 25.5 - + + -
586A TYR* 3.8 34.3 - + + -
600A 16C 4.0 8.1 - - - -
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ARG* 2.9 30.9 + - + +
443A ASN* 4.1 14.9 + - - +
445A TRP* 1.3 92.4 - - + +
447A THR* 1.3 66.2 + - - +
448A THR* 2.8 40.0 + - - +
449A ILE* 3.8 34.1 - - + +
579A PHE* 5.9 0.5 - - - +
582A ARG* 5.4 0.7 + - - -
600A 16C 2.7 48.7 + - - +
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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