Contacts of the helix formed by residues 444 - 456 (chain A) in PDB entry 2EBT
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 ARG 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A PHE* 3.9 7.4 - - - +
442A PHE* 3.8 16.6 - - - +
443A SER* 1.3 88.7 - - - +
445A SER* 1.3 64.1 + - - +
446A ASP* 4.6 19.9 + - - +
447A HIS* 3.5 45.3 + - + +
448A LEU 3.8 4.7 + - - -
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Residues in contact with SER 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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433A PHE* 3.3 36.3 - - - -
444A ARG* 1.3 69.7 - - - +
446A ASP* 1.3 78.0 + - - +
447A HIS 3.0 1.6 - - - -
448A LEU* 2.7 19.2 + - - +
449A ALA* 3.1 12.0 + - - +
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Residues in contact with ASP 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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444A ARG* 4.6 21.0 + - - +
445A SER* 1.3 82.3 + - - +
447A HIS* 1.3 76.0 + - - +
449A ALA* 3.2 6.8 + - - +
450A LEU* 2.9 50.8 + - - +
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Residues in contact with HIS 447 (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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409A GLY* 6.4 2.5 - - - -
442A PHE* 4.5 16.5 - + + -
443A SER* 5.6 1.6 + - - -
444A ARG* 3.5 54.4 + - + +
445A SER 2.9 0.6 + - - -
446A ASP* 1.3 89.1 + - - +
448A LEU* 1.3 53.4 + - - +
450A LEU* 3.7 2.9 - - + +
451A HIS* 2.7 37.3 + - - +
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Residues in contact with LEU 448 (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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433A PHE* 4.5 23.1 - - + -
434A GLN 4.0 9.4 - - - +
435A CYS* 3.7 45.3 - - + +
442A PHE* 4.0 21.2 - - + -
444A ARG 3.8 6.6 + - - +
445A SER* 2.7 16.4 + - - +
447A HIS* 1.3 75.0 - - - +
449A ALA* 1.3 64.2 + - - +
451A HIS* 3.1 7.6 + - + +
452A MET* 3.1 28.2 + - + +
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Residues in contact with ALA 449 (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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445A SER 3.1 7.3 + - - +
446A ASP* 3.6 10.8 - - - +
448A LEU* 1.3 83.5 - - - +
450A LEU* 1.3 67.5 + - + +
452A MET* 3.3 21.1 - - - +
453A LYS* 4.2 3.1 + - - +
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Residues in contact with LEU 450 (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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446A ASP* 2.9 56.8 + - - +
447A HIS* 4.0 3.1 - - - +
449A ALA* 1.3 75.0 - - + +
451A HIS* 1.3 66.5 + - - +
453A LYS* 2.9 34.9 - - + +
454A ARG 4.4 0.2 + - - -
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Residues in contact with HIS 451 (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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300A ZN 2.0 37.8 - - - -
435A CYS* 3.5 9.9 - - - -
438A CYS* 4.0 5.8 - - + -
440A ARG* 4.9 5.6 - - - -
442A PHE* 3.4 29.1 - + + -
447A HIS 2.7 25.5 + - - +
448A LEU* 3.1 10.1 + - + +
450A LEU* 1.3 72.3 - - - +
452A MET* 1.3 71.4 + - - +
454A ARG* 2.7 37.7 + - + +
455A HIS* 3.2 7.1 + + - -
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Residues in contact with MET 452 (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 CYS* 3.8 25.1 - - - -
436A GLY* 4.3 11.0 - - - +
437A VAL* 5.3 6.1 - - + +
448A LEU* 3.1 19.0 + - + +
449A ALA* 3.3 14.1 - - - +
450A LEU 3.2 0.2 - - - -
451A HIS* 1.3 83.1 - - - +
453A LYS* 1.3 53.5 + - - +
455A HIS* 2.6 49.2 + - + +
456A GLN* 3.2 15.1 + - - +
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Residues in contact with LYS 453 (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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449A ALA 4.7 2.2 - - - +
450A LEU* 2.9 31.4 - - + +
451A HIS 2.7 3.6 + - - -
452A MET* 1.3 75.0 - - - +
454A ARG* 1.3 53.4 + - - +
456A GLN* 2.6 59.4 + - - +
457A ASN 4.5 3.7 - - - +
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Residues in contact with ARG 454 (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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451A HIS* 2.7 32.7 + - + +
453A LYS* 1.3 72.3 - - - +
455A HIS* 1.3 67.8 + - + +
456A GLN 3.3 3.5 - - - +
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Residues in contact with HIS 455 (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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300A ZN 2.1 36.9 - - - -
435A CYS* 3.8 8.5 - - - -
437A VAL* 3.4 45.7 - - + +
438A CYS* 3.6 12.6 - - + -
451A HIS* 3.2 14.1 + + - -
452A MET* 2.6 25.4 + - - +
454A ARG* 1.3 80.4 - - + +
456A GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 456 (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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452A MET* 3.9 9.2 - - - +
453A LYS* 2.6 64.5 + - + +
454A ARG 3.3 4.7 - - - +
455A HIS* 1.3 84.2 - - - +
457A ASN* 1.3 85.2 + - - +
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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