Contacts of the helix formed by residues 436 - 445 (chain A) in PDB entry 2DB3
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 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ASP* 4.1 7.0 - - + +
435A PHE* 1.3 86.4 - - - +
437A GLU* 1.3 56.6 + - - +
438A GLU* 3.1 29.2 - - + +
439A ILE* 2.6 50.1 + - + -
440A GLN 3.0 8.8 + - - -
569A LYS* 6.2 1.8 - - - +
571A ASP* 3.1 25.8 - - - +
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Residues in contact with GLU 437 (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 PHE 3.3 3.0 + - - -
436A PRO* 1.3 68.9 - - - +
438A GLU* 1.3 70.1 + - - +
440A GLN* 3.0 26.5 + - + +
441A ARG* 3.0 44.8 + - + +
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Residues in contact with GLU 438 (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 PRO* 3.2 24.4 - - + +
437A GLU* 1.3 83.5 + - - +
439A ILE* 1.3 68.8 + - + +
441A ARG* 3.5 13.4 + - - +
442A MET* 3.4 29.9 + - + +
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Residues in contact with ILE 439 (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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402A ASP* 3.3 35.4 - - + +
405A LEU* 4.1 14.4 - - + -
406A ASP* 4.1 22.4 - - + +
435A PHE* 3.4 20.9 - - + -
436A PRO* 2.6 35.8 + - + +
438A GLU* 1.3 78.3 - - + +
440A GLN* 1.3 63.0 + - - +
441A ARG 3.1 1.3 - - - -
442A MET* 3.2 23.2 + - + +
443A ALA* 3.0 21.7 + - - +
569A LYS* 6.0 0.7 - - - +
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Residues in contact with GLN 440 (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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286A MET* 3.7 18.2 - - + +
435A PHE* 2.9 50.1 + - + +
436A PRO 3.0 6.4 + - - +
437A GLU* 3.0 30.2 + - + +
439A ILE* 1.3 77.1 - - - +
441A ARG* 1.3 63.1 + - + +
443A ALA* 3.4 3.1 + - - +
444A GLY* 3.3 17.5 + - - -
450A TYR* 4.4 6.7 + - - +
452A PHE* 3.4 31.5 - - - -
458A VAL* 4.3 11.1 - - - +
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Residues in contact with ARG 441 (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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437A GLU* 3.0 34.8 + - + +
438A GLU* 3.7 13.0 - - - +
439A ILE 3.1 0.2 - - - -
440A GLN* 1.3 77.2 - - + +
442A MET* 1.3 64.0 + - + +
444A GLY* 3.4 12.0 + - - -
445A GLU* 4.0 3.6 + - - +
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Residues in contact with MET 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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405A LEU* 3.7 28.5 - - + +
406A ASP* 4.9 5.2 - - - +
407A MET 5.8 0.4 - - - +
410A SER* 5.8 3.4 - - - -
438A GLU* 3.4 13.7 + - + +
439A ILE* 3.2 42.5 + - + +
441A ARG* 1.3 77.2 - - + +
443A ALA* 1.3 62.7 + - - +
445A GLU* 3.4 20.3 + - - +
446A PHE* 3.6 15.0 - - + -
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Residues in contact with ALA 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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286A MET* 3.6 20.9 - - + -
405A LEU* 3.5 18.8 - - + +
430A MET* 3.4 29.1 - - - +
435A PHE* 4.2 3.4 - - + -
439A ILE 3.0 12.7 + - - +
440A GLN 3.6 0.7 - - - +
442A MET* 1.3 77.5 - - - +
444A GLY* 1.3 53.5 + - - +
446A PHE* 2.7 35.0 + - - +
447A LEU* 3.5 8.6 + - - +
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Residues in contact with GLY 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 GLN 3.3 9.5 + - - -
441A ARG 3.4 5.6 + - - -
442A MET 3.3 1.4 - - - -
443A ALA* 1.3 78.0 - - - +
445A GLU* 1.3 62.3 + - - +
446A PHE 3.1 0.2 - - - -
447A LEU* 3.1 22.8 - - - +
450A TYR* 4.1 24.6 - - - -
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Residues in contact with GLU 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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414A ARG* 3.0 41.8 + - - -
441A ARG 4.0 4.5 + - - +
442A MET* 3.4 14.8 + - - +
443A ALA 2.9 1.0 + - - -
444A GLY* 1.3 77.2 - - - +
446A PHE* 1.3 74.3 + - + +
447A LEU 3.4 2.6 + - - +
448A LYS* 5.3 6.2 - - - -
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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