Contacts of the helix formed by residues 436 - 444 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D ASP* 3.9 19.5 - - + +
435D PHE* 1.3 90.9 - - - +
437D GLU* 1.3 67.3 + - - +
438D GLU* 4.4 6.5 - - + +
439D ILE* 3.0 35.9 + - + -
440D GLN* 3.0 9.2 + - - +
571D ASP* 3.2 27.8 - - - +
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D PHE 3.5 2.5 + - - -
436D PRO* 1.3 70.5 - - - +
438D GLU* 1.3 63.0 + - - +
440D GLN* 3.0 24.6 + - + +
441D ARG* 3.0 43.6 + - - +
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Residues in contact with GLU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D PRO* 3.2 4.9 - - + +
437D GLU* 1.3 77.6 - - - +
439D ILE* 1.3 69.9 + - + +
441D ARG* 3.6 16.8 + - - +
442D MET* 3.5 38.1 + - + +
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Residues in contact with ILE 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ASP* 3.6 44.2 - - + +
405D LEU* 3.8 16.9 - - + +
406D ASP* 4.1 22.9 - - + +
435D PHE* 3.7 8.5 - - + -
436D PRO* 3.0 35.7 + - + +
438D GLU* 1.3 79.7 - - + +
440D GLN* 1.3 61.1 + - - +
441D ARG 3.1 2.2 - - - -
442D MET* 3.3 19.2 + - + +
443D ALA* 3.0 26.3 + - - +
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Residues in contact with GLN 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D MET* 3.7 19.1 - - - +
435D PHE* 2.8 48.7 + - + +
436D PRO 3.0 8.9 + - - +
437D GLU* 3.0 27.4 + - + +
439D ILE* 1.3 77.1 - - - +
441D ARG* 1.3 62.9 + - + +
443D ALA* 3.4 2.8 + - - +
444D GLY* 3.2 18.7 + - - -
450D TYR* 4.3 6.8 + - - +
452D PHE* 3.4 32.4 - - - -
458D VAL* 4.3 10.9 - - - +
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Residues in contact with ARG 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D GLU* 3.0 32.2 + - + +
438D GLU* 3.7 19.7 - - - +
440D GLN* 1.3 76.0 - - + +
442D MET* 1.3 65.7 + - + +
444D GLY* 3.4 11.4 + - - -
445D GLU* 4.0 4.3 + - - +
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Residues in contact with MET 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D LEU* 3.4 32.1 - - + +
406D ASP* 4.7 5.4 - - - +
410D SER* 5.8 3.4 - - - -
438D GLU* 3.5 29.8 + - + +
439D ILE* 3.3 35.3 + - + +
441D ARG* 1.3 76.7 - - + +
443D ALA* 1.3 64.4 + - - +
445D GLU* 3.4 11.9 + - - +
446D PHE* 3.3 25.1 - - + -
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Residues in contact with ALA 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D MET* 3.4 26.7 - - + -
405D LEU* 3.4 27.5 - - + +
430D MET* 3.5 14.2 - - - +
435D PHE* 4.1 3.6 - - + -
439D ILE 3.0 9.9 + - - +
440D GLN 3.5 2.9 - - - +
442D MET* 1.3 78.3 - - - +
444D GLY* 1.3 57.1 + - - +
446D PHE* 2.9 24.8 + - - +
447D LEU* 3.4 14.0 + - - +
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Residues in contact with GLY 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D GLN 3.2 10.6 + - - -
441D ARG* 3.4 6.0 + - - -
442D MET 3.3 1.0 - - - -
443D ALA* 1.3 78.6 - - - +
445D GLU* 1.3 59.4 + - - +
446D PHE 3.2 0.4 - - - -
447D LEU* 3.1 21.3 - - - +
450D TYR* 4.0 25.5 - - - -
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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