Contacts of the helix formed by residues 436 - 450 (chain V) in PDB entry 1UW9
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 ASP 436 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392V GLU* 5.8 0.5 - - - +
434V GLY 3.7 1.9 + - - +
435V ARG* 1.3 70.2 - - - +
437V LEU* 1.3 59.6 + - - +
438V ALA* 3.0 22.7 + - - +
439V ARG* 3.1 37.9 + - + -
440V GLU* 2.8 45.3 + - + +
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Residues in contact with LEU 437 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388V PRO* 3.8 33.1 - - + +
389V ALA* 5.9 0.2 - - - -
391V VAL* 3.6 33.0 - - + -
392V GLU* 4.2 14.1 - - + +
427V CYS* 3.7 35.2 - - + +
430V ALA* 4.3 12.3 - - + -
431V ARG* 3.9 25.6 - - + +
435V ARG* 3.6 3.6 + - + +
436V ASP* 1.3 73.7 + - - +
438V ALA* 1.3 62.2 + - - +
440V GLU 4.9 0.2 - - - -
441V GLY* 3.1 23.5 + - - +
444V VAL* 4.5 9.6 - - + -
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Residues in contact with ALA 438 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389V ALA* 6.3 1.6 - - - +
392V GLU* 4.6 20.6 - - + +
436V ASP* 3.0 11.5 + - - +
437V LEU* 1.3 78.5 - - - +
439V ARG* 1.3 71.3 + - - +
441V GLY 5.0 0.2 + - - -
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Residues in contact with ARG 439 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436V ASP* 3.1 35.1 + - + +
438V ALA* 1.3 89.9 - - - +
440V GLU* 1.3 67.4 + - + +
441V GLY 3.4 1.3 + - - -
442V GLY 4.9 1.9 + - - -
443V ASP* 5.3 1.9 + - - +
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Residues in contact with GLU 440 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435V ARG* 3.0 44.7 + - + +
436V ASP* 2.8 42.8 + - + +
439V ARG* 1.3 79.1 - - + +
441V GLY* 1.3 64.8 + - - +
442V GLY 3.3 2.9 - - - -
443V ASP* 3.0 17.1 + - + +
444V VAL* 2.9 26.7 + - + +
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Residues in contact with GLY 441 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388V PRO* 3.6 24.2 - - - +
437V LEU* 3.1 23.5 + - - -
438V ALA 4.7 0.2 - - - -
439V ARG 3.4 2.0 - - - -
440V GLU* 1.3 76.8 - - - +
442V GLY* 1.3 62.8 + - - +
444V VAL* 3.1 10.1 + - - +
445V ILE* 3.0 27.4 + - - +
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Residues in contact with GLY 442 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385V TRP* 4.1 13.3 - - - -
388V PRO* 4.6 0.2 - - - +
439V ARG 4.9 2.0 + - - -
440V GLU 3.3 0.8 - - - -
441V GLY* 1.3 72.9 - - - +
443V ASP* 1.3 56.6 + - - +
445V ILE* 3.4 3.3 + - - +
446V ARG* 3.0 54.5 + - - +
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Residues in contact with ASP 443 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435V ARG* 4.3 12.7 + - - +
439V ARG 5.3 2.0 + - - +
440V GLU* 3.0 20.5 + - - +
442V GLY* 1.3 73.4 - - - +
444V VAL* 1.3 60.0 + - - +
446V ARG* 2.9 27.8 + - - +
447V SER* 2.9 35.9 + - - +
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Residues in contact with VAL 444 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426V ALA* 3.6 38.5 - - + +
427V CYS* 3.9 11.9 - - - +
430V ALA* 3.6 22.7 - - + -
435V ARG* 3.8 27.4 - - + +
437V LEU* 4.5 5.6 - - + -
440V GLU* 2.9 24.1 + - + +
441V GLY* 3.1 9.4 + - - +
443V ASP* 1.3 76.8 - - - +
445V ILE* 1.3 62.7 + - - +
447V SER* 3.4 3.2 + - - -
448V ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 445 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384V VAL 3.9 13.7 - - - +
385V TRP* 3.7 22.7 - - + -
388V PRO* 3.9 14.1 - - + -
423V ALA* 3.9 32.1 - - + +
426V ALA* 5.5 1.6 - - + -
427V CYS* 3.9 19.5 - - - -
441V GLY 3.0 19.5 + - - +
442V GLY 3.8 3.8 - - - +
444V VAL* 1.3 77.5 - - + +
446V ARG* 1.3 57.0 + - - +
448V ALA* 3.2 6.6 + - - +
449V CYS* 2.9 28.1 + - - -
455V LEU* 3.9 6.2 - - + +
459V CYS* 3.4 31.2 - - - -
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Residues in contact with ARG 446 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385V TRP* 4.0 28.8 - - + -
442V GLY* 3.0 34.0 + - - +
443V ASP* 2.9 32.1 + - - +
445V ILE* 1.3 77.2 - - - +
447V SER* 1.3 62.0 + - - +
449V CYS* 3.3 22.6 + - - +
450V LYS* 3.6 17.7 + - - +
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Residues in contact with SER 447 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435V ARG* 4.6 10.8 + - - -
443V ASP* 2.9 21.7 + - - +
444V VAL* 3.6 7.6 - - - -
446V ARG* 1.3 75.4 - - - +
448V ALA* 1.3 63.2 + - - +
450V LYS* 3.1 32.7 + - - +
451V TRP* 3.7 9.8 - - - -
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Residues in contact with ALA 448 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422V VAL* 4.2 1.6 - - + -
426V ALA* 4.0 17.5 - - + -
444V VAL 3.1 13.7 + - - +
445V ILE* 3.2 4.7 + - - +
447V SER* 1.3 77.1 - - - +
449V CYS* 1.3 62.4 + - - +
450V LYS 3.2 0.7 + - - -
451V TRP* 3.3 30.4 + - + +
452V SER* 3.1 24.4 + - - -
455V LEU* 3.5 23.3 - - + -
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Residues in contact with CYS 449 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385V TRP* 5.6 0.7 - - - -
445V ILE* 2.9 19.4 + - - -
446V ARG* 3.3 16.8 - - - +
447V SER 3.2 0.2 - - - -
448V ALA* 1.3 76.9 - - - +
450V LYS* 1.3 61.4 + - + +
452V SER 3.4 20.9 + - - +
453V PRO* 5.0 0.3 - - - +
455V LEU* 3.9 5.8 - - - +
456V ALA* 3.7 28.9 - - + +
459V CYS* 3.5 33.9 - - - -
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Residues in contact with LYS 450 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446V ARG* 3.9 14.3 + - - +
447V SER* 3.4 20.9 + - - +
448V ALA 3.1 1.0 - - - -
449V CYS* 1.3 78.3 - - - +
451V TRP* 1.3 60.7 + - + +
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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