Contacts of the helix formed by residues 436 - 450 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392R GLU* 5.8 0.5 - - - +
434R GLY 3.7 1.9 + - - +
435R ARG* 1.3 70.9 - - - +
437R LEU* 1.3 54.0 + - - +
438R ALA* 3.0 22.3 + - - +
439R ARG* 3.1 36.5 + - + -
440R GLU* 2.7 49.8 + - - +
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Residues in contact with LEU 437 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R PRO* 3.8 32.8 - - + +
389R ALA 5.2 0.2 + - - -
391R VAL* 3.6 32.1 - - + -
392R GLU* 4.2 14.3 - - + +
427R CYS* 3.7 41.5 - - + +
430R ALA* 4.4 13.0 - - + -
431R ARG* 3.9 20.6 - - + +
435R ARG* 3.5 3.8 + - + +
436R ASP* 1.3 73.8 + - - +
438R ALA* 1.3 62.8 + - - +
440R GLU 4.9 0.2 - - - -
441R GLY* 3.1 23.4 + - - +
444R VAL* 4.5 9.6 - - + -
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Residues in contact with ALA 438 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389R ALA* 6.4 1.8 - - - +
392R GLU* 4.6 20.4 - - + +
436R ASP* 3.0 12.1 + - - +
437R LEU* 1.3 79.2 - - - +
439R ARG* 1.3 71.6 + - - +
441R GLY 5.0 0.2 + - - -
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Residues in contact with ARG 439 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436R ASP* 3.1 35.4 + - + +
438R ALA* 1.3 88.1 - - - +
440R GLU* 1.3 66.9 + - + +
441R GLY 3.4 2.6 + - - -
442R GLY 4.9 1.7 + - - -
443R ASP* 5.3 1.9 - - - +
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Residues in contact with GLU 440 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435R ARG* 3.0 44.1 + - + +
436R ASP* 2.7 42.0 + - - +
437R LEU* 4.9 0.2 - - - -
439R ARG* 1.3 79.1 - - + +
441R GLY* 1.3 63.3 + - - +
442R GLY 3.3 2.7 - - - -
443R ASP* 3.0 17.1 + - + +
444R VAL* 2.9 26.9 + - + +
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Residues in contact with GLY 441 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388R PRO* 3.6 24.1 - - - +
437R LEU* 3.1 23.7 + - - -
439R ARG 3.4 2.2 - - - -
440R GLU* 1.3 76.9 - - - +
442R GLY* 1.3 60.7 + - - +
444R VAL* 3.2 9.8 + - - +
445R ILE* 3.0 28.1 + - - +
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Residues in contact with GLY 442 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R TRP* 4.0 12.6 - - - -
439R ARG 4.9 2.2 + - - -
440R GLU 3.3 0.6 - - - -
441R GLY* 1.3 72.8 - - - +
443R ASP* 1.3 56.2 + - - +
445R ILE* 3.5 4.0 + - - +
446R ARG* 3.0 53.1 + - - +
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Residues in contact with ASP 443 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435R ARG* 4.3 13.7 - - - +
439R ARG 5.3 1.6 - - - +
440R GLU* 3.0 19.8 + - - +
442R GLY* 1.3 72.9 - - - +
444R VAL* 1.3 60.9 + - - +
446R ARG* 2.9 28.8 + - - +
447R SER* 2.9 35.2 + - - +
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Residues in contact with VAL 444 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426R ALA* 3.6 38.5 - - + +
427R CYS* 3.9 12.3 - - - +
430R ALA* 3.6 23.3 - - + -
435R ARG* 3.8 25.4 - - + +
437R LEU* 4.5 5.2 - - + -
440R GLU* 2.9 25.2 + - + +
441R GLY* 3.5 10.5 - - - +
443R ASP* 1.3 77.0 - - - +
445R ILE* 1.3 61.9 + - - +
447R SER* 3.4 3.2 + - - -
448R ALA* 3.1 22.0 + - - +
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Residues in contact with ILE 445 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384R VAL 4.0 12.6 - - - +
385R TRP* 3.7 22.9 - - + -
388R PRO* 3.9 14.8 - - + -
423R ALA* 3.9 31.2 - - + +
426R ALA* 5.5 1.3 - - + -
427R CYS* 4.0 19.7 - - - -
441R GLY 3.0 20.1 + - - +
442R GLY 3.8 3.8 - - - +
444R VAL* 1.3 75.8 - - + +
446R ARG* 1.3 56.9 + - - +
448R ALA* 3.1 7.4 + - - +
449R CYS* 2.9 27.6 + - - -
455R LEU* 3.9 6.3 - - + +
459R CYS* 3.3 32.3 - - - -
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Residues in contact with ARG 446 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R TRP* 4.0 27.9 - - + -
442R GLY* 3.0 34.8 + - - +
443R ASP* 2.9 31.3 + - - +
444R VAL 3.4 0.2 - - - -
445R ILE* 1.3 74.7 - - - +
447R SER* 1.3 62.5 + - - +
449R CYS* 3.3 22.8 + - + +
450R LYS* 3.6 16.8 + - - +
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Residues in contact with SER 447 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435R ARG* 4.6 10.6 + - - -
443R ASP* 2.9 20.0 + - - +
444R VAL* 3.6 7.4 - - - -
446R ARG* 1.3 75.4 - - - +
448R ALA* 1.3 62.8 + - - +
450R LYS* 3.2 32.2 + - - +
451R TRP* 3.7 9.7 - - - -
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Residues in contact with ALA 448 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422R VAL* 4.2 1.8 - - + -
426R ALA* 4.0 16.8 - - + -
444R VAL 3.1 13.1 + - - +
445R ILE* 3.1 5.9 + - - +
447R SER* 1.3 76.2 - - - +
449R CYS* 1.3 62.6 + - - +
450R LYS 3.2 0.5 + - - -
451R TRP* 3.3 30.8 + - + +
452R SER* 3.0 23.7 + - - -
455R LEU* 3.5 23.8 - - + -
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Residues in contact with CYS 449 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R TRP* 5.6 0.9 - - - -
445R ILE 2.9 19.3 + - - -
446R ARG* 3.3 16.6 - - - +
447R SER 3.2 0.4 - - - -
448R ALA* 1.3 76.5 - - - +
450R LYS* 1.3 60.5 + - + +
451R TRP 3.3 0.2 - - - -
452R SER 3.4 21.1 + - - +
453R PRO* 5.0 0.3 - - - +
455R LEU* 3.9 6.5 - - - +
456R ALA* 3.7 29.6 - - + +
459R CYS* 3.5 32.1 - - - -
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Residues in contact with LYS 450 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446R ARG* 3.9 15.2 + - - +
447R SER* 3.4 22.1 + - - +
448R ALA 3.1 1.2 - - - -
449R CYS* 1.3 77.8 - - - +
451R TRP* 1.3 61.0 + - + +
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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
------------------------------------------------------------
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