Contacts of the helix formed by residues 436 - 450 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392H GLU* 5.8 0.3 - - - +
434H GLY 3.8 1.7 + - - +
435H ARG* 1.3 70.0 - - - +
437H LEU* 1.3 56.8 + - - +
438H ALA* 3.1 22.5 + - - +
439H ARG* 3.1 35.3 + - + -
440H GLU* 2.7 50.0 + - - +
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Residues in contact with LEU 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H PRO* 3.7 27.5 - - + +
389H ALA 5.1 0.5 + - - -
391H VAL* 3.7 36.6 - - + -
392H GLU* 4.3 14.5 - - + +
427H CYS* 3.6 36.3 - - + +
430H ALA* 4.4 12.8 - - + -
431H ARG* 3.9 26.9 - - + -
435H ARG* 3.5 3.6 + - + +
436H ASP* 1.3 72.9 + - - +
438H ALA* 1.3 62.1 + - - +
440H GLU 5.0 0.2 - - - -
441H GLY* 3.3 21.7 + - - +
444H VAL* 4.5 9.9 - - + -
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Residues in contact with ALA 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389H ALA* 6.3 1.6 - - - +
392H GLU* 4.5 22.1 - - + +
436H ASP* 3.1 11.9 + - - +
437H LEU* 1.3 77.5 - - - +
439H ARG* 1.3 71.9 + - - +
441H GLY 5.0 0.2 + - - -
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Residues in contact with ARG 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436H ASP* 3.1 33.5 + - + +
438H ALA* 1.3 89.0 - - - +
440H GLU* 1.3 67.7 + - + +
441H GLY 3.4 2.8 + - - -
442H GLY 5.0 1.6 + - - -
443H ASP* 5.3 2.1 - - - +
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Residues in contact with GLU 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434H GLY 5.0 0.3 - - - +
435H ARG* 3.1 42.6 + - + +
436H ASP* 2.7 41.8 + - + +
437H LEU* 5.0 0.2 - - - -
439H ARG* 1.3 80.6 - - + +
441H GLY* 1.3 59.4 + - - +
442H GLY 3.3 2.7 - - - -
443H ASP* 2.9 18.9 + - + +
444H VAL* 2.9 31.8 + - + +
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Residues in contact with GLY 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H PRO* 3.6 23.1 - - - +
437H LEU* 3.3 23.5 + - - -
438H ALA 4.8 0.4 + - - -
439H ARG 3.4 2.6 - - - -
440H GLU* 1.3 77.1 - - - +
442H GLY* 1.3 61.6 + - - +
444H VAL* 3.2 9.5 + - - +
445H ILE* 3.0 27.9 + - - +
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Residues in contact with GLY 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H TRP* 4.1 12.9 - - - -
439H ARG 5.0 1.4 + - - -
440H GLU 3.3 0.4 - - - -
441H GLY* 1.3 74.8 - - - +
443H ASP* 1.3 57.4 + - - +
445H ILE* 3.4 3.4 + - - +
446H ARG* 3.0 54.7 + - - +
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Residues in contact with ASP 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435H ARG* 4.4 13.2 - - - +
439H ARG 5.3 1.4 - - - +
440H GLU* 2.9 20.5 + - + +
442H GLY* 1.3 73.6 - - - +
444H VAL* 1.3 60.9 + - - +
446H ARG* 2.8 34.2 + - - +
447H SER* 2.9 34.5 + - - +
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Residues in contact with VAL 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426H ALA* 3.6 37.9 - - + +
427H CYS* 3.9 11.2 - - - +
430H ALA* 3.6 23.6 - - + -
435H ARG* 3.8 26.0 - - + +
437H LEU* 4.5 7.4 - - + -
440H GLU* 2.9 23.7 + - + +
441H GLY* 3.2 10.1 + - - +
443H ASP* 1.3 76.4 - - - +
445H ILE* 1.3 61.7 + - - +
447H SER* 3.4 3.4 + - - -
448H ALA* 3.1 21.3 + - - +
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Residues in contact with ILE 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H VAL 4.0 13.7 - - - +
385H TRP* 3.8 21.5 - - + -
388H PRO* 3.8 13.9 - - + -
423H ALA* 3.9 31.2 - - + +
426H ALA* 5.5 1.3 - - + -
427H CYS* 3.9 20.4 - - - -
441H GLY 3.0 16.2 + - - +
442H GLY 3.8 4.7 - - - +
444H VAL* 1.3 78.2 - - + +
446H ARG* 1.3 57.1 + - - +
448H ALA* 3.2 6.9 + - - +
449H CYS* 3.0 27.4 + - - -
455H LEU* 3.9 6.8 - - + +
459H CYS* 3.4 31.6 - - - -
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Residues in contact with ARG 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H TRP* 4.0 29.4 - - + -
442H GLY* 3.0 32.4 + - - +
443H ASP* 2.8 32.9 + - - +
445H ILE* 1.3 76.0 - - - +
447H SER* 1.3 63.3 + - - +
449H CYS* 3.3 23.2 - - + +
450H LYS* 3.7 16.8 + - - +
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Residues in contact with SER 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435H ARG* 4.6 11.3 + - - -
443H ASP* 2.9 19.8 + - - +
444H VAL* 3.6 7.0 - - - -
445H ILE 3.3 0.2 - - - -
446H ARG* 1.3 76.8 - - - +
448H ALA* 1.3 62.6 + - - +
450H LYS* 3.2 31.8 + - - +
451H TRP* 3.6 9.7 - - - -
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Residues in contact with ALA 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422H VAL* 4.3 1.3 - - + -
426H ALA* 3.9 22.7 - - + -
444H VAL 3.1 11.6 + - - +
445H ILE* 3.6 4.7 - - - +
447H SER* 1.3 79.1 - - - +
449H CYS* 1.3 63.1 + - - +
450H LYS 3.2 0.7 + - - -
451H TRP* 3.3 26.8 + - + +
452H SER* 3.0 23.9 + - - -
455H LEU* 3.5 23.3 - - + -
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Residues in contact with CYS 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H TRP* 5.6 0.7 - - - -
445H ILE* 3.0 20.5 + - - -
446H ARG* 3.3 17.7 - - + +
448H ALA* 1.3 76.7 - - - +
450H LYS* 1.3 60.1 - - + +
451H TRP 3.3 0.2 - - - -
452H SER 3.4 21.0 + - - +
453H PRO* 5.0 0.3 - - - +
455H LEU* 3.9 6.0 - - - +
456H ALA* 3.8 29.0 - - + +
459H CYS* 3.5 32.8 - - - -
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Residues in contact with LYS 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446H ARG* 3.9 14.3 + - - +
447H SER* 3.4 21.2 + - - +
448H ALA 3.1 1.2 - - - -
449H CYS* 1.3 78.0 - - + +
451H TRP* 1.3 61.2 + - + +
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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