Contacts of the helix formed by residues 452 - 463 (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 SER 452 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422R VAL* 3.9 20.4 - - - +
448R ALA 3.0 15.6 + - - -
449R CYS* 3.4 10.5 - - - +
450R LYS 3.6 0.6 - - - -
451R TRP* 1.3 92.9 - - - +
453R PRO* 1.3 59.5 - - - +
454R GLU* 3.7 9.3 + - - +
455R LEU* 3.1 26.5 + - - +
456R ALA 3.0 22.2 + - - -
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Residues in contact with PRO 453 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M MET* 3.7 32.3 - - + -
135M ALA 6.0 1.3 - - - +
139M SER* 5.0 2.2 - - - +
411R TRP* 3.5 19.0 - - + -
449R CYS 5.0 0.7 - - - +
451R TRP 3.5 11.0 - - - +
452R SER* 1.3 84.9 - - - +
454R GLU* 1.3 69.2 + - - +
456R ALA* 3.3 8.1 + - + +
457R ALA* 3.0 23.7 + - - +
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Residues in contact with GLU 454 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M MET* 4.0 1.0 - - - +
4M TRP* 3.7 24.2 - - + -
139M SER* 2.7 34.1 + - - -
409R HIS* 2.9 23.8 + - - -
411R TRP* 3.7 18.3 - - + -
415R PRO* 3.6 41.7 - - + +
418R ALA* 4.2 2.2 - - + -
419R ALA* 3.6 11.0 - - - +
452R SER* 3.2 8.5 + - - +
453R PRO* 1.3 92.4 - - - +
455R LEU* 1.3 60.7 + - - +
458R ALA 3.2 7.3 + - - -
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Residues in contact with LEU 455 (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* 3.6 35.2 - - + -
419R ALA* 3.7 16.5 - - - +
422R VAL* 3.8 14.6 - - + -
423R ALA* 4.1 11.9 - - + +
445R ILE* 3.9 16.6 - - + +
448R ALA* 3.5 33.0 - - + -
449R CYS* 3.9 10.8 - - - +
452R SER* 3.1 20.2 + - - +
454R GLU* 1.3 75.3 - - - +
456R ALA* 1.3 60.4 + - - +
458R ALA* 3.1 1.9 + - - +
459R CYS* 2.8 35.3 + - - +
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Residues in contact with ALA 456 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449R CYS* 3.7 29.1 - - + +
452R SER 3.0 13.8 + - - +
453R PRO* 3.3 12.3 + - + +
455R LEU* 1.3 76.2 - - - +
457R ALA* 1.3 58.0 + - - +
459R CYS* 3.4 3.1 + - - +
460R GLU* 3.0 33.2 + - + +
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Residues in contact with ALA 457 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R HIS* 3.8 14.8 - - + -
410R PRO* 4.2 6.1 - - + -
411R TRP* 3.8 27.4 - - + +
453R PRO 3.0 16.8 + - - +
454R GLU 3.7 4.5 - - - +
456R ALA* 1.3 72.7 - - - +
458R ALA* 1.3 64.9 + - - +
460R GLU* 3.5 7.0 + - - +
461R VAL* 3.3 27.5 + - - +
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Residues in contact with ALA 458 (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 14.8 - - + -
405R GLY 5.9 0.2 - - - +
409R HIS* 3.6 24.8 + - + -
410R PRO* 5.0 0.7 - - - -
419R ALA* 3.8 12.8 - - + -
454R GLU 3.2 8.4 + - - +
455R LEU 3.1 8.6 + - - +
457R ALA* 1.3 76.0 - - - +
459R CYS* 1.3 63.8 + - - +
461R VAL* 3.2 11.1 + - - -
462R TRP* 3.2 37.4 + - + +
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Residues in contact with CYS 459 (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* 3.8 7.6 - - - +
385R TRP* 2.8 44.4 + - + +
445R ILE* 3.3 33.7 - - - -
449R CYS* 3.5 17.7 - - - -
455R LEU* 2.8 31.8 + - - +
456R ALA 3.6 5.4 - - - +
458R ALA* 1.3 73.4 - - - +
460R GLU* 1.3 56.9 + - - +
463R LYS* 3.0 19.3 + - - +
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Residues in contact with GLU 460 (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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456R ALA 3.0 19.2 + - - +
457R ALA* 3.7 7.6 - - - +
458R ALA 3.2 0.4 - - - -
459R CYS* 1.3 78.5 - - + +
461R VAL* 1.3 64.0 + - + +
463R LYS* 3.8 30.1 + - - +
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Residues in contact with VAL 461 (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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15H ALA* 4.2 12.6 - - + +
16H GLY* 3.7 27.1 - - - +
17H VAL 5.5 0.3 + - - -
408R GLY 4.8 0.4 - - - +
410R PRO* 3.9 24.9 - - + -
457R ALA 3.3 15.0 + - - +
458R ALA 3.2 5.8 + - - +
460R GLU* 1.3 79.5 - - + +
462R TRP* 1.3 90.7 + - + +
463R LYS 3.8 0.2 + - - -
464R GLU 5.2 0.5 + - - -
465R ILE* 4.6 5.2 - - - +
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Residues in contact with TRP 462 (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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16H GLY* 4.6 0.9 - - - -
17H VAL* 4.3 2.7 - - + -
66H TRP* 3.3 30.3 - + - -
67H THR* 3.1 24.0 + - + -
383R HIS* 3.4 42.1 - - + +
384R VAL* 4.7 4.7 - - + -
385R TRP* 3.9 4.0 - - + -
404R GLY 3.6 13.9 - - - -
405R GLY* 3.6 29.8 - - - -
408R GLY 3.5 18.2 - - - -
409R HIS* 3.7 22.7 - + - -
458R ALA* 3.2 43.9 + - + +
459R CYS 3.9 1.1 - - - -
461R VAL* 1.3 93.1 - - + +
463R LYS* 1.3 66.1 + - - +
464R GLU 3.3 2.9 - - - -
465R ILE* 3.1 23.0 + - + -
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Residues in contact with LYS 463 (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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383R HIS* 5.4 0.5 - - - -
385R TRP* 3.5 27.9 - - + +
459R CYS 3.0 18.3 + - - +
460R GLU* 3.9 28.1 + - - +
461R VAL 3.5 1.8 - - - -
462R TRP* 1.3 77.6 - - - +
464R GLU* 1.3 82.3 + - + +
465R ILE 3.5 1.2 + - - +
466R LYS* 5.5 5.2 - - - +
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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