Contacts of the helix formed by residues 386 - 395 (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 HIS 386 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332R VAL* 3.6 43.4 + - + +
381R GLY 3.7 10.1 + - - -
382R ILE* 3.4 10.5 - - + -
383R HIS* 2.8 63.5 + + - +
385R TRP* 1.3 77.5 - - + +
387R MET* 1.3 65.0 + - - +
388R PRO* 3.4 0.9 - - - -
389R ALA* 3.1 10.4 + - - +
390R LEU* 3.0 34.7 + - + +
465R ILE 4.2 8.4 + - - -
466R LYS* 5.0 6.7 - - + -
467R PHE* 4.5 5.3 - + - -
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Residues in contact with MET 387 (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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170R LEU* 4.5 1.1 - - + -
383R HIS 3.7 2.2 + - - -
384R VAL* 3.0 17.3 + - - +
386R HIS* 1.3 77.0 - - - +
388R PRO* 1.3 66.8 - - + +
390R LEU* 3.2 4.9 + - - +
391R VAL* 3.0 30.7 + - + +
400R LEU* 3.7 29.2 - - - -
402R PHE* 3.5 32.3 - - + -
420R ASN* 3.4 32.1 - - - +
423R ALA* 3.7 15.5 - - + +
424R LEU* 3.7 31.4 - - + +
427R CYS* 3.9 7.4 - - - -
445R ILE* 4.4 0.7 - - + -
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Residues in contact with PRO 388 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384R VAL 4.0 2.0 - - - +
385R TRP 3.4 17.3 - - - +
386R HIS 3.5 0.9 - - - -
387R MET* 1.3 93.5 - - + +
389R ALA* 1.3 56.0 + - - +
392R GLU* 3.0 29.7 + - - +
427R CYS* 3.7 21.5 - - + -
437R LEU* 3.8 23.0 - - + +
441R GLY* 3.6 42.4 - - - +
442R GLY* 5.5 0.2 - - - -
445R ILE* 3.9 6.3 - - + -
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Residues in contact with ALA 389 (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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332R VAL* 4.4 23.3 - - + -
339R ARG* 6.2 0.4 - - - +
385R TRP 5.3 0.4 + - - +
386R HIS* 3.1 11.4 + - - +
388R PRO* 1.3 77.0 - - - +
390R LEU* 1.3 60.1 + - - +
392R GLU* 3.3 8.2 + - - +
393R ILE* 2.8 42.7 + - + +
437R LEU 5.2 0.6 + - - -
438R ALA* 6.4 1.3 - - - +
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Residues in contact with LEU 390 (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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330R THR* 3.7 28.5 - - - +
332R VAL* 4.2 9.0 - - + -
378R ALA* 4.3 12.1 - - + -
382R ILE* 3.7 24.0 - - + -
386R HIS* 3.0 33.1 + - + +
387R MET* 3.6 6.5 - - - +
389R ALA* 1.3 75.0 - - - +
391R VAL* 1.3 59.5 + - - +
393R ILE* 3.3 1.9 + - + -
394R PHE* 2.9 52.4 + - + +
400R LEU* 4.1 20.4 - - + -
402R PHE* 3.9 17.7 - - + -
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Residues in contact with VAL 391 (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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387R MET* 3.0 25.0 + - + +
390R LEU* 1.3 76.1 - - - +
392R GLU* 1.3 58.0 + - - +
395R GLY* 2.8 35.6 + - - +
396R ASP* 5.1 2.5 - - - +
400R LEU* 4.5 4.3 - - + -
424R LEU* 3.7 30.3 - - + +
427R CYS* 4.2 17.5 - - + +
428R THR* 4.8 8.1 - - - +
431R ARG* 4.0 23.8 + - - +
437R LEU* 3.6 24.2 - - + -
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Residues in contact with GLU 392 (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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339R ARG* 2.8 44.2 + - - -
388R PRO 3.0 18.9 + - - +
389R ALA* 3.6 7.6 - - - +
390R LEU 3.3 0.2 - - - -
391R VAL* 1.3 80.2 - - - +
393R ILE* 1.3 64.5 + - - +
395R GLY 4.4 1.6 + - - -
436R ASP* 5.8 0.4 - - - +
437R LEU* 4.2 13.0 - - + +
438R ALA* 4.6 25.0 - - + +
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Residues in contact with ILE 393 (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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330R THR 4.3 7.0 - - - +
331R VAL* 4.0 36.6 - - + -
332R VAL* 4.8 4.7 - - + -
339R ARG* 3.4 32.3 - - + +
342R THR* 5.2 2.5 - - + -
343R LEU* 3.5 34.2 - - + +
346R VAL* 5.9 1.0 - - - +
350R ARG* 5.2 2.6 + - - -
389R ALA* 2.8 35.7 + - + +
390R LEU* 3.8 4.3 - - + +
392R GLU* 1.3 79.4 - - - +
394R PHE* 1.3 87.2 + - + +
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Residues in contact with PHE 394 (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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328R SER* 3.4 19.7 - - - -
329R GLY 3.3 23.6 - - - -
330R THR* 4.2 7.4 - - - -
342R THR* 4.4 8.1 - - + -
346R VAL* 3.9 26.9 - - + -
350R ARG* 2.8 33.6 + - - +
376R PRO* 4.5 6.7 - - + -
378R ALA* 3.7 20.9 - - + -
390R LEU* 2.9 40.9 + - + +
393R ILE* 1.3 98.3 - - + +
395R GLY* 1.3 63.4 + - - +
396R ASP 4.0 0.2 + - - -
397R ASP 4.4 0.2 + - - -
398R ALA* 3.7 27.6 - - + -
400R LEU* 4.4 4.0 - - + -
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Residues in contact with GLY 395 (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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168R GLY* 4.9 3.8 + - - -
391R VAL* 2.8 27.3 + - - +
392R GLU 4.4 1.6 + - - -
393R ILE 3.7 0.6 - - - -
394R PHE* 1.3 87.1 - - - +
396R ASP* 1.3 66.2 + - - -
398R ALA* 4.4 3.3 - - - +
400R LEU* 5.9 1.7 - - - +
431R ARG* 4.4 9.0 - - - -
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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
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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