Contacts of the helix formed by residues 415 - 428 (chain A) in PDB entry 5DO7
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 ALA 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A VAL* 4.0 2.9 - - - +
408A ARG 3.3 10.1 - - - +
409A SER 4.3 5.8 - - - +
411A VAL 3.2 24.2 - - - +
412A LEU* 3.4 23.1 + - + -
414A GLY* 1.3 76.4 - - - +
416A ILE* 1.3 68.0 + - - +
417A GLN* 3.2 3.4 + - - +
418A ASP 3.8 0.2 + - - -
419A ARG* 3.3 37.7 + - - +
585A PHE* 4.5 5.2 - - + -
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 4.2 18.8 - - + +
415A ALA* 1.3 77.9 - - - +
417A GLN* 1.3 85.8 + - + +
419A ARG* 2.8 13.2 + - - +
420A VAL* 2.8 34.9 + - + +
580A PHE* 3.9 21.7 - - + -
585A PHE* 3.4 33.0 - - + -
602A PHE* 4.9 20.9 - - + -
608A PHE* 4.5 22.8 - - + -
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU 5.9 1.3 - - - +
413A LYS 5.6 1.8 - - - +
414A GLY 5.5 0.2 - - - -
415A ALA 3.2 4.2 - - - +
416A ILE* 1.3 94.0 - - + +
418A ASP* 1.3 60.7 + - - +
420A VAL* 3.5 23.4 - - + +
421A GLY 3.6 3.5 + - - -
575B GLY 4.2 0.8 + - - -
576B PHE* 2.9 40.1 + - + +
577B MET 3.6 8.7 - - - +
579B ASN* 3.5 34.9 - - + +
633B MET* 4.6 14.1 - - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 4.6 21.5 - - + +
405A LEU* 5.3 1.4 - - - +
406A ARG 5.0 0.9 - - - +
407A VAL* 5.0 10.3 - - + -
408A ARG* 4.6 9.0 + - - +
414A GLY* 2.9 25.6 + - - +
415A ALA 3.8 4.1 + - - +
416A ILE 3.3 0.4 - - - -
417A GLN* 1.3 78.6 - - - +
419A ARG* 1.3 60.8 - - - +
421A GLY* 4.0 1.8 + - - -
422A LEU* 3.4 23.7 + - - +
577B MET 4.9 3.4 - - - +
578B ILE* 2.9 22.1 - - + +
579B ASN* 2.6 32.4 + - - -
582B SER* 4.7 7.0 + - - +
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Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A VAL* 3.4 29.6 - - + +
409A SER* 3.6 20.7 + - - -
415A ALA* 3.3 21.4 + - - +
416A ILE* 2.8 9.1 + - - +
418A ASP* 1.3 76.3 - - - +
420A VAL* 1.3 68.9 + - - +
421A GLY 3.1 0.9 - - - -
422A LEU* 2.8 7.1 + - + +
423A LEU* 2.8 34.3 + - + +
492A LEU* 4.4 16.9 - - + +
493A HIS 5.1 0.2 - - - +
579A GLU* 3.3 36.8 + - - -
580A PHE* 4.5 13.7 - - + -
583A LEU* 3.6 20.4 - - - +
585A PHE* 3.1 35.8 - - - -
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ILE* 2.8 14.1 + - + +
417A GLN* 3.5 20.9 - - + +
419A ARG* 1.3 75.1 - - - +
421A GLY* 1.3 71.5 + - - +
423A LEU* 3.3 7.0 + - - +
424A TYR* 2.8 32.2 + - + +
548A PHE* 3.2 46.0 - - + +
549A LEU* 6.5 1.1 - - + -
580A PHE* 5.5 1.2 - - - -
608A PHE* 3.9 21.8 - - + -
576B PHE* 5.2 17.0 - - + -
577B MET* 5.2 1.3 - - + +
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Residues in contact with GLY 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A GLN 3.6 4.0 + - - -
418A ASP 4.3 0.9 - - - -
419A ARG 3.1 1.0 - - - -
420A VAL* 1.3 85.6 - - - +
422A LEU* 1.3 52.9 + - - +
424A TYR* 3.3 5.0 - - - +
425A GLN* 2.8 38.5 + - - +
577B MET* 3.5 36.0 - - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 4.5 12.3 - - + +
404A VAL* 3.9 31.6 - - + +
418A ASP 3.4 14.4 + - - +
419A ARG* 2.8 11.5 + - + +
421A GLY* 1.3 72.3 - - - +
423A LEU* 1.3 68.0 - - + +
425A GLN* 3.2 6.6 + - - +
426A PHE* 2.9 53.6 + - + -
490A LEU* 3.4 27.1 - - + -
492A LEU* 3.2 35.0 - - + -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ARG* 2.8 31.8 + - + +
420A VAL* 3.8 4.9 - - - +
422A LEU* 1.3 77.3 - - + +
424A TYR* 1.3 66.0 + - - +
426A PHE* 2.8 11.6 + - + +
427A VAL* 2.8 27.4 + - + +
492A LEU* 5.5 3.1 - - + -
502A PHE* 4.6 13.9 - - + -
548A PHE* 4.3 21.8 - - + -
575A LEU* 3.5 50.7 - - + +
576A VAL* 4.9 3.6 - - - -
579A GLU* 5.0 10.3 - - + +
580A PHE* 4.4 21.8 - - + -
608A PHE* 6.5 0.2 - - + -
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Residues in contact with TYR 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A VAL 2.8 22.6 + - - +
421A GLY* 3.3 7.2 - - - +
423A LEU* 1.3 73.6 - - - +
425A GLN* 1.3 68.4 + - - +
427A VAL* 3.0 5.3 + - + +
428A GLY* 2.8 21.2 + - - -
539A ILE 4.6 0.2 + - - -
542A VAL* 3.1 47.6 - - + +
543A LEU* 3.8 19.0 - - - +
546A SER* 4.1 12.1 - - - -
548A PHE* 4.1 16.9 - + + -
549A LEU* 3.4 32.6 - - + +
454B MET* 5.4 6.2 - - - +
571B TYR* 4.4 10.3 - - - -
577B MET* 3.5 32.8 - - + -
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Residues in contact with GLN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 4.9 10.0 - - - -
400A LEU* 3.8 32.1 - - + -
421A GLY 2.8 18.0 + - - +
422A LEU* 3.2 4.5 + - - +
424A TYR* 1.3 74.6 - - - +
426A PHE* 1.3 63.9 + - - +
428A GLY* 3.1 5.9 + - - +
429A ALA* 2.8 31.5 + - + +
568B ASN* 3.3 27.4 + - - +
571B TYR* 3.1 40.3 + - - -
572B LEU* 4.4 8.5 - - + +
577B MET* 3.6 12.5 - - - +
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 4.9 4.9 - - + -
397A GLY* 4.3 7.2 - - - -
400A LEU* 3.5 24.7 - - + -
422A LEU* 2.9 48.0 + - + -
423A LEU* 2.8 17.6 + - + +
425A GLN* 1.3 70.8 - - - +
427A VAL* 1.3 52.4 + - + +
429A ALA* 3.1 3.1 + - - -
430A THR* 2.6 45.5 + - + -
482A PHE* 3.1 36.8 - + - -
486A CYS* 5.0 3.6 - - + -
487A TYR* 6.4 0.2 - - - -
490A LEU* 4.3 13.0 - - + -
502A PHE* 3.6 33.9 - + - -
506A LEU* 3.9 17.7 - - + -
575A LEU* 5.2 0.9 - - + -
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 2.8 22.2 + - + +
424A TYR* 3.7 7.6 - - + +
426A PHE* 1.3 70.5 - - - +
428A GLY* 1.3 57.2 + - - +
429A ALA 3.4 0.4 - - - -
430A THR* 3.9 5.2 - - - -
431A PRO* 3.2 20.9 - - - +
506A LEU* 4.7 2.0 - - + -
509A PRO* 4.8 1.7 - - + +
542A VAL* 3.6 18.0 - - + +
546A SER* 5.5 0.9 - - - -
567A PHE* 4.6 3.5 - - + -
568A GLN* 4.1 23.3 - - + +
571A CYS* 3.7 17.0 - - + -
572A SER* 3.6 25.8 - - - +
575A LEU* 3.6 27.6 - - + -
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Residues in contact with GLY 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TYR* 2.8 13.2 + - - -
425A GLN* 3.3 9.4 + - - -
427A VAL* 1.3 78.1 - - - +
429A ALA* 1.3 54.8 + - - +
431A PRO* 4.2 4.0 - - - +
432A TYR* 4.6 7.8 - - - +
538A SER* 4.0 13.1 + - - +
539A ILE* 4.9 10.0 - - - +
542A VAL* 3.4 22.6 - - - +
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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