Contacts of the helix formed by residues 444 - 458 (chain B) 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 SER 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A ARG* 4.0 0.2 + - - -
554A GLU* 2.5 33.8 + - - -
442B GLN 3.5 1.8 + - - -
443B LEU* 1.3 74.1 - - - +
445B PHE* 1.3 55.3 + - - +
446B MET* 3.0 30.3 - - - -
447B ASP* 2.1 57.4 + - - +
448B THR* 2.8 7.7 + - - -
617B LEU 4.9 7.0 - - - -
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LEU* 3.9 4.6 + - - +
444B SER* 1.3 72.1 - - - +
446B MET* 1.3 88.9 + - + +
448B THR* 3.0 24.2 - - + +
449B ALA* 3.1 12.8 + - - +
608B PHE* 3.3 29.2 - + + -
614B LYS* 4.8 3.7 - - - +
616B PRO* 3.3 36.2 - - + +
617B LEU 5.1 2.2 - - - +
629B ILE* 3.6 24.9 - - + -
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Residues in contact with MET 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A ASN* 4.0 20.4 - - - +
554A GLU* 5.5 2.9 - - - +
602A PHE* 6.3 1.6 - - - -
611A LYS* 4.7 22.0 - - + +
444B SER* 2.7 28.1 + - - -
445B PHE* 1.3 98.6 - - + +
447B ASP* 1.3 64.5 + - - +
449B ALA* 4.1 5.1 - - - +
450B ALA* 4.0 8.3 + - - +
576B PHE* 4.2 12.5 - - - -
617B LEU 4.3 17.5 - - - +
618B GLY* 5.1 5.8 - - - -
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Residues in contact with ASP 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A PHE 5.0 1.0 - - - +
549A LEU 4.1 13.5 - - - +
550A ARG* 3.7 15.3 + - - +
551A ASN* 3.4 25.6 - - - +
554A GLU* 3.2 9.0 - - - +
435B TYR* 3.5 18.5 - - + -
443B LEU* 5.5 0.9 - - + -
444B SER* 2.1 51.0 + - - +
446B MET* 1.3 73.9 - - - +
448B THR* 1.3 59.5 + - - +
449B ALA 3.1 2.5 - - - -
450B ALA* 2.8 32.3 + - - +
451B LEU 3.1 5.0 + - - -
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B TYR* 5.1 1.6 - - - -
443B LEU* 3.3 34.7 - - + +
444B SER 2.8 9.1 + - - +
445B PHE* 3.0 37.7 - - + +
447B ASP* 1.3 72.1 - - - +
449B ALA* 1.3 64.8 + - - +
451B LEU* 3.7 7.4 + - - +
452B LEU* 3.3 33.4 + - - +
521B LEU* 5.4 4.7 - - - +
604B MET* 5.6 0.2 - - - -
607B GLN* 5.7 2.1 - - - +
608B PHE* 4.5 19.9 - - + +
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE 3.1 15.0 + - - +
446B MET 4.1 5.8 - - - +
447B ASP 3.1 0.4 - - - -
448B THR* 1.3 75.9 - - + +
450B ALA* 1.3 68.9 + - - +
452B LEU* 2.8 17.0 + - - +
453B PHE* 2.9 11.1 + - - +
576B PHE* 4.4 7.9 - - + -
600B PHE* 4.0 9.8 - - + -
604B MET* 3.5 33.9 - - + -
608B PHE* 6.0 1.1 - - + -
633B MET* 6.3 1.6 - - + -
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A LEU* 3.4 35.0 - - + +
435B TYR* 3.6 10.3 - - + +
446B MET 4.0 0.2 + - - -
447B ASP* 2.8 21.6 + - - +
449B ALA* 1.3 71.7 - - - +
451B LEU* 1.3 63.9 + - - +
453B PHE* 2.8 6.0 + - - +
454B MET* 2.8 25.9 + - - +
576B PHE* 3.9 23.7 - - + -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B ILE* 3.9 20.9 - - + +
435B TYR* 3.3 43.9 - - + -
447B ASP 3.1 4.6 + - - +
448B THR* 3.8 9.0 - - - +
450B ALA* 1.3 76.9 - - - +
452B LEU* 1.3 79.5 + - + +
454B MET* 2.8 9.2 + - - +
455B ILE* 2.8 40.4 + - + +
515B THR* 4.3 12.3 - - + -
519B ALA* 3.3 29.6 - - + -
521B LEU* 4.4 12.1 - - + -
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B THR* 3.3 19.7 + - - +
449B ALA* 2.8 16.8 + - - +
451B LEU* 1.3 86.2 - - + +
453B PHE* 1.3 58.9 + - - +
455B ILE* 3.2 18.5 - - + +
456B GLY 4.0 0.9 + - - -
521B LEU* 3.5 32.3 - - + -
599B CYS* 4.5 1.0 - - - -
600B PHE* 4.2 13.9 - - + -
603B LEU* 3.5 29.1 - - + +
604B MET* 3.7 43.5 - - + +
607B GLN* 3.8 16.8 - - + -
608B PHE* 4.7 2.5 - - + -
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A LEU* 5.9 0.4 - - + -
449B ALA 2.9 6.0 + - - +
450B ALA 2.8 11.9 + - - +
452B LEU* 1.3 70.7 - - - +
454B MET* 1.3 75.4 + - + +
456B GLY* 2.8 10.9 + - - -
457B ALA* 2.8 44.6 + - + +
571B TYR* 4.0 33.4 - + + -
574B GLY* 4.2 15.0 - - - -
575B GLY 4.8 0.4 - - - -
576B PHE* 3.9 32.3 - + + -
577B MET* 3.4 37.5 - - + -
596B LEU* 4.7 6.5 - - + +
599B CYS* 5.1 0.7 - - - -
600B PHE* 3.5 32.5 - + + -
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Residues in contact with MET 454 (chain B).
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* 5.4 5.8 - - - +
539A ILE* 6.4 0.2 - - + -
543A LEU* 4.0 20.4 - - + -
549A LEU* 5.0 13.0 - - + -
431B ILE* 4.3 11.4 - - + -
435B TYR* 4.3 14.6 - - + +
450B ALA* 2.8 20.3 + - - +
451B LEU* 2.8 9.1 + - - +
453B PHE* 1.3 94.6 - - - +
455B ILE* 1.3 65.1 + - - +
456B GLY 2.7 6.4 + - - -
457B ALA 4.3 7.9 - - - +
458B LEU* 2.8 65.0 + - + +
571B TYR* 6.3 2.7 - - + -
577B MET* 5.4 3.6 - - - -
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Residues in contact with ILE 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B ILE* 4.1 6.6 - - + +
451B LEU* 2.8 26.7 + - + +
452B LEU* 3.2 28.7 - - - +
454B MET* 1.3 72.0 - - - +
456B GLY* 1.3 59.5 + - - +
459B ILE* 3.7 4.2 - - - +
511B TYR* 2.6 47.3 + - + +
512B GLY* 4.6 6.3 - - - +
515B THR* 3.6 31.2 - - + -
531B HIS* 3.4 31.0 - - + +
535B VAL* 4.6 11.8 - - + +
603B LEU* 3.6 11.2 - - + -
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Residues in contact with GLY 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PHE 2.8 9.2 + - - -
454B MET 2.7 0.4 + - - -
455B ILE* 1.3 82.3 - - - +
457B ALA* 1.3 56.6 + - - -
458B LEU 3.0 9.8 + - - -
459B ILE* 3.7 3.1 + - - +
460B PRO* 3.1 18.9 - - - +
535B VAL* 5.9 1.8 - - - -
538B VAL* 5.2 6.0 - - - +
539B VAL* 5.6 1.2 - - - +
596B LEU* 4.3 6.4 - - - +
599B CYS* 3.5 28.5 - - - -
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PHE* 2.8 39.2 + - + +
454B MET* 3.4 9.9 - - - +
456B GLY* 1.3 69.8 - - - +
458B LEU* 1.3 57.9 + - - +
460B PRO* 4.2 1.8 - - - -
567B TYR* 2.7 21.6 + - - -
571B TYR* 4.1 8.8 - - + -
596B LEU* 3.5 44.1 + - + +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A ILE* 5.1 17.3 - - + -
543A LEU* 4.5 11.0 - - + -
427B MET* 3.7 43.1 - - + +
431B ILE* 3.8 26.7 - - + -
454B MET* 2.8 46.3 + - + +
457B ALA* 1.3 74.0 - - - +
459B ILE* 1.3 56.8 + - - +
460B PRO* 3.2 2.2 - - - -
461B PHE* 2.8 37.4 + - - +
462B ASN 4.1 0.7 + - - -
511B TYR* 4.1 7.0 - - - +
567B TYR* 4.1 1.2 + - - -
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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