Contacts of the helix formed by residues 440 - 452 (chain A) in PDB entry 1DNC
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 CYS 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A VAL* 4.4 3.8 - - - +
376A PRO* 3.6 15.7 - - - +
378A GLY* 4.5 5.9 - - - +
417A CYS* 4.6 7.2 - - - -
419A MET* 5.0 0.2 - - - -
435A MET* 3.9 33.3 - - + +
436A GLN 3.8 5.2 - - - -
437A GLY* 3.1 37.8 + - - +
438A LEU 4.6 0.2 - - - -
439A GLY* 1.3 77.2 - - - +
441A ASP* 1.3 63.4 + - - +
443A MET* 3.5 28.4 + - - +
444A LEU* 3.6 13.0 + - - +
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Residues in contact with ASP 441 (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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67A LYS* 4.8 3.5 + - - -
70A TRP* 3.8 22.2 - - - -
370A VAL* 3.9 26.1 - - + +
372A PHE* 3.7 28.0 - - + -
376A PRO* 3.6 19.1 - - + +
439A GLY* 3.4 17.3 + - - -
440A CYS* 1.3 74.3 - - - +
442A GLU* 1.3 78.2 + - - +
443A MET 3.8 0.3 + - - -
444A LEU* 4.4 3.8 + - - +
445A GLN 5.3 1.2 + - - -
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Residues in contact with GLU 442 (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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67A LYS* 4.9 9.5 + - - -
439A GLY* 3.3 6.7 + - - +
441A ASP* 1.3 96.3 - - - +
443A MET* 1.3 61.2 + - - +
444A LEU 3.5 1.1 - - - -
445A GLN* 4.7 7.6 + - - +
446A GLY 5.6 0.3 + - - -
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Residues in contact with MET 443 (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 MET* 3.8 16.2 - - + -
435A MET* 3.9 17.0 - - + +
438A LEU 4.3 2.9 - - - +
439A GLY* 3.2 26.7 + - - +
440A CYS* 3.8 15.9 - - - +
441A ASP 3.4 0.4 - - - -
442A GLU* 1.3 79.3 - - - +
444A LEU* 1.3 62.7 + - - +
445A GLN 3.7 0.6 + - - -
446A GLY* 4.2 4.9 + - - -
447A PHE* 3.4 25.2 + - + -
470A SER* 4.0 15.3 - - - -
471A SER* 3.6 46.9 - - - +
474A LEU* 5.1 0.4 - - - -
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Residues in contact with LEU 444 (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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368A PRO* 3.8 20.6 - - + -
369A THR 3.5 13.5 - - - +
370A VAL* 4.2 10.3 - - + -
378A GLY* 3.9 3.1 - - - -
379A THR* 3.5 38.6 - - - +
380A VAL* 4.1 23.3 - - + -
433A ILE* 4.9 6.3 - - + -
435A MET* 3.8 23.8 - - + +
440A CYS 3.6 8.9 + - - +
441A ASP 4.4 1.9 + - - +
442A GLU 3.5 0.8 - - - -
443A MET* 1.3 79.4 - - - +
445A GLN* 1.3 68.3 + - - +
447A PHE* 3.0 12.1 + - + -
448A ALA* 3.0 18.2 + - + +
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Residues in contact with GLN 445 (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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368A PRO* 4.4 19.8 - - - +
441A ASP 5.3 1.2 + - - -
442A GLU 4.7 6.4 + - - +
443A MET 3.7 1.2 - - - -
444A LEU* 1.3 75.6 - - - +
446A GLY* 1.3 62.6 + - - +
448A ALA* 3.2 10.8 + - - +
449A VAL* 3.2 28.6 + - + +
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Residues in contact with GLY 446 (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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442A GLU 5.6 0.6 + - - -
443A MET 4.2 4.1 + - - -
444A LEU 3.3 1.0 - - - -
445A GLN* 1.3 74.5 - - - +
447A PHE* 1.3 66.3 + - - +
449A VAL* 3.3 18.9 + - - +
450A ALA* 3.3 12.0 + - - +
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Residues in contact with PHE 447 (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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380A VAL* 5.3 0.2 - - - -
433A ILE* 4.1 14.1 - - + -
435A MET* 5.0 2.5 - - + -
443A MET* 3.4 40.4 - - + -
444A LEU* 3.0 12.8 + - + +
446A GLY* 1.3 77.9 - - - +
448A ALA* 1.3 58.7 + - - +
450A ALA* 3.1 8.7 + - + +
451A VAL* 2.9 32.2 + - - +
460A PHE* 3.4 33.4 - + - -
471A SER* 4.0 16.2 - - - -
474A LEU* 3.6 38.1 - - + -
475A VAL* 4.2 12.6 - - + -
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Residues in contact with ALA 448 (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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366A ASN* 5.2 4.2 - - - +
368A PRO* 3.9 34.1 - - + -
380A VAL* 4.4 19.1 - - + +
444A LEU* 3.0 12.0 + - + +
445A GLN* 3.4 14.8 - - - +
446A GLY 3.2 0.2 - - - -
447A PHE* 1.3 74.9 - - - +
449A VAL* 1.3 58.8 + - - +
451A VAL* 3.9 2.8 - - - +
452A LYS* 3.0 29.6 + - - +
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Residues in contact with VAL 449 (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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445A GLN* 3.2 25.3 + - + +
446A GLY* 3.5 12.1 - - - +
447A PHE 3.2 0.4 - - - -
448A ALA* 1.3 74.7 - - - +
450A ALA* 1.3 58.3 + - - +
452A LYS* 3.2 9.5 + - + +
453A MET* 3.0 42.1 + - + +
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Residues in contact with ALA 450 (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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446A GLY 3.3 8.6 + - - +
447A PHE* 3.1 14.7 + - + +
449A VAL* 1.3 80.3 - - - +
451A VAL* 1.3 60.8 + - - +
453A MET* 3.2 18.4 + - - +
454A GLY 3.4 0.2 + - - -
455A ALA* 3.2 36.4 + - + +
460A PHE* 4.5 11.2 - - + -
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Residues in contact with VAL 451 (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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366A ASN* 3.7 33.7 - - + +
380A VAL* 4.4 13.5 - - + -
381A GLY* 5.3 0.7 - - - -
429A LYS* 5.8 0.7 - - - -
430A VAL* 3.8 33.6 - - + +
431A VAL* 4.9 5.2 - - - -
432A GLY 5.4 0.7 - - - +
433A ILE* 3.6 27.1 - - + -
447A PHE 2.9 19.1 + - - +
448A ALA* 4.0 6.1 - - - +
450A ALA* 1.3 73.3 - - - +
452A LYS* 1.3 65.7 + - - +
453A MET 3.1 0.4 - - - -
454A GLY* 3.0 14.8 + - - +
455A ALA* 4.6 4.0 - - - +
460A PHE* 4.7 2.9 - - + -
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Residues in contact with LYS 452 (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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362A LEU* 6.0 2.4 - - - +
363A ASP* 3.5 37.4 + - - +
365A ASN 4.4 6.7 + - - +
366A ASN* 4.2 27.3 - - + +
448A ALA 3.0 18.8 + - - +
449A VAL* 3.2 9.6 + - - +
451A VAL* 1.3 78.3 - - - +
453A MET* 1.3 60.1 + - + +
454A GLY 3.6 0.3 + - - -
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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