Contacts of the helix formed by residues 441 - 454 (chain A) in PDB entry 6MOL
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 ASN 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A ALA 5.0 3.0 + - - -
405A ARG 5.9 0.2 + - - -
407A GLY* 5.5 4.9 - - - -
436A SER* 2.9 20.2 + - - +
437A ILE* 5.2 0.8 - - - +
439A ASN* 3.5 27.3 - - - +
440A GLY* 1.3 79.7 - - - +
442A GLU* 1.3 65.8 + - - +
443A ASP* 3.2 6.3 - - + +
444A LEU* 3.8 32.5 - - + +
445A ALA* 3.5 17.5 + - - +
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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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437A ILE* 6.0 3.8 - - + -
440A GLY 4.0 3.0 + - - +
441A ASN* 1.3 71.7 - - - +
443A ASP* 1.3 67.9 + - - +
444A LEU 3.4 0.2 - - - -
445A ALA* 3.5 8.1 + - + +
446A GLU* 3.2 23.6 + - - +
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Residues in contact with ASP 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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409A VAL* 4.5 18.3 - - + +
441A ASN* 3.2 4.9 - - + +
442A GLU* 1.3 84.6 + - - +
444A LEU* 1.3 63.0 + - + +
446A GLU* 3.4 17.6 + - - +
447A ILE* 3.9 11.1 + - - +
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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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404A ALA* 3.7 30.5 - - + +
407A GLY* 3.8 16.6 - - - -
408A HIS 4.1 17.9 - - - +
409A VAL* 3.6 26.9 - - + -
412A VAL* 4.2 18.3 - - + +
436A SER* 3.6 18.6 - - - +
441A ASN* 3.6 28.5 + - + +
442A GLU 3.4 0.2 - - - -
443A ASP* 1.3 77.3 - - + +
445A ALA* 1.3 62.7 + - - +
446A GLU 3.3 0.3 + - - -
447A ILE* 3.4 5.5 + - - +
448A LEU* 3.2 28.0 + - + +
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Residues in contact with ALA 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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433A PHE* 3.4 36.6 - - + -
436A SER* 4.2 4.6 - - - -
437A ILE* 4.1 15.0 - - + -
441A ASN 3.5 15.1 + - - +
442A GLU* 3.9 8.5 - - + +
443A ASP 3.3 0.6 - - - -
444A LEU* 1.3 78.1 - - - +
446A GLU* 1.3 61.5 + - - +
448A LEU 4.0 0.7 - - - -
449A GLN* 3.3 24.6 + - - +
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Residues in contact with GLU 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 3.2 13.9 + - - +
443A ASP* 3.5 13.2 - - - +
444A LEU 3.1 1.0 - - - -
445A ALA* 1.3 79.7 - - - +
447A ILE* 1.3 70.8 + - + +
449A GLN* 4.6 2.2 - - - +
450A ALA* 3.9 16.5 + - - +
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Residues in contact with ILE 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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409A VAL* 6.0 6.1 - - + +
412A VAL* 4.9 9.4 - - + -
413A GLU* 4.8 27.1 - - + +
416A LEU* 3.7 24.5 - - + -
443A ASP 4.0 11.7 - - - +
444A LEU* 3.4 6.3 + - - +
446A GLU* 1.3 85.4 - - + +
448A LEU* 1.3 66.0 + - - +
450A ALA* 3.4 5.8 + - - +
451A ALA* 3.3 20.8 + - + +
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Residues in contact with LEU 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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400A LEU* 4.1 9.4 - - + -
404A ALA* 5.0 4.7 - - + -
412A VAL* 4.5 18.4 - - + -
416A LEU* 4.9 2.7 - - + -
422A VAL* 3.9 33.8 - - + +
432A ALA* 3.3 41.7 - - + +
433A PHE* 3.6 19.5 - - + -
436A SER* 3.3 17.9 - - - +
444A LEU* 3.2 18.8 + - + +
446A GLU 3.5 0.2 - - - -
447A ILE* 1.3 77.1 - - - +
449A GLN* 1.3 61.7 + - - +
451A ALA* 3.4 2.1 + - - +
452A ALA* 3.1 27.1 + - - +
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Residues in contact with GLN 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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433A PHE* 3.7 31.6 - - + -
445A ALA* 3.3 16.9 + - - +
446A GLU* 4.6 2.9 - - - +
447A ILE 3.3 0.2 - - - -
448A LEU* 1.3 79.3 - - - +
450A ALA* 1.3 59.5 + - - +
452A ALA* 4.1 12.3 + - + +
453A LEU* 4.5 15.3 + - + +
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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 GLU 3.9 11.9 + - - +
447A ILE* 3.4 8.0 + - - +
448A LEU 3.2 0.6 - - - -
449A GLN* 1.3 79.7 - - - +
451A ALA* 1.3 59.8 + - - +
452A ALA 3.4 0.4 + - - -
453A LEU* 4.4 2.1 + - - +
454A GLU* 4.0 17.8 + - - +
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Residues in contact with ALA 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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416A LEU* 4.1 32.1 - - + -
422A VAL* 4.5 6.1 - - + +
447A ILE* 3.3 15.1 + - + +
448A LEU 3.4 2.7 + - - +
450A ALA* 1.3 77.3 - - - +
452A ALA* 1.3 64.0 + - - +
453A LEU 3.5 0.9 - - - -
454A GLU 4.0 15.9 - - - +
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Residues in contact with ALA 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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422A VAL* 4.2 22.7 - - + -
423A ASN* 3.9 27.7 + - - +
433A PHE* 6.5 0.4 - - + -
448A LEU 3.1 17.1 + - - +
449A GLN* 4.4 7.6 - - - +
450A ALA 3.4 0.6 - - - -
451A ALA* 1.3 79.5 - - - +
453A LEU* 1.3 67.7 + - + +
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Residues in contact with LEU 453 (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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449A GLN* 4.5 13.6 + - + +
450A ALA 4.4 2.5 + - - +
452A ALA* 1.3 86.9 - - + +
454A GLU* 1.3 59.8 + - + +
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Residues in contact with GLU 454 (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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450A ALA 4.0 14.7 + - - +
451A ALA* 4.0 16.9 - - - +
453A LEU* 1.3 82.8 - - + +
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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