Contacts of the helix formed by residues 444 - 451 (chain D) in PDB entry 2W93
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 ASP 444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442D ILE 3.8 0.2 + - - -
443D GLY* 1.3 73.3 - - - +
445D GLY* 1.3 61.3 + - - +
447D LEU* 3.7 6.7 + - - +
448D GLN* 3.5 18.0 + - - +
468D VAL* 4.2 8.0 - - - +
469D LEU 3.1 19.7 + - - +
470D ASN* 3.6 5.4 - - - +
471D ASN* 3.0 3.0 + - - +
472D ASP* 3.0 26.2 + - - -
473D GLY 3.1 7.8 + - - +
490D ILE* 3.6 13.6 - - + +
495D HIS* 3.8 30.2 + - + +
600D TPP 2.9 2.9 + - - -
601D MG 2.1 32.7 - - - -
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Residues in contact with GLY 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D ILE* 4.7 0.4 - - - -
444D ASP* 1.3 76.7 + - - +
446D SER* 1.3 61.4 + - - +
448D GLN* 3.2 15.9 + - - +
449D LEU* 3.4 14.3 - - - +
474D TYR* 3.5 28.3 + - - -
490D ILE* 4.0 9.9 - - - -
600D TPP 2.9 23.3 + - - -
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Residues in contact with SER 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D GLU* 3.3 29.0 - - - +
388D THR 3.7 0.3 + - - -
415D ILE* 3.2 32.5 - - - +
416D GLY* 3.6 23.4 - - - +
442D ILE* 3.8 10.8 - - - -
443D GLY 3.3 0.6 + - - -
445D GLY* 1.3 69.8 - - - +
447D LEU* 1.3 66.7 + - - +
448D GLN 3.1 0.9 + - - -
449D LEU* 3.1 11.6 + - - +
450D THR* 4.0 0.9 + - - -
600D TPP 2.7 27.4 + - - -
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Residues in contact with LEU 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D THR* 4.0 16.6 - - + +
440D LEU* 5.9 1.1 - - + -
442D ILE* 3.7 23.0 - - + +
443D GLY 3.0 17.0 + - - +
444D ASP 3.8 6.5 - - - +
445D GLY 3.3 0.2 - - - -
446D SER* 1.3 77.2 - - - +
448D GLN* 1.3 62.2 + - + +
449D LEU 3.2 0.3 + - - -
450D THR 3.3 1.4 + - - -
451D VAL* 2.9 32.7 + - + +
454D ILE* 4.2 21.3 - - + -
468D VAL* 4.2 19.7 - - + -
493D TRP* 5.0 3.1 - - + -
495D HIS* 3.8 20.2 - - + -
498D LEU* 3.7 27.1 - - + -
535D MET* 4.8 1.1 - - + -
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Residues in contact with GLN 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN 5.6 0.2 - - - +
49C ALA* 3.7 19.6 - - + +
452C GLN* 2.9 32.7 + - - +
455C SER* 4.6 2.6 + - - -
444D ASP 3.5 12.8 + - - +
445D GLY 3.5 8.1 - - - +
446D SER 3.1 1.4 + - - -
447D LEU* 1.3 77.3 - - + +
449D LEU* 1.3 58.5 + - + +
451D VAL 4.0 0.5 + - - -
474D TYR* 4.9 3.5 + - - -
490D ILE* 3.8 30.0 - - - +
491D GLN* 3.0 30.5 + - - +
493D TRP* 3.3 51.0 - - + +
495D HIS* 5.8 1.6 + - - +
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Residues in contact with LEU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.9 12.6 - - + -
49C ALA* 3.1 21.8 - - - +
50C ASN* 2.9 33.3 + - + +
51C GLU* 3.8 21.8 - - - +
452C GLN* 3.1 3.5 + - - -
50D ASN* 5.3 0.9 + - - -
52D LEU* 5.7 2.1 - - + +
53D ASN* 4.7 0.9 - - - +
415D ILE* 3.4 48.0 - - + +
445D GLY 3.4 20.4 - - - +
446D SER 3.1 8.9 + - - +
448D GLN* 1.3 79.5 - - + +
450D THR* 1.3 69.8 + - + +
452D GLN* 4.0 1.0 - - - +
474D TYR* 4.8 4.5 - - - +
600D TPP 3.9 5.8 - - + -
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Residues in contact with THR 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.1 4.5 - - + -
53D ASN* 3.2 26.4 + - - +
56D TYR* 3.6 18.4 - - + -
416D GLY* 2.7 39.9 + - - +
419D THR* 2.7 31.2 + - - +
420D GLY 5.0 0.9 - - - -
446D SER 4.1 1.2 + - - -
447D LEU 3.3 1.0 + - - -
449D LEU* 1.3 85.5 - - + +
451D VAL* 1.3 66.2 + - - +
452D GLN* 2.9 12.4 + - - -
453D GLU* 3.0 12.0 + - - +
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Residues in contact with VAL 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C VAL* 4.8 5.2 - - + -
452C GLN* 4.1 17.0 - - + +
502C PHE* 4.9 3.4 - - + -
419D THR* 4.6 0.9 - - - -
447D LEU* 2.9 28.9 + - + +
450D THR* 1.3 76.5 - - - +
452D GLN* 1.3 69.6 + - + +
453D GLU 3.0 1.4 + - - -
454D ILE* 3.2 18.7 + - + +
493D TRP* 3.8 26.7 - - + -
498D LEU* 3.7 40.2 - - + -
502D PHE* 3.5 17.2 - - + -
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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