Contacts of the helix formed by residues 444 - 451 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A ILE 3.9 0.2 + - - -
443A GLY* 1.3 71.1 - - - +
445A GLY* 1.3 60.3 + - - +
447A LEU* 3.6 7.2 + - - +
448A GLN* 3.4 19.4 + - - +
468A VAL* 4.2 9.6 - - + +
469A LEU 3.1 19.0 + - - +
470A ASN* 3.5 6.2 - - - +
471A ASN* 3.0 2.7 + - - +
472A ASP* 3.0 26.7 + - - -
473A GLY 3.1 7.3 + - - +
490A ILE* 3.6 15.3 - - + +
495A HIS* 3.8 28.6 + - + +
600A TPP 2.8 3.5 + - - -
601A MG 2.0 34.2 - - - -
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Residues in contact with GLY 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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415A ILE* 4.7 0.7 - - - -
444A ASP* 1.3 74.2 + - - +
446A SER* 1.3 60.6 + - - +
448A GLN* 3.1 20.9 + - - +
449A LEU* 3.5 9.9 - - - +
474A TYR* 3.5 28.7 - - - -
490A ILE* 4.0 11.0 - - - -
600A TPP 2.9 23.2 + - - -
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Residues in contact with SER 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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387A GLU* 3.3 27.2 - - - +
388A THR 3.7 0.7 + - - -
415A ILE* 3.1 35.3 - - - +
416A GLY* 3.5 25.0 - - - +
442A ILE* 3.9 5.2 - - - -
443A GLY 3.3 4.2 + - - -
445A GLY* 1.3 69.5 - - - +
447A LEU* 1.3 66.8 + - - +
448A GLN 3.1 0.9 + - - -
449A LEU* 3.1 11.3 + - - +
450A THR* 4.0 0.7 + - - -
600A TPP 2.7 27.7 + - - -
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Residues in contact with LEU 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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419A THR* 4.0 17.0 - - + +
440A LEU* 5.9 1.6 - - + -
442A ILE* 3.6 21.3 - - + +
443A GLY 3.0 16.0 + - - +
444A ASP 3.8 5.6 - - - +
445A GLY 3.2 0.2 - - - -
446A SER* 1.3 78.1 - - - +
448A GLN* 1.3 62.3 + - + +
449A LEU 3.2 0.5 + - - -
450A THR 3.3 1.4 + - - -
451A VAL* 3.0 33.5 + - + +
454A ILE* 4.2 22.0 - - + -
468A VAL* 4.0 22.2 - - + -
493A TRP* 5.0 2.5 - - + -
495A HIS* 3.8 29.6 - - + +
498A LEU* 3.9 15.3 - - + -
535A MET* 4.8 1.1 - - + -
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Residues in contact with GLN 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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444A ASP 3.4 16.1 + - - +
445A GLY 3.4 8.5 - - - +
446A SER 3.0 1.4 - - - -
447A LEU* 1.3 79.7 - - - +
449A LEU* 1.3 58.5 + - + +
451A VAL 4.0 0.7 + - - -
474A TYR* 5.0 3.1 + - - -
490A ILE* 3.8 28.6 - - - +
491A GLN* 2.9 29.8 + - - +
493A TRP* 3.3 48.9 - - + +
495A HIS* 5.7 1.2 + - - -
48B ASN 5.6 0.2 - - - +
49B ALA* 3.7 20.0 - - + +
452B GLN* 2.9 33.1 + - - +
455B SER* 4.6 2.7 + - - -
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Residues in contact with LEU 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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50A ASN* 5.3 1.0 + - - -
52A LEU* 5.6 2.5 - - + +
53A ASN* 4.6 0.9 - - - +
415A ILE* 3.4 46.4 - - + +
416A GLY* 4.3 2.0 - - - -
445A GLY 3.5 18.8 - - - +
446A SER 3.1 9.7 + - - +
448A GLN* 1.3 79.7 - - + +
450A THR* 1.3 70.4 + - + +
452A GLN* 4.1 0.7 - - - +
474A TYR* 4.8 4.0 - - - +
600A TPP 4.0 4.9 - - + -
25B LEU* 4.0 12.6 - - + -
49B ALA* 3.2 20.9 - - - +
50B ASN* 2.9 33.1 + - + +
51B GLU* 3.8 22.2 - - - +
452B GLN* 3.1 3.4 + - - -
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Residues in contact with THR 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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52A LEU* 5.1 4.5 - - + -
53A ASN* 3.1 25.1 + - - +
56A TYR* 3.6 19.1 - - + -
416A GLY* 2.7 39.7 + - - +
419A THR* 2.7 31.4 + - - +
420A GLY 5.0 0.7 - - - -
446A SER 4.0 1.9 + - - -
447A LEU 3.3 0.8 + - - -
449A LEU* 1.3 84.0 - - + +
451A VAL* 1.3 66.8 + - - +
452A GLN* 3.0 11.6 + - - -
453A GLU* 3.1 11.4 + - - +
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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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419A THR* 4.6 0.2 - - - -
447A LEU* 3.0 31.4 + - + +
448A GLN 4.2 0.2 - - - +
450A THR* 1.3 76.6 - - - +
452A GLN* 1.3 69.1 + - - +
453A GLU 3.0 1.6 + - - -
454A ILE* 3.1 23.3 + - + +
493A TRP* 3.8 28.7 - - + -
498A LEU* 3.6 38.4 - - + -
502A PHE* 3.5 11.7 - - + -
451B VAL* 4.7 7.4 - - + -
452B GLN* 4.1 17.0 - - + +
502B PHE* 4.8 3.1 - - + -
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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