Contacts of the helix formed by residues 444 - 451 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442C ILE 3.9 0.2 + - - -
443C GLY* 1.3 72.8 - - - +
445C GLY* 1.3 61.3 + - - +
447C LEU* 3.7 6.8 + - - +
448C GLN* 3.4 18.9 + - - +
468C VAL* 4.1 8.7 - - + +
469C LEU 3.1 17.6 + - - +
470C ASN* 3.5 7.3 - - - +
471C ASN* 3.8 2.5 - - - -
472C ASP* 3.0 26.3 + - - -
473C GLY 3.1 7.6 + - - +
490C ILE* 3.6 15.5 - - + +
495C HIS* 3.8 28.6 + - + +
600C TPP 2.8 4.3 + - - -
601C MG 2.1 33.0 - - - -
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Residues in contact with GLY 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ILE* 4.7 0.7 - - - -
444C ASP* 1.3 80.4 + - - +
446C SER* 1.3 61.1 + - - +
448C GLN* 3.1 16.9 + - - +
449C LEU* 3.3 13.7 - - - +
474C TYR* 3.6 28.4 + - - -
490C ILE* 4.0 9.6 - - - -
600C TPP 2.8 18.6 + - - -
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Residues in contact with SER 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C GLU* 3.4 27.1 - - - +
388C THR 3.7 0.7 + - - -
415C ILE* 3.1 33.5 - - - +
416C GLY* 3.6 24.7 - - - +
442C ILE* 3.9 6.3 - - - -
443C GLY 3.3 4.2 + - - -
445C GLY* 1.3 70.6 - - - +
447C LEU* 1.3 67.3 + - - +
448C GLN 3.1 1.2 + - - -
449C LEU* 3.1 11.8 + - - +
450C THR* 4.0 0.9 + - - -
600C TPP 2.7 26.5 + - - -
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Residues in contact with LEU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C THR* 4.1 15.7 - - + +
440C LEU* 6.0 1.3 - - + -
442C ILE* 3.6 22.6 - - + +
443C GLY 3.0 17.4 + - - +
444C ASP* 3.8 5.2 - - - +
446C SER* 1.3 77.1 - - - +
448C GLN* 1.3 62.6 + - - +
449C LEU 3.2 0.3 + - - -
450C THR 3.3 1.6 + - - -
451C VAL* 2.9 38.3 + - + +
454C ILE* 4.1 23.6 - - + -
468C VAL* 4.0 20.9 - - + -
493C TRP* 4.9 2.7 - - + -
495C HIS* 3.7 29.8 - - + +
498C LEU* 3.9 16.4 - - + -
535C MET* 4.8 1.1 - - + -
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Residues in contact with GLN 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASP 3.4 16.1 + - - +
445C GLY 3.1 9.7 + - - +
446C SER 3.1 0.4 + - - -
447C LEU* 1.3 78.3 - - - +
449C LEU* 1.3 58.2 + - + +
450C THR 3.3 0.2 + - - -
451C VAL 4.0 0.7 + - - -
474C TYR* 5.0 2.8 + - - -
490C ILE* 3.8 28.6 - - - +
491C GLN* 2.9 30.7 + - - +
493C TRP* 3.2 50.5 - - + +
495C HIS* 5.7 1.6 + - - +
48D ASN 5.6 0.2 - - - +
49D ALA* 3.7 19.9 - - + +
452D GLN* 2.9 32.9 + - - +
455D SER* 4.9 2.1 + - - -
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASN* 5.2 1.0 + - - -
52C LEU* 5.5 3.6 - - + +
53C ASN* 4.6 1.0 - - - +
415C ILE* 3.4 46.9 - - + +
416C GLY* 4.2 2.5 - - - -
445C GLY 3.3 20.2 - - - +
446C SER 3.1 10.2 + - - +
448C GLN* 1.3 78.7 - - + +
450C THR* 1.3 70.2 + - + +
452C GLN* 4.1 0.9 - - - +
474C TYR* 4.8 4.3 - - - +
600C TPP 4.0 4.5 - - + -
25D LEU* 3.9 13.0 - - + -
49D ALA* 3.2 22.0 - - - +
50D ASN* 2.9 31.6 + - + +
51D GLU* 3.8 21.5 - - - +
452D GLN* 3.1 4.3 + - - -
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Residues in contact with THR 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 5.0 4.3 - - + -
53C ASN* 3.2 26.6 + - - +
56C TYR* 3.6 15.0 - - + -
415C ILE 5.1 0.2 - - - +
416C GLY* 2.6 44.0 + - - +
419C THR* 2.8 29.7 + - - +
420C GLY 4.9 0.4 - - - -
446C SER 4.0 1.6 + - - -
447C LEU 3.3 1.0 + - - -
449C LEU* 1.3 89.0 - - + +
451C VAL* 1.3 63.7 + - - +
452C GLN* 3.0 11.7 + - - -
453C GLU* 3.1 12.0 + - - +
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Residues in contact with VAL 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C THR* 4.6 1.1 - - - -
447C LEU* 2.9 30.7 + - + +
448C GLN 4.1 0.2 - - - +
450C THR* 1.3 76.9 - - - +
452C GLN* 1.3 68.3 + - - +
453C GLU 3.0 1.6 + - - -
454C ILE* 3.1 20.8 + - + +
493C TRP* 3.8 29.4 - - + -
498C LEU* 3.8 37.5 - - + -
502C PHE* 3.5 15.0 - - + -
451D VAL* 4.8 5.8 - - + -
452D GLN* 4.1 16.8 - - + +
502D 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