Contacts of the helix formed by residues 410 - 418 (chain C) in PDB entry 2WMZ
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 GLN 410 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C MET* 5.5 0.2 - - - +
408C ASN* 2.5 30.5 + - - +
409C GLU* 1.3 77.7 - - + +
411C ASP* 1.3 52.8 + - - +
412C LEU 2.8 4.9 - - - -
413C LEU* 2.5 46.6 + - - +
414C ALA* 3.0 11.3 + - - +
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Residues in contact with ASP 411 (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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398C LEU* 4.1 9.0 - - + +
401C LYS* 2.9 45.9 + - + +
407C LEU* 3.5 15.5 - - + -
408C ASN* 3.0 39.8 + - - +
410C GLN* 1.3 76.7 - - - +
412C LEU* 1.3 59.7 + - - +
413C LEU 3.2 0.6 + - - -
414C ALA* 3.8 9.8 + - - +
415C LEU* 3.4 27.2 + - - +
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Residues in contact with LEU 412 (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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3C LEU* 3.4 38.0 - - + +
4C MET* 3.0 13.8 - - + +
7C TYR* 3.1 56.8 - - + -
106C ILE* 4.3 17.0 - - + +
109C THR* 5.6 0.7 - - + -
110C ALA* 4.1 17.9 - - + -
398C LEU* 4.6 6.7 - - + -
407C LEU* 5.8 0.2 - - - +
408C ASN 3.6 5.2 + - - +
409C GLU* 3.4 15.3 - - - +
410C GLN 2.8 0.6 - - - -
411C ASP* 1.3 78.6 - - - +
413C LEU* 1.3 58.3 + - - +
415C LEU* 4.1 2.0 - - - -
416C ASN* 3.4 19.1 + - - +
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Residues in contact with LEU 413 (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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4C MET* 3.0 33.7 - - + +
409C GLU 4.1 0.7 - - - +
410C GLN* 2.5 38.8 + - - +
412C LEU* 1.3 71.2 - - - +
414C ALA* 1.3 65.4 + - - +
415C LEU 2.9 1.6 - - - -
416C ASN* 2.8 20.6 + - + +
417C ASN* 2.8 29.8 + - - +
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Residues in contact with ALA 414 (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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410C GLN 3.0 8.6 + - - +
411C ASP* 4.0 12.8 - - - +
413C LEU* 1.3 78.4 - - - +
415C LEU* 1.3 63.7 + - + +
417C ASN* 3.6 21.9 - - - +
418C ALA* 4.4 2.3 + - - +
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Residues in contact with LEU 415 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.2 16.2 - - + -
114C PHE* 4.3 20.4 - - + -
394C LEU* 3.7 35.4 - - + +
397C GLN* 3.7 18.8 - - - +
398C LEU* 3.3 39.5 - - + -
411C ASP 3.4 15.0 + - - +
412C LEU* 4.4 0.7 - - + +
413C LEU 2.9 0.4 - - - -
414C ALA* 1.3 80.4 - - + +
416C ASN* 1.3 58.4 + - - +
417C ASN 2.8 12.1 + - - -
418C ALA* 3.2 17.1 + - + +
419C LEU* 3.4 14.2 - - - +
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Residues in contact with ASN 416 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ASN* 2.6 52.0 + - - +
3C LEU* 3.6 1.9 + - - +
4C MET* 3.5 20.3 + - + +
412C LEU 3.4 15.5 + - - +
413C LEU* 2.8 21.8 + - - +
415C LEU* 1.3 76.8 - - - +
417C ASN* 1.3 63.5 + - - +
419C LEU* 3.4 23.1 + - - +
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Residues in contact with ASN 417 (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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197C ASN* 5.0 1.4 - - - +
413C LEU* 2.8 27.6 + - - +
414C ALA* 3.6 16.7 - - - +
415C LEU 2.8 2.0 + - - -
416C ASN* 1.3 83.6 - - - +
418C ALA* 1.3 51.6 + - - +
419C LEU 2.6 28.0 + - - +
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Residues in contact with ALA 418 (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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196C LEU* 3.1 23.7 - - + +
197C ASN* 2.5 41.9 + - - +
200C ASN* 5.5 9.6 - - - +
201C PHE* 4.7 10.3 - - + -
394C LEU* 5.2 9.0 - - + -
414C ALA 4.4 1.7 + - - +
415C LEU* 3.2 11.7 + - + +
417C ASN* 1.3 75.4 - - - +
419C LEU* 1.3 53.3 + - + +
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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