Contacts of the helix formed by residues 593 - 599 (chain C) in PDB entry 2W4V
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 GLY 593 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544C ASP* 3.3 9.5 + - - +
592C THR* 1.3 72.5 - - - +
594C TRP* 1.3 60.7 + - - +
595C LEU* 3.1 21.7 + - - +
596C GLU* 3.4 3.1 + - - +
597C LYS* 3.3 22.2 + - - +
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Residues in contact with TRP 594 (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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471C SER 3.9 1.3 - - - -
472C PHE* 2.3 81.2 - + + -
475C LEU* 3.5 36.3 - - + -
529C ILE* 4.2 5.4 - - + -
530C LEU* 3.8 11.4 - - + +
533C LEU* 1.6 54.8 - - + +
544C ASP* 4.8 0.2 + - - -
547C PHE* 6.4 0.7 - - + -
578C PHE* 6.2 0.7 - + - -
589C TYR* 6.3 0.4 - - + -
590C SER 5.2 0.7 - - - -
591C ILE* 3.4 31.7 + - + +
592C THR 3.3 2.6 + - - -
593C GLY* 1.3 76.9 - - - +
595C LEU* 1.3 61.2 + - - +
596C GLU 3.5 0.2 - - - -
597C LYS* 3.9 8.4 - - - +
598C ASN* 3.5 21.0 + - + +
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Residues in contact with LEU 595 (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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533C LEU* 5.4 2.2 - - - +
537C CYS* 4.8 9.5 - - - +
542C ALA 5.8 2.2 - - - +
543C ASP* 5.5 6.5 - - - -
544C ASP* 5.6 4.0 - - + +
547C PHE* 4.0 34.3 - - + -
593C GLY* 3.3 20.4 - - - +
594C TRP* 1.3 75.2 - - - +
596C GLU* 1.3 138.3 + - + +
598C ASN* 3.8 2.9 + - - +
599C LYS* 3.5 24.6 + - + +
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Residues in contact with GLU 596 (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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593C GLY* 4.1 2.9 - - - +
595C LEU* 1.3 127.0 - - + +
597C LYS* 1.3 64.8 + - - +
598C ASN 3.1 2.9 + - - -
599C LYS* 3.3 16.9 + - - +
600C ASP* 3.3 11.8 + - - -
601C PRO* 4.0 24.9 - - + +
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Residues in contact with LYS 597 (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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270C SER* 5.2 4.0 - - - -
471C SER* 3.3 11.8 + - - +
472C PHE* 2.9 32.7 - - + +
473C GLU* 2.2 74.0 - - - +
593C GLY 3.3 16.8 + - - +
594C TRP* 3.9 8.1 - - - +
596C GLU* 1.3 80.1 - - - +
598C ASN* 1.3 56.7 + - - +
599C LYS 3.5 0.4 + - - -
600C ASP* 4.6 2.6 + - - -
645C ILE* 4.2 9.2 - - - +
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Residues in contact with ASN 598 (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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472C PHE* 3.8 9.1 - - + -
533C LEU* 5.1 3.8 - - + +
534C GLU* 2.5 23.1 + - - +
537C CYS* 4.7 9.3 - - + +
594C TRP* 3.5 25.0 + - + +
595C LEU* 4.3 4.0 - - - +
596C GLU 3.1 0.4 - - - -
597C LYS* 1.3 78.6 - - - +
599C LYS* 1.3 56.7 + - + +
644C THR* 3.3 16.9 - - - +
645C ILE* 2.7 39.6 + - + +
646C SER* 2.2 29.6 + - - -
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Residues in contact with LYS 599 (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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537C CYS* 3.8 40.1 + - + +
538C MET* 4.9 13.1 - - - +
595C LEU* 3.5 16.5 + - + +
596C GLU* 3.3 12.5 + - - +
598C ASN* 1.3 81.2 - - - +
600C ASP* 1.3 78.0 - - - +
601C PRO* 3.8 0.9 - - + -
644C THR* 5.8 3.4 - - + +
645C ILE* 5.2 0.4 - - - -
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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