Contacts of the helix formed by residues 559 - 568 (chain C) in PDB entry 2VZE
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 559 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551C PRO* 2.8 37.9 + - + +
552C LYS 3.5 12.5 + - - +
553C THR* 3.7 36.7 - - + +
558C ILE* 1.3 74.3 - - - +
560C ARG* 1.3 63.2 + - - +
561C ALA* 3.5 2.2 - - + +
562C LYS* 3.4 35.9 + - + +
563C LEU* 3.2 21.5 + - - +
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Residues in contact with ARG 560 (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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224C THR 5.8 0.2 - - - -
464C ASP* 3.8 29.6 + - - +
475C PRO* 4.4 10.5 - - - +
476C SER* 5.7 0.8 + - - -
479C GLU* 2.8 41.5 + - - +
491C THR 4.9 0.2 + - - -
492C ALA* 4.5 11.2 - - + -
493C VAL 3.9 16.8 - - - +
494C ILE* 4.1 12.4 - - + +
557C LYS* 4.7 8.7 - - - +
558C ILE* 3.1 54.0 + - + +
559C GLN* 1.3 71.2 - - - +
561C ALA* 1.3 60.4 + - - +
563C LEU* 3.0 10.2 + - - +
564C ARG* 2.8 32.5 + - - +
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Residues in contact with ALA 561 (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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464C ASP* 4.5 4.9 + - - +
559C GLN* 3.5 1.1 - - + +
560C ARG* 1.3 77.1 - - - +
562C LYS* 1.3 57.4 + - - +
564C ARG* 3.1 24.7 + - - +
565C ASP* 2.8 41.0 + - - +
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Residues in contact with LYS 562 (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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551C PRO* 5.0 9.6 - - + -
559C GLN* 3.4 45.9 + - + +
560C ARG 3.1 0.4 - - - -
561C ALA* 1.3 78.8 - - - +
563C LEU* 1.3 61.4 + - - +
565C ASP* 3.4 9.3 + - - +
566C LYS* 3.3 20.4 + - - +
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Residues in contact with LEU 563 (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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492C ALA* 3.6 24.2 - - + -
494C ILE* 3.8 7.4 - - + +
508C PHE* 3.4 55.8 - - + -
550C LEU* 4.1 9.6 - - + -
551C PRO* 3.9 29.4 - - + +
558C ILE* 4.9 1.3 - - + -
559C GLN 3.2 8.3 + - - +
560C ARG* 3.0 10.4 + - - +
562C LYS* 1.3 78.7 - - - +
564C ARG* 1.3 58.0 + - - +
566C LYS* 3.7 11.0 + - + +
567C GLU* 3.2 27.0 + - - +
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Residues in contact with ARG 564 (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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461C ARG 5.3 2.8 + - - -
462C ALA 4.5 7.9 + - - -
463C ASP* 3.4 19.1 + - - +
464C ASP* 3.1 39.6 + - - +
494C ILE* 4.0 18.9 - - + +
495C SER* 4.0 22.2 - - - +
560C ARG* 2.8 18.9 + - - +
561C ALA* 3.1 24.9 + - - +
563C LEU* 1.3 76.9 - - - +
565C ASP* 1.3 71.4 + - - +
566C LYS 3.2 0.2 - - - -
567C GLU* 3.3 0.6 + - - -
568C TRP* 3.1 40.5 + - + +
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Residues in contact with ASP 565 (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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561C ALA* 2.8 26.3 + - - +
562C LYS* 3.4 8.3 + - - +
564C ARG* 1.3 85.2 + - - +
566C LYS* 1.3 61.8 + - - +
568C TRP* 3.8 7.6 + - - +
569C LYS 3.9 14.4 - - - +
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Residues in contact with LYS 566 (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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562C LYS 3.3 10.0 + - - +
563C LEU* 3.9 15.5 - - + +
564C ARG 3.2 0.6 - - - -
565C ASP* 1.3 78.2 - - - +
567C GLU* 1.3 65.8 + - - +
568C TRP 3.4 0.5 + - - -
569C LYS* 3.5 16.0 + - - +
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Residues in contact with GLU 567 (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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494C ILE* 3.8 15.7 - - + -
495C SER 4.1 3.1 - - - +
496C SER* 3.3 33.8 + - - +
497C PRO* 4.3 7.7 - - + +
506C LYS* 2.6 41.5 + - - +
508C PHE* 3.7 8.1 - - - -
543C LYS* 4.6 5.2 + - - +
545C GLU* 4.4 0.3 - - - +
563C LEU 3.2 15.4 + - - +
564C ARG 3.3 3.8 + - - +
566C LYS* 1.3 79.9 - - - +
568C TRP* 1.3 58.4 + - + +
569C LYS* 3.1 7.4 + - - +
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Residues in contact with TRP 568 (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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495C SER* 3.0 37.8 + - - -
496C SER* 3.9 1.0 - - - +
497C PRO* 3.4 41.1 - - + -
502C GLY 5.0 2.0 - - - -
503C GLU* 3.8 37.7 - - + -
564C ARG* 3.1 33.0 + - + +
565C ASP* 4.2 4.8 - - - +
566C LYS 3.3 0.6 - - - -
567C GLU* 1.3 77.9 - - + +
569C LYS* 1.3 70.4 + - - +
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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