Contacts of the helix formed by residues 584 - 595 (chain C) in PDB entry 4BUR
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 ARG 584 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493C GLU* 5.3 0.6 + - - -
578C LEU* 4.0 24.3 - - + +
581C ILE* 3.3 39.6 + - + +
582C PHE* 2.8 36.7 + - - +
583C ASN* 1.3 80.7 - - - +
585C MET* 1.3 66.0 + - - +
586C PRO* 3.3 3.8 - - - -
587C ILE* 2.9 28.3 + - + +
588C ALA* 3.2 10.0 + - - +
608C PHE* 2.8 29.0 + - + +
609C ASN* 3.0 32.3 + - - +
612C GLU* 3.0 28.9 + - - +
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Residues in contact with MET 585 (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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481C MET* 4.0 28.3 - - + -
493C GLU* 3.7 39.7 + - + +
494C ALA 4.1 9.9 - - - +
495C ILE* 4.0 31.4 - - + -
578C LEU* 3.8 15.5 - - + +
583C ASN* 3.5 0.6 - - - +
584C ARG* 1.3 76.6 - - - +
586C PRO* 1.4 69.1 - - + +
588C ALA* 3.1 5.9 + - - +
589C ARG* 3.0 45.9 + - - +
701C NAD 5.0 9.0 - - - +
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Residues in contact with PRO 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C ASN* 4.0 14.4 - - - +
584C ARG 3.4 4.9 - - - -
585C MET* 1.4 94.0 - - + +
587C ILE* 1.3 63.5 + - + +
589C ARG* 3.7 13.8 + - + +
590C LYS* 3.4 20.3 + - - +
701C NAD 5.4 1.8 - - - +
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Residues in contact with ILE 587 (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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583C ASN 5.2 2.5 - - - +
584C ARG* 2.9 28.4 + - + +
586C PRO* 1.3 78.5 - - + +
588C ALA* 1.3 64.4 + - - +
590C LYS* 3.3 9.9 + - + +
591C ILE* 3.1 25.5 + - + +
607C LEU* 3.5 43.1 - - + +
608C PHE* 4.0 21.5 - - + -
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Residues in contact with ALA 588 (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 ILE* 3.8 20.6 - - + -
576C ILE* 3.7 33.1 - - + +
578C LEU* 4.7 4.3 - - + -
584C ARG 3.2 7.7 + - - +
585C MET* 3.1 15.4 + - - +
587C ILE* 1.3 73.9 - - - +
589C ARG* 1.3 55.9 + - - +
591C ILE* 2.7 23.7 + - - +
592C ILE* 3.0 16.5 + - - +
608C PHE* 4.1 7.4 - - + -
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Residues in contact with ARG 589 (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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456C ASP* 4.9 1.8 + - - -
478C HIS* 3.5 34.4 + - - -
479C GLN* 2.6 34.0 + - + +
480C SER* 4.5 1.0 - - - +
481C MET* 4.1 19.0 - - - +
495C ILE* 4.0 21.9 - - + +
585C MET* 3.0 42.8 + - + +
586C PRO* 3.7 13.5 - - - +
588C ALA* 1.3 77.2 - - - +
590C LYS* 1.3 58.3 + - - +
592C ILE* 3.4 2.9 + - - +
593C LYS* 2.9 32.1 + - - +
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Residues in contact with LYS 590 (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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586C PRO 3.4 10.1 + - - +
587C ILE* 3.3 13.4 + - + +
588C ALA 3.1 0.8 - - - -
589C ARG* 1.3 79.3 - - - +
591C ILE* 1.3 61.3 + - + +
593C LYS* 3.8 7.7 - - + +
594C ASP* 2.7 68.9 + - - +
607C LEU* 6.2 3.6 - - + -
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Residues in contact with ILE 591 (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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566C PHE* 5.0 0.7 - - + -
573C VAL* 4.0 36.9 - - + +
576C ILE* 4.3 5.6 - - + -
587C ILE* 3.1 12.6 + - + +
588C ALA 2.7 13.9 + - - +
590C LYS* 1.3 76.3 - - + +
592C ILE* 1.3 59.9 + - - +
594C ASP* 3.5 7.0 + - - +
595C GLY* 3.4 15.8 + - - -
596C GLU 4.8 1.6 + - - -
598C HIS* 4.4 15.8 + - + +
604C VAL* 3.7 18.8 - - + -
607C LEU* 4.1 20.2 - - + -
608C PHE* 3.5 38.1 - - + -
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Residues in contact with ILE 592 (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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446C LYS* 4.3 9.6 - - + +
447C LEU* 4.1 30.7 - - + +
479C GLN* 4.5 15.5 - - + +
495C ILE* 4.5 18.6 - - + +
496C GLY* 4.9 1.3 - - - -
573C VAL* 3.9 14.3 - - + +
574C VAL 3.6 6.3 - - - +
575C GLY* 3.6 32.8 - - - +
576C ILE* 4.1 15.5 - - + +
588C ALA 3.0 20.2 + - - +
589C ARG* 3.8 6.3 - - - +
591C ILE* 1.3 72.8 - - - +
593C LYS* 1.3 65.7 + - - +
595C GLY* 3.0 15.8 + - - -
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Residues in contact with LYS 593 (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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446C LYS* 3.1 30.7 + - + +
477C TRP* 4.3 36.1 - - + +
589C ARG 2.9 21.0 + - - +
590C LYS* 4.0 7.4 - - + +
592C ILE* 1.3 75.4 - - - +
594C ASP* 1.3 69.3 + - - +
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Residues in contact with ASP 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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446C LYS* 5.0 1.6 + - - -
590C LYS* 2.7 56.2 + - - +
591C ILE* 3.8 7.7 - - - +
593C LYS* 1.3 85.9 - - - +
595C GLY* 1.3 64.5 + - - +
596C GLU* 3.0 30.4 + - + +
598C HIS* 6.2 1.6 - - + +
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Residues in contact with GLY 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LYS* 5.0 7.6 - - - -
572C VAL* 3.9 26.8 - - - +
573C VAL 5.2 1.1 - - - -
591C ILE 3.4 6.5 + - - -
592C ILE 3.0 16.6 + - - -
593C LYS 3.2 1.5 - - - -
594C ASP* 1.3 77.1 - - - +
596C GLU* 1.3 63.2 + - - +
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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