Contacts of the helix formed by residues 572 - 585 (chain C) in PDB entry 5VOT
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 572 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541C PHE* 3.3 6.1 - - - -
569C ASN 4.4 2.2 + - - -
570C GLU 2.7 14.3 + - - +
571C PHE* 1.3 75.2 - - - +
573C ILE* 1.3 66.6 + - - -
574C PHE* 3.2 3.9 + - - -
575C ASN* 3.5 11.7 + - - +
576C SER* 3.3 15.1 + - - -
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Residues in contact with ILE 573 (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 SER* 4.6 7.0 - - - +
538C VAL* 4.5 18.4 - - + -
541C PHE* 3.1 48.0 - - + -
572C GLY* 1.3 72.8 - - - -
574C PHE* 1.3 70.4 + - + +
576C SER* 3.1 4.7 + - - -
577C LEU* 2.9 26.9 + - + +
195H VAL* 4.6 21.1 - - + -
199H HIS* 6.3 3.6 - - + -
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Residues in contact with PHE 574 (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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594B ARG* 5.2 7.2 - - - -
596B LEU* 3.4 46.4 - - + -
599B ARG* 4.0 21.5 - - + -
572C GLY* 3.2 1.4 - - - -
573C ILE* 1.3 86.5 - - + +
575C ASN* 1.3 78.0 + - - +
577C LEU* 3.3 14.0 + - + +
578C TRP* 2.9 32.6 + + + +
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Residues in contact with ASN 575 (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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594B ARG* 5.2 14.8 - - - +
569C ASN 4.4 13.3 - - - +
570C GLU* 5.0 3.8 - - + -
572C GLY* 3.5 14.9 + - - +
573C ILE 3.4 0.4 - - - -
574C PHE* 1.3 87.6 - - - +
576C SER* 1.3 58.6 + - - +
578C TRP* 3.3 15.2 + - - +
579C PHE* 2.9 26.5 + - - +
591C ILE* 4.2 28.0 - - + +
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Residues in contact with SER 576 (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 SER* 4.6 17.3 - - - -
540C LEU* 5.1 8.5 - - - +
541C PHE* 4.3 13.1 + - - -
570C GLU* 3.4 30.7 + - - +
572C GLY 3.3 12.1 + - - -
573C ILE* 3.1 12.1 + - - -
575C ASN* 1.3 74.8 - - - +
577C LEU* 1.3 67.1 + - - +
579C PHE* 2.9 20.8 + - - +
580C SER* 3.0 12.1 + - - -
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Residues in contact with LEU 577 (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 TYR* 3.4 35.2 + - + +
534C ILE* 5.3 6.3 - - + -
537C SER* 3.3 33.4 - - - +
573C ILE* 2.9 17.1 + - + +
574C PHE* 3.6 17.7 - - + +
576C SER* 1.3 73.4 - - - +
578C TRP* 1.3 65.2 + - - +
580C SER* 2.9 13.7 + - - -
581C LEU 3.0 10.7 + - - -
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Residues in contact with TRP 578 (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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592B SER* 4.7 2.2 + - - -
593B PRO* 4.5 29.5 + - + -
599B ARG* 3.1 53.6 - - + -
602B GLY* 4.7 3.4 - - - -
603B GLY 4.3 4.9 - - - -
606B TRP* 3.7 32.4 - + - -
574C PHE* 2.9 24.5 + + + +
575C ASN* 3.3 19.5 - - - +
577C LEU* 1.3 76.5 - - - +
579C PHE* 1.3 63.2 + - - +
581C LEU* 3.2 26.4 + - + +
582C GLY* 2.9 21.2 + - - -
590C ASP* 3.7 26.1 + - + -
591C ILE* 6.3 2.7 - - + -
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Residues in contact with PHE 579 (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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540C LEU* 4.6 19.7 - - + -
570C GLU* 5.6 5.4 - - + -
575C ASN 2.9 14.1 + - - +
576C SER* 2.9 13.4 + - - +
578C TRP* 1.3 76.5 - - - +
580C SER* 1.3 67.0 + - - +
582C GLY* 3.9 1.5 - - - +
583C ALA* 2.9 36.3 + - + +
589C CYS* 3.6 24.7 - - + -
590C ASP 5.2 1.3 - - - -
591C ILE* 3.5 33.7 - - + +
593C PRO* 3.9 26.2 - - + -
602C GLY* 5.0 10.8 - - - -
605C TRP* 5.4 4.5 - + - -
606C TRP* 4.2 23.8 - + - -
578D TRP* 6.2 0.2 - + - -
587D GLN* 5.8 0.9 - - - -
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Residues in contact with SER 580 (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 TYR* 3.1 25.6 + - - -
536C VAL* 5.1 2.7 - - - +
537C SER* 3.2 27.8 + - - -
540C LEU* 5.6 4.5 - - - -
576C SER 3.0 8.3 + - - -
577C LEU 2.9 7.9 + - - -
579C PHE* 1.3 84.4 - - - +
581C LEU* 1.3 62.9 + - - +
583C ALA* 4.7 0.2 - - - -
584C PHE* 2.9 23.4 + - - +
605C TRP* 3.6 22.3 + - - +
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Residues in contact with LEU 581 (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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599B ARG 5.2 0.2 - - - +
603B GLY* 4.1 20.0 - - - -
606B TRP* 4.6 9.9 - - + -
533C TYR* 3.2 27.0 + - + +
577C LEU 3.0 7.3 + - - +
578C TRP* 3.6 35.7 - - + +
580C SER* 1.3 76.5 - - - +
582C GLY* 1.3 60.4 + - - +
584C PHE* 2.8 25.9 + - + +
585C MET* 3.0 33.1 + - + +
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Residues in contact with GLY 582 (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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606B TRP* 3.8 27.3 - - - -
578C TRP* 2.9 20.0 + - - -
579C PHE* 3.9 1.3 - - - -
581C LEU* 1.3 73.2 - - - +
583C ALA* 1.3 56.5 + - - +
585C MET* 2.8 20.7 - - - +
587C GLN* 3.0 19.9 + - - +
588C GLY 5.3 4.3 - - - -
589C CYS* 6.2 1.1 - - - -
587D GLN* 5.7 0.4 - - - -
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Residues in contact with ALA 583 (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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579C PHE* 2.9 32.3 + - + +
580C SER 3.8 2.9 - - - +
582C GLY* 1.3 72.6 - - - +
584C PHE* 1.3 62.4 + - - +
585C MET 2.8 12.6 - - - +
605C TRP* 4.0 18.2 - - + -
606C TRP* 4.0 15.7 - - + +
609C THR* 3.8 14.4 + - - +
587D GLN* 3.5 21.9 - - - +
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Residues in contact with PHE 584 (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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607B PHE* 5.9 1.1 - + - -
610B LEU* 5.6 1.3 - - + -
526C TRP* 4.5 17.9 - + - -
529C ILE* 4.1 26.5 - - + -
533C TYR* 5.0 7.0 - + + -
580C SER 2.9 13.7 + - - +
581C LEU* 2.8 16.3 + - + +
583C ALA* 1.3 75.8 - - - +
585C MET* 1.3 90.6 + - + +
586C ARG* 5.4 1.9 - - - +
605C TRP* 4.1 25.7 - + + +
608C PHE* 4.7 3.1 - + - -
609C THR* 3.1 25.2 + - - -
612C ILE* 4.3 15.3 - - + -
613C ILE* 3.5 38.4 - - + +
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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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603B GLY 5.8 0.4 - - - +
606B TRP* 4.3 32.3 - - + -
607B PHE* 3.5 38.8 - - + -
610B LEU* 4.3 26.7 - - + -
581C LEU* 3.0 27.3 + - + +
582C GLY 2.8 11.7 - - - +
583C ALA* 2.8 17.5 - - - +
584C PHE* 1.3 106.5 - - + +
586C ARG* 1.3 63.0 + - - +
587C GLN 3.2 8.6 - - - +
613C ILE* 5.7 0.4 - - - -
587D GLN* 4.7 1.2 - - - +
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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