Contacts of the helix formed by residues 572 - 585 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B PHE* 3.5 11.3 - - - -
571B PHE* 1.3 76.0 - - - +
573B ILE* 1.3 54.4 + - - +
574B PHE 3.2 2.9 - - - -
575B ASN* 3.2 10.9 + - - -
576B SER* 2.6 41.8 + - - -
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B SER* 5.1 5.6 - - - +
538B VAL* 5.3 4.3 - - + -
541B PHE* 3.1 51.8 - - + -
572B GLY* 1.3 70.7 - - - -
574B PHE* 1.3 64.5 + - + +
576B SER* 3.7 2.3 - - - -
577B LEU* 2.9 31.3 + - + +
195G VAL* 3.8 27.8 - - + -
199G HIS* 5.9 4.9 - - + -
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Residues in contact with PHE 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ARG 4.1 13.7 - - - -
596A LEU* 3.5 44.0 - - + -
599A ARG* 4.2 15.7 - - + -
572B GLY 3.2 0.6 - - - -
573B ILE* 1.3 85.5 - - + +
575B ASN* 1.3 70.2 + - - +
577B LEU* 3.2 12.5 + - + +
578B TRP* 2.9 32.8 + + + +
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Residues in contact with ASN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ARG* 5.0 16.4 + - - +
569B ASN 5.4 2.5 - - - +
570B GLU 5.7 0.2 - - - +
571B PHE 4.1 9.8 - - - +
572B GLY* 3.2 13.2 + - - +
574B PHE* 1.3 87.9 - - - +
576B SER* 1.3 57.4 + - - +
578B TRP* 3.3 15.3 + - + +
579B PHE* 2.9 27.7 + - - +
591B ILE* 5.6 9.1 - - + +
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Residues in contact with SER 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B SER* 4.9 3.8 - - - -
540B LEU* 4.8 15.7 - - - +
541B PHE* 3.7 21.3 - - - +
544B SER* 5.6 0.2 - - - -
570B GLU 3.1 22.0 + - - -
571B PHE 4.8 0.2 + - - -
572B GLY 2.6 29.1 + - - -
573B ILE* 3.7 7.4 - - - -
575B ASN* 1.3 73.4 - - - +
577B LEU* 1.3 63.1 + - - +
579B PHE* 3.0 13.5 + - - +
580B SER* 2.9 22.4 + - - -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B TYR* 3.0 41.6 + - + +
534B ILE* 4.7 9.9 - - + -
537B SER* 3.3 30.2 - - - +
573B ILE* 2.9 21.1 + - + +
574B PHE* 3.7 12.1 - - + +
576B SER* 1.3 75.4 - - - +
578B TRP* 1.3 58.8 + - - +
580B SER* 2.8 25.7 + - - -
581B LEU* 3.0 1.2 + - - +
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Residues in contact with TRP 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A CYS* 5.7 4.3 - - + -
592A SER* 3.7 29.4 - - - -
593A PRO* 4.4 21.1 - - + -
599A ARG* 3.4 39.5 + - + +
606A TRP* 3.4 42.2 - + - -
574B PHE* 2.9 19.9 + + + +
575B ASN* 3.5 18.8 - - + +
576B SER 3.2 0.2 - - - -
577B LEU* 1.3 76.9 - - - +
579B PHE* 1.3 60.7 + - + +
581B LEU* 3.3 8.4 + - + +
582B GLY* 2.9 31.3 + - - -
588B GLY 5.3 2.9 - - - -
589B CYS* 3.6 33.2 - - + -
590B ASP 5.6 0.2 - - - -
591B ILE* 5.7 1.8 - - + -
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Residues in contact with PHE 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B LEU* 4.1 26.0 - - + -
575B ASN 2.9 13.7 + - - +
576B SER* 3.0 11.4 + - - +
578B TRP* 1.3 84.2 - - + +
580B SER* 1.3 51.1 + - - +
582B GLY* 5.2 0.2 - - - -
583B ALA* 2.6 54.4 + - + +
589B CYS* 3.7 32.5 - - + -
591B ILE* 3.7 26.7 - - + -
592B SER* 4.9 1.3 - - - -
593B PRO* 4.3 24.2 - - + -
602B GLY* 5.0 11.9 - - - -
605B TRP* 5.4 4.0 - + - -
606B TRP* 4.5 21.5 - + - -
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Residues in contact with SER 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B TYR* 3.4 18.8 - - - -
536B VAL* 5.7 2.6 - - - +
537B SER* 2.6 38.5 + - - -
540B LEU* 5.1 4.3 - - - +
576B SER 2.9 13.4 + - - -
577B LEU 2.8 14.4 + - - -
579B PHE* 1.3 77.8 - - - +
581B LEU* 1.3 63.6 + - - -
583B ALA* 3.1 5.8 + - - +
584B PHE* 2.9 20.1 + - - +
605B TRP* 3.8 9.1 + - - +
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A ARG 5.6 1.1 - - - +
603A GLY* 4.2 25.1 - - - +
606A TRP* 5.0 7.4 - - + -
607A PHE* 3.6 39.0 - - + -
533B TYR* 2.8 31.8 + - + +
577B LEU 3.0 3.6 + - - +
578B TRP* 4.1 10.8 - - + +
580B SER* 1.3 72.4 - - - +
582B GLY* 1.3 66.1 + - - +
584B PHE* 2.8 24.4 + - + +
585B MET* 3.1 14.9 + - + +
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Residues in contact with GLY 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A TRP* 4.5 26.7 - - - -
578B TRP* 2.9 22.3 + - - -
579B PHE* 4.8 0.7 - - - -
581B LEU* 1.3 74.8 - - - +
583B ALA* 1.3 54.9 + - - +
585B MET* 3.2 8.2 + - - +
587B GLN* 2.7 30.4 - - - +
588B GLY 4.6 9.2 - - - -
589B CYS* 5.6 2.2 - - - -
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Residues in contact with ALA 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B PHE* 2.6 44.4 + - + +
580B SER* 3.3 4.7 - - - +
582B GLY* 1.3 77.6 - - - +
584B PHE* 1.3 64.4 + - - +
585B MET 3.1 8.0 - - - +
587B GLN 4.1 3.2 - - - +
588B GLY* 5.7 2.5 - - - -
589B CYS* 5.5 0.6 - - - +
605B TRP* 3.7 22.9 - - + +
606B TRP* 4.5 14.2 + - - +
609B THR* 4.2 7.9 + - - +
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Residues in contact with PHE 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A PHE* 5.6 7.0 - + - -
610A LEU* 5.3 9.2 - - + -
526B TRP* 5.7 8.5 - + - -
529B ILE* 4.6 21.5 - - + -
533B TYR* 5.1 4.7 - + + -
580B SER 2.9 10.6 + - - +
581B LEU* 2.8 21.8 + - + +
583B ALA* 1.3 78.1 - - - +
585B MET* 1.3 70.1 + - + +
586B ARG 3.7 0.2 + - - -
605B TRP* 4.0 23.7 - + + +
608B PHE* 4.9 4.5 - + - -
609B THR* 3.2 38.7 - - - +
612B ILE* 4.3 20.2 - - + -
613B ILE* 3.5 32.7 - - + +
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Residues in contact with MET 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A TRP* 3.9 34.1 - - + +
607A PHE* 5.8 4.9 - - + -
609A THR* 6.1 0.9 - - + -
610A LEU* 5.7 10.3 - - + -
581B LEU* 3.1 14.8 + - + +
582B GLY 3.2 3.8 - - - +
583B ALA 3.1 5.5 - - - +
584B PHE* 1.3 94.4 - - + +
586B ARG* 1.3 68.5 + - - +
587B GLN 2.9 15.8 + - - +
609B THR* 5.3 0.2 - - - +
613B ILE* 5.9 1.3 - - - -
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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