Contacts of the helix formed by residues 582 - 597 (chain F) in PDB entry 5G04
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 GLU 582 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F PHE* 3.3 18.9 + - + +
580F GLN* 2.9 17.3 + - + +
581F ARG* 1.3 75.0 - - - +
583F HIS* 1.3 64.0 + - - +
584F ASP* 3.3 13.2 - - - +
585F ILE* 3.3 36.1 + - + +
586F ALA 3.2 16.3 + - - -
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Residues in contact with HIS 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F SER 4.3 5.7 + - - -
581F ARG* 3.0 40.5 + - + +
582F GLU* 1.3 71.4 - - - +
584F ASP* 1.3 70.6 + - - +
586F ALA* 3.1 3.9 + - - +
587F ILE* 2.9 31.1 + - + +
610F GLU* 3.0 30.3 - - - +
613F LEU* 3.8 42.4 + - + +
614F THR* 3.8 31.2 + - + +
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Residues in contact with ASP 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581F ARG 5.5 0.3 - - - +
582F GLU* 4.4 9.4 - - - +
583F HIS* 1.3 82.1 + - - +
585F ILE* 1.3 65.0 + - + +
587F ILE* 3.4 15.6 + - - +
588F LYS* 3.5 18.7 + - - +
614F THR* 5.5 7.8 - - - +
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Residues in contact with ILE 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577F PHE* 3.5 36.6 - - + -
582F GLU* 3.3 38.2 + - + +
583F HIS 3.3 0.6 - - - -
584F ASP* 1.3 74.9 - - + +
586F ALA* 1.3 65.0 + - - +
587F ILE 3.5 0.3 + - - -
588F LYS* 3.6 31.5 + - - +
589F PHE* 3.3 34.1 + - + -
66M HIS* 5.3 5.8 - - + +
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Residues in contact with ALA 586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F GLY* 3.6 8.2 - - - +
577F PHE* 3.7 11.3 - - - +
578F SER* 3.5 35.0 - - - +
582F GLU 3.2 7.2 + - - +
583F HIS 3.1 10.3 + - - +
585F ILE* 1.3 76.4 - - - +
587F ILE* 1.3 57.6 + - - +
589F PHE* 3.4 6.5 + - - +
590F PHE* 2.9 38.0 + - + -
610F GLU* 4.1 8.3 - - + +
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Residues in contact with ILE 587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583F HIS* 2.9 23.3 + - + +
584F ASP* 3.7 9.0 - - - +
585F ILE 3.3 0.2 - - - -
586F ALA* 1.3 74.2 - - - +
588F LYS* 1.3 55.8 + - - +
590F PHE* 3.7 0.4 - - - +
591F GLN* 2.8 59.9 + - - +
607F LEU* 3.9 15.5 - - + -
610F GLU* 3.8 25.1 - - + -
611F PHE* 4.0 22.9 - - + -
614F THR* 3.7 26.7 - - + +
616F GLU* 5.6 1.1 - - - +
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Residues in contact with LYS 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584F ASP* 3.5 13.9 - - - +
585F ILE* 3.6 39.6 - - + +
587F ILE* 1.3 76.4 - - - +
589F PHE* 1.3 67.2 + - + +
591F GLN* 3.7 12.4 - - - +
592F ARG* 3.0 40.1 + - - +
66M HIS* 3.8 28.8 + - + +
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Residues in contact with PHE 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F TRP* 3.5 41.7 - + + +
573F ALA* 3.5 34.3 - - + -
574F GLY* 3.8 12.8 - - - +
577F PHE* 4.1 7.6 - + - -
585F ILE* 3.3 30.3 - - + +
586F ALA 3.4 8.7 + - - +
587F ILE 3.3 0.4 - - - -
588F LYS* 1.3 87.4 - - + +
590F PHE* 1.3 57.8 + - - +
592F ARG* 3.1 20.9 - - - +
593F ALA* 3.0 21.8 + - - +
65M LEU* 3.6 40.6 - - + -
66M HIS* 4.0 14.6 - - + -
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Residues in contact with PHE 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F TRP 5.0 0.2 - - - -
571F CYS* 3.5 29.6 - - + -
574F GLY* 3.3 30.7 - - - -
575F ASN* 3.5 18.4 - - - -
578F SER* 4.3 4.9 - - - -
586F ALA* 2.9 24.8 + - + +
587F ILE* 3.3 3.6 + - - +
589F PHE* 1.3 71.7 - - - +
591F GLN* 1.3 65.6 + - - +
592F ARG 3.0 1.1 - - - -
593F ALA* 3.0 22.3 + - + +
594F ILE* 3.3 11.8 + - - +
603F ALA 4.6 4.9 - - - +
606F LEU* 3.5 35.2 - - + -
607F LEU* 3.8 21.3 - - + -
610F GLU* 3.7 31.2 - - + -
499R ARG* 4.6 1.1 - - - -
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Residues in contact with GLN 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587F ILE* 2.8 40.2 + - - +
588F LYS* 3.7 13.2 - - - +
590F PHE* 1.3 72.7 - - - +
592F ARG* 1.3 50.9 - - - +
594F ILE* 3.3 14.8 - - - +
595F GLN* 2.7 34.7 + - - +
607F LEU* 3.8 18.7 - - + +
611F PHE* 4.3 11.7 - - - -
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Residues in contact with ARG 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E TRP* 3.2 72.5 - - + +
570F TRP* 3.3 46.7 - - + -
588F LYS* 3.0 26.2 + - - +
589F PHE* 3.1 29.3 - - - +
590F PHE 3.0 0.2 - - - -
591F GLN* 1.3 73.3 - - - +
593F ALA* 1.3 53.5 + - - +
595F GLN* 3.0 14.5 + - - +
596F VAL* 2.7 40.3 + - - +
66M HIS* 5.7 9.7 - - - +
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Residues in contact with ALA 593 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567F PRO* 3.5 30.8 - - - +
570F TRP* 3.8 10.0 - - + +
571F CYS* 3.9 17.5 - - + +
589F PHE 3.0 8.1 + - - +
590F PHE* 3.0 13.4 + - + +
592F ARG* 1.3 72.2 - - - +
594F ILE* 1.3 56.9 + - - +
596F VAL* 2.9 21.6 + - - +
597F ASP 2.9 14.2 + - - +
603F ALA* 4.1 15.9 - - + -
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Residues in contact with ILE 594 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590F PHE 3.3 7.1 + - - +
591F GLN* 3.3 9.0 - - - +
593F ALA* 1.3 78.2 - - - +
595F GLN* 1.3 65.4 + - - +
597F ASP 2.9 28.6 - - - -
598F PRO* 3.0 9.0 - - + +
603F ALA* 3.8 22.8 - - + +
604F TYR* 3.4 62.8 - - + +
607F LEU* 3.7 30.5 - - + -
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Residues in contact with GLN 595 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ALA* 4.2 8.5 + - - +
92E ASP* 3.4 28.2 + - - +
94E TRP* 2.8 31.4 + - + +
95E ARG* 3.3 16.8 + - - +
591F GLN 2.7 17.6 + - - +
592F ARG* 3.3 21.5 - - - +
594F ILE* 1.3 75.9 - - - +
596F VAL* 1.3 63.2 + - - +
598F PRO* 4.4 7.9 - - - +
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Residues in contact with VAL 596 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E TRP* 3.7 21.1 - - + -
95E ARG* 3.6 25.3 + - - +
565F ASN* 3.7 28.7 - - + -
566F SER* 3.7 20.4 - - - +
567F PRO* 4.0 2.5 - - + -
570F TRP* 4.0 13.9 - - + -
592F ARG 2.7 20.5 + - - +
593F ALA 2.9 7.8 + - - +
595F GLN* 1.3 76.3 - - - +
597F ASP* 1.3 59.1 + - + +
598F PRO* 3.8 4.9 - - - +
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Residues in contact with ASP 597 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567F PRO* 3.9 28.6 - - + +
593F ALA 2.9 11.1 + - - +
594F ILE* 2.9 15.6 - - - +
596F VAL* 1.3 73.4 - - + +
598F PRO* 1.3 67.1 - - - +
599F ASN* 2.8 36.2 + - - +
600F TYR* 3.4 32.6 + - + +
603F ALA* 5.2 0.3 - - - +
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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