Contacts of the helix formed by residues 605 - 613 (chain A) in PDB entry 5DO7
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 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A PHE* 3.5 40.6 - - - -
582A GLY* 4.6 0.6 - - - -
583A LEU* 2.8 23.4 + - - +
585A PHE* 4.5 3.6 - - - -
604A GLN* 1.3 73.1 - - - +
606A ILE* 1.3 62.9 + - - +
608A PHE 3.5 2.4 + - - -
609A ILE* 3.4 21.0 + - - +
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A TYR 4.0 19.3 - - - +
582A GLY* 5.2 3.4 - - - -
604A GLN* 3.5 3.9 - - + +
605A GLY* 1.3 71.6 - - - +
607A GLN* 1.3 64.0 + - + +
608A PHE 3.0 2.7 - - - -
609A ILE* 2.8 32.5 + - + -
610A GLU* 2.8 39.5 + - + +
617A THR* 6.3 1.8 - - - -
105C ARG* 4.4 30.3 - - + +
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Residues in contact with GLN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A PHE* 3.8 27.7 - - + -
603A THR* 3.4 15.8 + - - -
604A GLN* 3.1 41.9 + - + +
605A GLY 3.4 0.6 - - - -
606A ILE* 1.3 83.2 - - + +
608A PHE* 1.3 58.5 + - - +
610A GLU* 4.3 6.6 - - - +
611A LYS* 3.8 9.9 + - - +
105C ARG 5.3 3.8 - - - +
107C GLY* 4.5 29.3 + - - +
108C THR* 4.8 8.9 - - - +
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Residues in contact with PHE 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ILE* 4.5 22.7 - - + -
420A VAL* 3.9 28.3 - - + -
423A LEU* 6.5 0.2 - - + -
548A PHE* 4.5 5.8 - + - -
576A VAL* 3.8 22.2 - - + -
580A PHE* 3.2 38.4 - + + -
602A PHE* 4.4 21.7 - + + -
604A GLN 4.0 6.8 + - - +
605A GLY 3.5 7.4 + - - +
606A ILE 3.0 0.8 - - - -
607A GLN* 1.3 76.0 - - - +
609A ILE* 1.3 67.8 + - - +
610A GLU 3.0 1.8 - - - -
611A LYS* 2.8 21.4 + - + +
612A THR* 3.3 39.9 + - + -
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Residues in contact with ILE 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A VAL* 4.2 17.7 - - + +
577A VAL* 4.1 28.7 - - + -
580A PHE* 3.7 33.9 - - + +
581A TYR* 4.4 6.5 - - - +
605A GLY 3.4 16.8 + - - +
606A ILE* 2.8 27.6 + - + +
608A PHE* 1.3 77.2 - - - +
610A GLU* 1.3 72.7 + - - +
612A THR* 3.6 1.5 + - - -
613A CYS* 3.0 35.2 + - - +
614A PRO 5.0 0.7 - - - +
616A ALA* 4.7 0.2 - - + -
617A THR* 4.5 13.7 - - - +
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A GLN* 4.0 5.0 + - - +
606A ILE* 2.8 33.4 + - + +
607A GLN* 4.3 5.4 - - - +
609A ILE* 1.3 82.5 - - - +
611A LYS* 1.3 64.3 + - - +
612A THR 3.2 0.9 + - - -
613A CYS 3.8 0.2 + - - -
614A PRO* 3.6 51.9 - - - +
617A THR* 4.1 12.6 - - - +
105C ARG* 3.7 31.3 + - - +
106C ALA* 4.2 21.8 + - + +
107C GLY 5.7 0.2 - - - +
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Residues in contact with LYS 611 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A ASN* 3.6 30.4 - - - +
553A GLN* 3.6 20.7 + - - +
602A PHE* 4.2 30.0 - - + -
607A GLN 3.8 11.9 + - - +
608A PHE* 2.8 18.7 + - + +
610A GLU* 1.3 74.6 - - - +
612A THR* 1.3 64.7 + - + +
446B MET* 4.7 20.6 - - + +
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Residues in contact with THR 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A GLY* 4.5 13.2 - - - -
548A PHE* 4.9 14.7 - - + +
551A ASN* 4.8 14.8 - - - +
552A ILE* 3.4 25.5 + - - +
553A GLN* 4.0 9.4 - - - +
576A VAL* 4.6 1.6 - - - +
608A PHE* 3.3 45.6 + - + -
609A ILE* 3.6 4.7 + - - -
610A GLU 3.2 1.5 - - - -
611A LYS* 1.3 86.5 - - + +
613A CYS* 1.3 83.1 + - - +
614A PRO* 4.0 1.1 - - - +
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Residues in contact with CYS 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A GLY 5.4 6.1 - - - +
548A PHE* 5.9 0.2 - - - -
552A ILE* 4.9 2.5 - - + -
572A SER* 6.4 0.2 - - - -
573A GLU* 3.3 44.6 - - + +
576A VAL* 4.3 25.6 - - - -
609A ILE* 3.0 13.9 + - - +
612A THR* 1.3 98.2 + - - +
614A PRO* 1.3 64.0 - - - +
615A GLY 3.3 1.1 - - - -
616A ALA* 2.8 31.8 + - + +
619A ARG* 5.7 0.2 - - - -
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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