Contacts of the helix formed by residues 609 - 617 (chain A) in PDB entry 2DX0
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 SER 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A THR 3.6 20.9 - - - -
525A GLU* 3.5 10.1 - - - -
528A PHE* 3.8 13.3 - - - -
599A TYR* 3.6 9.2 - - - -
607A PHE* 3.1 9.9 - - - +
608A ASN* 1.3 84.1 - - - +
610A ILE* 1.3 63.9 + - - +
611A TYR* 3.5 5.5 - - - +
612A ALA* 3.0 25.7 + - - +
613A LEU* 3.2 15.6 + - - +
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Residues in contact with ILE 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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522A PRO* 4.1 17.9 - - + -
525A GLU* 2.8 23.5 + - + +
530A GLU* 5.3 0.2 - - - +
532A TRP* 3.7 25.6 - - + -
533A PHE* 4.4 8.7 - - + -
563A VAL* 4.2 12.8 - - + -
573A TYR* 4.2 24.5 - - + -
588A ILE* 4.5 12.3 - - + -
599A TYR* 3.8 32.8 - - + -
609A SER* 1.3 71.2 - - - +
611A TYR* 1.3 64.3 + - - +
613A LEU* 2.9 10.5 + - + +
614A ILE* 2.8 33.2 + - + +
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Residues in contact with TYR 611 (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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525A GLU* 3.1 5.5 + - - -
528A PHE* 3.5 56.3 - + + -
529A GLY 3.8 21.8 - - - -
530A GLU* 3.6 12.2 + - + +
532A TRP* 4.1 7.2 - + - -
609A SER* 3.5 8.7 - - - +
610A ILE* 1.3 78.0 - - - +
612A ALA* 1.3 62.0 + - + +
614A ILE* 3.3 0.7 + - - +
615A GLN* 3.0 69.0 + - + +
1002A SO4 5.6 2.2 - - - -
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Residues in contact with ALA 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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607A PHE* 3.7 21.4 - - + -
608A ASN* 5.0 2.0 - - + +
609A SER* 3.0 22.5 + - - +
611A TYR* 1.3 80.3 - - + +
613A LEU* 1.3 65.1 + - - +
615A GLN* 4.0 5.3 - - - +
616A HIS* 3.0 24.9 + - - +
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Residues in contact with LEU 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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575A LEU* 5.7 2.5 - - + -
588A ILE* 4.0 29.8 - - + -
599A TYR* 4.0 6.1 - - + -
600A TYR* 3.8 36.8 - - - +
601A LEU* 4.3 11.7 - - + +
607A PHE* 3.6 24.8 - - + -
609A SER 3.2 9.6 + - - +
610A ILE* 2.9 11.3 + - + +
612A ALA* 1.3 77.1 - - - +
614A ILE* 1.3 79.8 + - + +
616A HIS* 3.4 1.2 + - - +
617A TYR* 3.1 49.3 + - + -
631B LEU* 5.6 1.3 - - + -
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Residues in contact with ILE 614 (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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532A TRP* 3.5 27.6 - - + +
561A PHE* 3.4 42.6 - - + -
563A VAL* 3.8 16.4 - - + -
575A LEU* 4.2 4.3 - - + -
610A ILE* 2.8 19.7 + - + +
611A TYR 3.5 7.0 - - - +
613A LEU* 1.3 85.8 - - + +
615A GLN* 1.3 75.7 + - - +
617A TYR* 3.1 4.5 + - - +
618A ARG* 3.1 29.2 + - - +
631B LEU* 3.9 16.1 - - + +
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Residues in contact with GLN 615 (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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532A TRP* 4.4 4.8 - - - +
611A TYR* 3.0 74.7 + - + +
612A ALA* 4.1 5.4 - - - +
614A ILE* 1.3 81.2 - - - +
616A HIS* 1.3 63.5 - - - +
618A ARG* 3.1 50.2 + - - +
619A GLU* 3.5 12.3 + - - +
1002A SO4 4.9 1.6 + - - -
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Residues in contact with HIS 616 (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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605A LEU* 3.3 21.8 - - + +
607A PHE* 3.6 22.3 - + + -
612A ALA 3.0 19.1 + - - +
613A LEU 3.5 4.0 - - - +
614A ILE 3.2 0.2 - - - -
615A GLN* 1.3 78.0 - - - +
617A TYR* 1.3 87.7 + + - +
619A GLU* 3.0 8.9 + - - +
620A ALA* 2.9 45.2 + - + +
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Residues in contact with TYR 617 (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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601A LEU* 3.6 30.4 + - + +
602A THR* 4.7 2.9 + - - -
605A LEU* 3.7 27.5 + - - +
607A PHE* 4.1 7.3 - + - -
613A LEU* 3.1 46.9 + - + +
614A ILE 3.1 4.7 + - - +
616A HIS* 1.3 96.9 - + - +
618A ARG* 1.3 52.3 + - - +
619A GLU 3.2 0.4 - - - -
620A ALA 3.4 23.9 - - - +
621A HIS 3.7 13.9 - - - -
622A LEU* 3.5 30.1 - - + -
623A ARG* 4.2 10.3 + - + +
629B LEU 4.6 0.5 - - - +
630B ARG* 3.5 2.3 - - - -
631B LEU* 2.7 38.9 + - + -
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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