Contacts of the helix formed by residues 611 - 624 (chain A) in PDB entry 1DQ8
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 THR 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A ALA* 3.4 16.4 - - + +
608A TRP* 2.7 26.2 + - + +
610A GLU* 1.3 79.9 - - - +
612A SER* 1.3 64.0 + - - +
613A GLU* 3.7 10.3 - - - +
614A GLY* 2.9 15.4 + - - -
615A PHE* 2.9 24.8 + - - +
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Residues in contact with SER 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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610A GLU 3.9 1.6 + - - -
611A THR* 1.3 72.5 - - - +
613A GLU* 1.3 65.9 + - - +
615A PHE* 4.0 6.6 - - - +
616A ALA* 3.1 26.0 + - - +
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Residues in contact with GLU 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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608A TRP* 5.8 5.2 - - + +
611A THR* 3.7 10.1 - - - +
612A SER* 1.3 85.3 + - - +
614A GLY* 1.3 63.6 + - - +
616A ALA* 3.4 4.2 + - - +
617A VAL* 3.3 32.4 + - + +
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Residues in contact with GLY 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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608A TRP* 3.7 37.2 - - - -
609A LEU* 4.7 1.3 - - - -
611A THR* 2.9 20.6 + - - -
613A GLU* 1.3 72.0 - - - +
615A PHE* 1.3 65.0 + - - +
617A VAL* 3.1 19.9 - - - +
618A ILE* 3.2 12.6 + - - +
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Residues in contact with PHE 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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609A LEU* 4.0 12.4 + - - +
610A GLU 5.6 0.2 - - - -
611A THR 2.9 16.6 + - - +
612A SER* 4.0 7.6 - - - +
614A GLY* 1.3 75.3 - - - +
616A ALA* 1.3 58.6 + - + +
618A ILE* 3.1 6.4 + - + +
619A LYS* 2.7 56.0 + - + +
631A LEU* 3.8 39.3 - - + -
632A GLN 3.9 13.9 - - - -
633A LYS* 4.1 40.2 - - + -
634A LEU* 4.1 20.6 - - + -
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Residues in contact with ALA 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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612A SER 3.1 18.8 + - - +
613A GLU* 3.7 5.6 - - - +
614A GLY 3.3 0.2 - - - -
615A PHE* 1.3 80.6 - - + +
617A VAL* 1.3 58.5 + - + +
619A LYS* 3.6 8.3 - - - +
620A GLU* 2.9 30.9 + - - +
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Residues in contact with VAL 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TRP* 3.2 27.6 - - + -
613A GLU* 3.3 24.9 - - + +
614A GLY* 3.1 14.8 - - - +
615A PHE 3.3 0.2 - - - -
616A ALA* 1.3 77.3 - - + +
618A ILE* 1.3 72.2 + - + +
620A GLU* 3.3 9.8 - - - +
621A ALA* 3.1 21.0 + - - +
670A LYS* 4.5 9.3 - - + +
674A TYR* 4.1 25.1 - - + +
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Residues in contact with ILE 618 (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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608A TRP* 3.8 17.3 - - + -
609A LEU* 3.8 13.2 - - + -
614A GLY 3.3 13.0 - - - +
615A PHE* 3.1 9.7 + - - +
617A VAL* 1.3 81.2 - - + +
619A LYS* 1.3 66.7 + - - +
621A ALA* 3.3 4.6 + - - +
622A PHE* 2.9 21.5 + - - +
631A LEU* 3.9 15.9 - - + -
634A LEU* 4.7 9.0 - - + -
647A PHE* 3.9 11.4 - - + -
667A ALA* 3.6 39.2 - - + +
670A LYS* 4.6 3.8 - - + -
671A LEU* 3.9 22.4 - - + +
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Residues in contact with LYS 619 (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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615A PHE* 2.7 43.7 + - + +
616A ALA* 3.6 7.9 - - - +
618A ILE* 1.3 72.1 - - - +
620A GLU* 1.3 65.7 + - - +
622A PHE* 3.0 2.3 + - - +
623A ASP* 2.7 59.3 + - - +
630A ARG* 3.9 6.3 - - - +
631A LEU* 3.0 45.5 + - + +
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Residues in contact with GLU 620 (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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616A ALA 2.9 14.4 + - - +
617A VAL* 3.3 14.5 - - - +
619A LYS* 1.3 78.4 - - - +
621A ALA* 1.3 64.3 + - - +
623A ASP* 3.4 3.8 + - - +
624A SER* 3.2 22.5 + - - -
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Residues in contact with ALA 621 (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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617A VAL 3.1 7.0 + - - +
618A ILE 3.8 6.7 - - - +
619A LYS 3.3 0.4 - - - -
620A GLU* 1.3 80.2 - - - +
622A PHE* 1.3 59.9 + - - +
624A SER* 2.7 24.5 + - - -
625A THR* 3.9 5.2 + - - -
666A LYS* 4.0 19.4 - - + +
667A ALA* 4.2 2.5 - - - -
670A LYS* 3.8 39.5 - - + -
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Residues in contact with PHE 622 (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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618A ILE 2.9 18.1 + - - +
619A LYS 3.4 4.3 - - - +
621A ALA* 1.3 76.5 - - - +
623A ASP* 1.3 73.5 + - - +
625A THR* 3.1 24.9 + - - -
629A ALA* 4.0 15.1 - - + +
631A LEU* 4.0 17.0 - - + -
647A PHE* 3.7 30.5 - + + -
649A SER* 3.8 25.1 - - - -
660A ILE* 3.8 33.0 - - + -
663A GLY* 3.2 39.8 - - - +
664A THR* 3.5 14.6 - - - -
667A ALA* 4.2 3.5 - - + +
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Residues in contact with ASP 623 (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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619A LYS* 2.7 53.3 + - - +
620A GLU* 4.1 3.8 - - - +
622A PHE* 1.3 72.1 - - - +
624A SER* 1.3 56.5 + - - +
625A THR 3.0 5.8 + - - -
626A SER 2.9 26.3 - - - +
629A ALA* 3.1 20.9 - - - +
630A ARG* 3.7 3.8 - - + +
631A LEU* 2.8 24.7 + - - +
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Residues in contact with SER 624 (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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620A GLU* 3.2 15.0 + - - -
621A ALA* 2.7 22.8 + - - -
622A PHE 3.2 0.4 - - - -
623A ASP* 1.3 74.0 - - - +
625A THR* 1.3 64.3 + - - +
626A SER* 3.3 1.8 + - - -
666A LYS* 5.2 5.2 - - - +
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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