Contacts of the helix formed by residues 611 - 624 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607D ALA 3.5 15.7 - - - +
608D TRP* 2.7 26.3 + - + +
610D GLU* 1.3 81.9 - - - +
612D SER* 1.3 58.8 + - - +
613D GLU* 3.6 21.9 + - - +
614D GLY* 2.9 14.9 + - - -
615D PHE* 3.0 28.6 + - - +
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Residues in contact with SER 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D GLU 4.0 1.0 + - - -
611D THR* 1.3 72.8 - - - +
613D GLU* 1.3 70.0 + - - +
615D PHE* 3.9 7.5 - - - +
616D ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D TRP* 6.2 0.9 - - - +
611D THR* 3.2 24.3 + - - +
612D SER* 1.3 88.5 + - - +
614D GLY* 1.3 64.4 + - - +
616D ALA* 3.1 8.0 + - - +
617D VAL* 3.1 30.0 + - + +
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Residues in contact with GLY 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D TRP* 3.4 37.6 - - - +
609D LEU* 4.7 2.0 - - - -
611D THR* 2.9 19.7 + - - -
613D GLU* 1.3 79.0 - - - +
615D PHE* 1.3 59.6 + - - +
617D VAL* 3.4 3.1 + - - +
618D ILE* 3.1 27.6 + - - +
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Residues in contact with PHE 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D LEU 4.0 11.2 + - - +
610D GLU 5.7 0.4 - - - -
611D THR 3.0 15.9 + - - +
612D SER* 3.9 7.9 - - - +
614D GLY* 1.3 71.9 - - - +
616D ALA* 1.3 64.6 + - - +
618D ILE* 3.2 6.1 + - - +
619D LYS* 2.8 61.2 + - + +
631D LEU* 3.8 25.1 - - + -
632D GLN 3.8 25.1 - - - -
633D LYS* 4.1 16.6 - - - -
634D LEU* 4.1 21.1 - - + -
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Residues in contact with ALA 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D SER 2.9 19.6 + - - +
613D GLU* 3.4 7.4 - - - +
615D PHE* 1.3 81.1 - - + +
617D VAL* 1.3 63.8 + - + +
619D LYS* 3.7 6.7 - - - +
620D GLU* 3.0 23.9 + - - +
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Residues in contact with VAL 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D TRP* 3.5 32.3 - - + -
613D GLU* 3.1 19.6 + - + +
614D GLY 4.1 0.7 - - - +
616D ALA* 1.3 76.4 - - + +
618D ILE* 1.3 70.8 + - + +
620D GLU* 3.2 8.6 + - - +
621D ALA* 3.1 22.0 + - - +
670D LYS* 4.3 17.2 - - + +
674D TYR* 4.2 25.8 - - + +
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Residues in contact with ILE 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D TRP* 3.6 22.7 - - + -
609D LEU* 3.9 11.0 - - + -
614D GLY 3.1 15.3 - - - +
615D PHE* 3.2 9.5 + - - +
617D VAL* 1.3 80.8 - - + +
619D LYS* 1.3 54.7 + - - +
621D ALA* 3.2 7.8 + - - +
622D PHE* 2.8 35.2 + - - +
631D LEU* 3.3 22.0 - - + -
634D LEU* 4.0 19.1 - - + -
647D PHE* 3.2 36.3 - - + -
667D ALA* 4.0 15.3 - - + +
670D LYS* 5.2 2.0 - - + -
671D LEU* 5.0 6.3 - - + +
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Residues in contact with LYS 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D PHE* 2.8 37.3 + - + +
616D ALA* 3.7 6.7 - - - +
618D ILE* 1.3 75.7 - - - +
620D GLU* 1.3 60.2 + - - +
622D PHE* 4.2 1.1 - - - -
623D ASP* 2.7 66.1 + - - +
630D ARG* 3.9 11.3 - - - +
631D LEU* 2.8 50.5 + - + +
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Residues in contact with GLU 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D ALA 3.0 14.6 + - - +
617D VAL* 3.2 11.8 + - - +
619D LYS* 1.3 78.3 - - - +
621D ALA* 1.3 62.4 + - - +
623D ASP* 3.9 2.9 - - - +
624D SER* 2.9 26.3 + - - -
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Residues in contact with ALA 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D VAL 3.1 9.5 + - - +
618D ILE 3.6 7.6 - - - +
620D GLU* 1.3 80.4 - - - +
622D PHE* 1.3 60.6 + - - +
624D SER* 2.6 25.5 + - - -
625D THR 3.9 0.2 + - - -
666D LYS* 3.6 26.7 - - + +
667D ALA* 4.1 2.5 - - - -
670D LYS* 3.8 31.9 - - + -
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Residues in contact with PHE 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D ILE 2.8 20.4 + - - +
619D LYS* 3.7 7.0 - - - +
621D ALA* 1.3 72.5 - - - +
623D ASP* 1.3 76.9 + - - +
625D THR* 3.1 25.3 - - - +
629D ALA* 4.1 14.9 - - + +
631D LEU* 3.9 11.9 - - + -
647D PHE* 3.7 31.0 - + + -
649D SER* 3.5 36.6 - - - -
660D ILE* 3.7 27.1 - - + -
663D GLY* 3.3 27.8 - - - +
664D THR* 3.5 21.5 - - - -
667D ALA* 4.2 3.5 - - + +
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Residues in contact with ASP 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D LYS* 2.7 52.2 + - - +
620D GLU* 4.1 2.9 - - - +
622D PHE* 1.3 72.2 - - - +
624D SER* 1.3 58.1 + - - +
625D THR 2.8 11.6 + - - -
626D SER 3.0 22.5 + - - +
629D ALA 3.2 19.8 - - - +
630D ARG* 3.4 18.8 + - - +
631D LEU* 2.8 25.1 + - - +
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Residues in contact with SER 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D GLU* 2.9 19.2 + - - -
621D ALA* 2.6 23.3 + - - -
623D ASP* 1.3 75.7 - - - +
625D THR* 1.3 61.1 + - - +
626D SER* 3.4 0.8 + - - -
666D LYS* 4.0 16.8 - - - +
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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