Contacts of the strand formed by residues 777 - 784 (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 CYS 777 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698D TRP* 3.7 5.5 - - - -
747D GLY 3.0 8.4 + - - +
749D TYR 3.1 14.9 + - - -
750D ASN* 3.0 28.3 + - - +
753D ALA* 3.9 6.1 - - + -
775D SER 3.1 9.9 + - - +
776D ASN* 1.3 77.8 - - - +
778D ILE* 1.3 64.2 + - - +
779D THR* 3.9 19.5 - - - -
795D CYS* 4.0 18.2 - - - -
796D THR 3.3 7.2 - - - -
797D MET* 3.8 20.9 - - + -
846D VAL* 4.2 12.1 - - - -
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Residues in contact with ILE 778 (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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639A ALA* 4.5 7.0 - - + -
738B VAL* 3.9 26.7 - - + -
741B ALA* 4.4 10.3 - - + -
742B MET* 4.1 21.3 - - + -
698D TRP* 3.8 16.4 - - + -
737D LEU* 4.0 19.1 - - + -
749D TYR* 3.3 17.9 - - + +
777D CYS* 1.3 74.1 - - - +
779D THR* 1.3 62.3 + - - +
780D LEU* 4.0 15.6 + - + +
794D SER* 3.7 1.4 + - - +
795D CYS* 3.4 3.8 - - - -
796D THR* 3.0 50.5 + - - +
798D PRO* 6.3 0.2 - - + -
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Residues in contact with THR 779 (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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732D ASN* 2.9 32.3 + - - +
736D ASN* 3.9 9.8 - - - +
737D LEU* 4.8 2.1 - - - +
749D TYR 2.8 16.9 + - - +
750D ASN* 3.5 6.6 - - - +
777D CYS* 3.9 1.2 - - - -
778D ILE* 1.3 72.6 - - - +
780D LEU* 1.3 68.6 + - - +
781D MET* 4.1 17.3 - - + -
793D ILE* 4.4 4.0 - - + -
794D SER 3.4 9.0 - - - +
795D CYS* 3.7 13.5 - - - -
850D GLU* 2.6 38.5 + - + +
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Residues in contact with LEU 780 (chain D).
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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639A ALA* 3.7 40.8 - - + +
642A ASN* 4.8 7.2 - - - +
733B ILE* 6.2 0.7 - - + -
734B ASN* 5.3 1.6 - - - +
738B VAL* 3.7 30.3 - - + -
732D ASN* 3.6 1.6 - - - +
737D LEU* 4.1 14.6 - - + -
778D ILE* 4.1 17.0 - - + +
779D THR* 1.3 81.4 - - - +
781D MET* 1.3 65.7 + - - +
792D TYR* 5.1 4.4 - - + -
793D ILE* 3.2 4.5 - - - +
794D SER* 2.8 45.2 + - - +
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Residues in contact with MET 781 (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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728D MET* 4.0 35.7 - - + +
729D ILE* 4.0 21.2 - - + +
732D ASN* 3.6 42.3 + - + +
733D ILE* 5.4 4.3 - - - +
779D THR* 4.1 4.3 - - + -
780D LEU* 1.3 79.6 - - - +
782D GLU* 1.3 64.0 + - - +
791D LEU* 3.9 15.5 - - + -
792D TYR 3.2 5.2 - - - +
793D ILE* 3.7 30.5 - - + -
850D GLU 4.4 2.5 - - - +
851D LEU* 4.6 0.2 - - + -
854D MET* 3.8 28.0 - - + -
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Residues in contact with GLU 782 (chain D).
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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595A ARG* 4.2 9.0 + - - -
641A ARG* 2.6 48.8 + - - +
730B GLU* 4.6 10.8 - - - +
729D ILE* 3.5 10.9 - - - +
781D MET* 1.3 77.1 - - - +
783D ALA* 1.3 72.7 + - - +
790D ASP 3.8 1.0 - - - +
791D LEU* 3.8 3.5 - - - +
792D TYR* 2.8 52.6 + - + +
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Residues in contact with ALA 783 (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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725D THR* 4.4 2.7 - - + -
729D ILE* 3.2 19.6 - - + +
782D GLU* 1.3 88.2 - - - +
784D SER* 1.3 59.9 + - - +
788D ASN* 3.5 46.4 - - - +
790D ASP 3.6 5.8 - - - +
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Residues in contact with SER 784 (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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598A ARG* 4.4 13.5 + - - -
711D VAL* 4.4 19.5 - - - +
783D ALA* 1.3 74.9 - - - +
785D GLY* 1.3 68.1 + - - +
788D ASN* 4.0 4.7 + - - -
789D GLU 3.3 9.0 + - - -
790D ASP* 2.8 37.1 + - - +
792D TYR* 3.9 24.2 - - - +
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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