Contacts of the strand formed by residues 777 - 784 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698C TRP* 3.8 5.6 - - - -
747C GLY 3.1 8.3 + - - +
749C TYR* 3.1 27.0 + - - +
750C ASN* 3.1 19.7 + - - +
753C ALA* 4.0 4.5 - - + -
775C SER 3.2 9.7 + - - +
776C ASN* 1.3 77.4 - - - +
778C ILE* 1.3 63.1 + - - +
779C THR* 3.7 19.7 - - - -
795C CYS* 4.0 18.2 - - - -
796C THR 3.3 7.2 - - - -
797C MET* 3.7 20.0 - - + -
846C VAL* 4.1 12.8 - - - -
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Residues in contact with ILE 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A VAL* 4.0 26.9 - - + -
741A ALA* 4.4 11.0 - - + -
742A MET* 4.2 20.4 - - + -
639B ALA* 4.6 6.7 - - + -
698C TRP* 3.9 16.1 - - + -
737C LEU* 4.1 17.3 - - + -
749C TYR* 3.3 17.9 - - + -
777C CYS* 1.3 74.0 - - - +
779C THR* 1.3 64.1 + - - +
780C LEU* 4.0 17.3 + - + +
794C SER* 3.8 1.4 + - - +
795C CYS* 3.5 2.6 - - - -
796C THR* 3.1 46.3 + - - +
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Residues in contact with THR 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732C ASN* 2.9 30.9 + - - +
736C ASN* 3.8 11.7 - - - +
737C LEU* 4.8 1.2 - - - +
749C TYR 2.9 10.0 + - - +
750C ASN* 3.5 7.6 - - - +
777C CYS* 3.7 1.7 - - - -
778C ILE* 1.3 73.5 - - - +
780C LEU* 1.3 68.3 + - - +
781C MET* 4.0 16.8 - - + -
793C ILE* 4.1 5.4 - - + -
794C SER 3.4 5.6 - - - +
795C CYS* 3.6 13.3 - - - -
850C GLU* 2.6 44.8 + - + +
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Residues in contact with LEU 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733A ILE* 6.1 0.4 - - + -
734A ASN* 5.5 0.9 - - - +
738A VAL* 3.8 31.0 - - + -
639B ALA* 3.6 41.1 - - + +
642B ASN* 4.7 7.2 - - - +
732C ASN* 3.6 2.0 - - - +
737C LEU* 4.0 20.0 - - + -
778C ILE* 4.1 11.9 - - + +
779C THR* 1.3 82.1 - - - +
781C MET* 1.3 66.3 + - - +
792C TYR* 5.0 4.8 - - + -
793C ILE* 3.3 5.0 - - - +
794C SER* 2.9 44.8 + - - +
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Residues in contact with MET 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728C MET* 3.9 33.4 - - + +
729C ILE* 4.1 18.3 - - + +
732C ASN* 3.5 42.2 + - + +
733C ILE* 5.2 5.5 - - - +
779C THR* 4.0 4.9 - - + -
780C LEU* 1.3 83.0 - - - +
782C GLU* 1.3 65.0 + - - +
791C LEU* 4.1 13.2 - - + -
792C TYR* 3.2 9.4 - - - +
793C ILE* 3.9 28.5 - - + -
850C GLU 4.3 2.2 - - - +
854C MET* 3.6 31.6 - - + -
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Residues in contact with GLU 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A GLU* 4.1 14.0 - - - +
595B ARG* 4.2 3.4 + - - -
641B ARG* 2.6 50.3 + - - +
642B ASN* 5.6 0.2 - - - +
729C ILE* 3.5 13.1 - - - +
781C MET* 1.3 77.3 - - - +
783C ALA* 1.3 68.5 + - - +
784C SER* 5.6 0.2 - - - -
790C ASP 3.8 0.9 - - - +
791C LEU* 3.9 2.4 - - - +
792C TYR* 2.9 58.9 + - + +
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Residues in contact with ALA 783 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725C THR* 4.4 1.6 - - + -
729C ILE* 3.3 18.2 - - + +
782C GLU* 1.3 86.3 - - - +
784C SER* 1.3 59.9 + - - +
788C ASN* 3.4 44.1 + - + +
790C ASP 3.6 5.2 - - - -
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Residues in contact with SER 784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C VAL* 4.4 15.5 - - - +
782C GLU* 5.6 0.2 - - - -
783C ALA* 1.3 76.6 - - - +
785C GLY* 1.3 71.0 + - - +
788C ASN* 3.1 16.0 - - - +
789C GLU 3.2 0.3 + - - -
790C ASP* 2.8 40.9 + - - -
792C TYR* 4.0 23.9 - - - +
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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