Contacts of the helix formed by residues 780 - 791 (chain C) in PDB entry 1DDJ
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 PHE 780 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C GLU* 3.7 27.1 - - + -
645C LYS* 3.6 39.7 - - + -
647C ILE* 4.1 20.4 - - + -
723C THR* 3.8 27.6 - - + -
775C VAL* 3.4 22.2 - - + -
776C ARG 3.0 31.6 - - - -
777C VAL 2.8 6.5 + - - +
779C ARG* 1.3 88.6 - - + +
781C VAL* 1.3 52.5 + - - +
782C THR 3.3 2.7 - - - -
783C TRP* 3.0 17.5 + + + +
784C ILE* 2.8 38.5 + - + +
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Residues in contact with VAL 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C LEU* 4.3 15.0 - - + -
668C PRO* 3.3 44.2 - - + +
670C PRO* 4.4 15.0 - - + -
777C VAL* 3.1 22.6 + - + +
778C SER* 3.8 11.6 + - - +
779C ARG 3.7 0.6 - - - -
780C PHE* 1.3 76.7 - - - +
782C THR* 1.3 59.4 + - - +
784C ILE* 3.1 7.5 + - + +
785C GLU* 2.8 53.9 + - + +
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Residues in contact with THR 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C PRO* 3.8 25.2 - - - +
778C SER 5.1 1.2 + - - -
779C ARG 5.3 1.7 - - - -
780C PHE 3.3 0.8 - - - +
781C VAL* 1.3 78.5 - - - +
783C TRP* 1.3 63.4 + - - +
785C GLU* 3.9 10.1 + - - +
786C GLY* 3.1 19.1 + - - -
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Residues in contact with TRP 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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599C LEU* 4.6 0.2 - - + -
639C PHE* 3.5 27.1 - - + -
640C LEU 3.7 4.2 + - - -
641C GLU* 3.5 34.8 - - + -
642C PRO* 3.1 33.0 - - + +
647C ILE* 4.4 14.1 - - + -
648C ALA* 4.2 1.6 - - - -
649C LEU* 4.0 20.6 - - + -
779C ARG 5.6 0.4 - - - +
780C PHE* 3.0 23.9 + - + +
782C THR* 1.3 80.6 - - - +
784C ILE* 1.3 90.8 + - + +
786C GLY* 3.2 3.1 + - - -
787C VAL* 3.1 42.6 + - + +
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Residues in contact with ILE 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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593C ILE* 3.8 24.2 - - + -
599C LEU* 3.5 33.9 - - + -
647C ILE* 4.7 0.7 - - + -
649C LEU* 3.8 18.7 - - + +
667C LEU* 4.4 12.8 - - + -
777C VAL* 4.5 9.2 - - + -
780C PHE* 2.8 34.7 + - + +
781C VAL* 3.5 9.6 - - - +
783C TRP* 1.3 91.1 - - + +
785C GLU* 1.3 61.8 + - - +
787C VAL* 3.3 3.6 + - - +
788C MET* 3.0 30.8 + - + +
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Residues in contact with GLU 785 (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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667C LEU* 5.7 3.3 - - + +
670C PRO* 5.6 4.6 - - - +
781C VAL* 2.8 41.0 + - + +
782C THR* 3.9 9.3 + - - +
784C ILE* 1.3 72.3 - - + +
786C GLY* 1.3 63.0 + - - +
788C MET* 3.2 20.2 + - + +
789C ARG* 2.9 53.6 + - - +
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Residues in contact with GLY 786 (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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782C THR 3.1 12.5 + - - -
783C TRP 3.2 3.6 + - - -
785C GLU* 1.3 78.6 - - - +
787C VAL* 1.3 61.7 + - - +
789C ARG* 3.3 14.8 + - - +
790C ASN* 3.0 32.4 + - - +
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Residues in contact with VAL 787 (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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597C TRP* 3.8 16.4 - - + -
639C PHE* 3.5 37.5 - - + -
649C LEU* 3.9 8.5 - - + -
783C TRP* 3.1 44.2 + - + +
784C ILE 3.9 5.8 - - - +
786C GLY* 1.3 74.0 - - - +
788C MET* 1.3 62.7 + - - +
790C ASN* 4.9 0.4 - - - -
791C ASN* 2.8 40.2 + - - +
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Residues in contact with MET 788 (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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593C ILE* 3.6 26.2 - - + -
594C SER* 4.5 9.0 - - - -
597C TRP* 3.5 48.1 + - + +
649C LEU* 4.9 1.1 - - + -
667C LEU* 5.2 5.4 - - + -
784C ILE* 3.0 23.8 + - + +
785C GLU* 3.6 30.3 - - + +
787C VAL* 1.3 78.6 - - - +
789C ARG* 1.3 60.6 + - - +
791C ASN 3.3 16.8 - - - +
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Residues in contact with ARG 789 (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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785C GLU* 2.9 54.2 + - - +
786C GLY* 3.3 15.4 - - - +
788C MET* 1.3 75.5 - - - +
790C ASN* 1.3 72.4 + - - +
791C ASN 3.5 2.0 - - - +
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Residues in contact with ASN 790 (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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786C GLY* 3.0 20.6 + - - +
787C VAL* 4.9 0.2 - - - -
789C ARG* 1.3 91.3 + - - +
791C ASN* 1.3 73.0 + - - +
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Residues in contact with ASN 791 (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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597C TRP* 3.8 13.0 - - + -
637C ARG* 3.7 15.0 + - - +
639C PHE* 3.3 28.7 - - + -
651C LYS* 2.6 43.5 + - - -
787C VAL* 2.8 41.9 + - - +
788C MET 3.3 15.2 - - - +
789C ARG 4.5 1.6 - - - +
790C ASN* 1.3 91.0 + - - +
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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