Contacts of the helix formed by residues 786 - 796 (chain D) in PDB entry 1XFV
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 GLU 786 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700D TYR* 4.9 4.9 + - - -
723D PHE* 3.9 25.2 - - + -
727D GLN* 3.4 25.0 - - - +
782D PHE* 3.7 27.5 - - - +
784D GLU 4.4 0.8 + - - -
785D ASN* 1.4 70.5 - - - +
787D THR* 1.3 70.5 + - - +
789D ASN* 3.6 18.9 + - - +
790D PHE* 3.7 7.2 + - + +
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Residues in contact with THR 787 (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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785D ASN* 3.1 29.1 + - + -
786D GLU* 1.3 85.1 - - - +
788D ASP* 1.3 72.3 + - - -
790D PHE* 3.4 12.1 + - - +
791D GLU* 4.0 8.8 + - - +
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Residues in contact with ASP 788 (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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785D ASN* 3.0 22.2 + - - +
787D THR* 1.3 80.6 + - - +
789D ASN* 1.3 55.5 + - - +
790D PHE 2.9 3.1 - - - -
791D GLU* 2.8 25.2 + - + +
792D VAL* 2.3 54.8 + - + +
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Residues in contact with ASN 789 (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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723D PHE* 4.2 8.1 - - + -
780D LEU* 3.3 24.9 - - - +
781D ASN* 2.6 42.6 + - + +
782D PHE* 3.8 7.9 - - - +
785D ASN* 4.0 4.8 + - - +
786D GLU* 3.6 38.0 + - + +
787D THR 3.1 0.2 - - - -
788D ASP* 1.3 81.9 + - - +
790D PHE* 1.3 57.0 + - - +
792D VAL* 3.1 11.1 - - - +
793D PHE* 2.9 24.1 + - - +
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Residues in contact with PHE 790 (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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716D LYS* 5.9 1.8 - - + -
719D LYS* 5.0 2.7 - - + -
720D ILE* 3.4 40.8 - - + -
723D PHE* 3.8 34.7 - + + -
786D GLU 3.7 5.8 + - - +
787D THR 3.4 10.4 + - - +
788D ASP 2.9 0.6 - - - -
789D ASN* 1.3 76.1 - - - +
791D GLU* 1.3 69.0 + - + +
792D VAL 3.0 1.3 - - - -
793D PHE* 2.9 47.7 + + - +
794D GLN* 2.9 12.6 + - + +
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Residues in contact with GLU 791 (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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787D THR* 4.2 5.6 - - - +
788D ASP* 2.8 32.8 + - + +
790D PHE* 1.3 72.9 - - + +
792D VAL* 1.4 70.1 - - - +
794D GLN* 2.8 32.0 + - - +
795D LYS* 3.2 6.1 + - - +
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Residues in contact with VAL 792 (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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779D GLN 4.5 12.3 - - - +
780D LEU* 4.6 4.3 - - + -
788D ASP* 2.3 62.2 + - + +
789D ASN* 3.1 14.1 - - - +
791D GLU* 1.4 69.7 - - - +
793D PHE* 1.3 65.5 + - - +
795D LYS* 2.9 6.9 + - - +
796D ILE* 2.8 45.1 + - + +
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Residues in contact with PHE 793 (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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719D LYS* 3.9 29.2 - - + -
722D ILE* 3.8 28.0 - - + -
723D PHE* 3.9 19.7 - + + -
726D ILE* 5.2 1.1 - - + -
764D LEU* 6.0 0.2 - - + -
776D LEU* 3.7 43.1 - - + -
780D LEU* 4.6 4.3 - - + -
789D ASN 2.9 11.0 + - - +
790D PHE* 2.9 43.9 + + + +
792D VAL* 1.3 80.1 - - - +
794D GLN* 1.3 64.9 + - - +
796D ILE* 3.1 18.7 - - + +
797D ILE* 3.4 20.1 - - + +
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Residues in contact with GLN 794 (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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719D LYS* 5.0 15.0 - - - +
790D PHE* 2.9 8.7 + - + +
791D GLU* 2.8 25.3 + - - +
793D PHE* 1.3 72.5 - - - +
795D LYS* 1.3 80.5 + - - +
797D ILE* 2.5 52.3 + - + +
798D ASP* 4.4 8.5 - - - +
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Residues in contact with LYS 795 (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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791D GLU 3.2 3.1 + - - +
792D VAL* 2.9 13.1 + - - +
794D GLN* 1.3 88.4 - - - +
796D ILE* 1.3 55.9 + - + +
797D ILE 2.5 18.0 + - - -
798D ASP* 2.8 35.7 + - - +
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Residues in contact with ILE 796 (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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771D ILE* 4.0 20.2 - - + +
776D LEU* 4.0 30.7 - - + +
779D GLN* 3.9 37.2 - - + +
780D LEU* 4.7 5.6 - - + -
792D VAL* 2.8 52.4 + - + +
793D PHE* 3.1 16.6 - - + +
794D GLN 3.0 0.2 + - - -
795D LYS* 1.3 76.6 - - + +
797D ILE* 1.3 60.6 + - + +
798D ASP 3.9 0.8 + - - -
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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