Contacts of the helix formed by residues 783 - 793 (chain A) in PDB entry 3L6X
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 ASN 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735A ALA* 6.1 1.0 - - - +
738A LYS* 2.6 58.4 + - + +
741A ILE* 5.3 2.4 - - - +
742A GLY 4.4 3.6 - - - +
779A VAL* 3.5 26.2 + - - +
780A ILE* 3.5 3.8 + - - +
782A GLU* 1.3 78.0 - - - +
784A LEU* 1.3 67.6 + - - +
785A GLU* 3.1 10.2 + - - +
786A ALA* 2.9 29.7 + - + +
787A ALA* 3.0 12.0 + - - +
826A TYR* 3.0 8.2 + - - -
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Residues in contact with LEU 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782A GLU 4.1 0.2 - - - -
783A ASN* 1.3 73.7 - - - +
785A GLU* 1.3 69.1 + - + +
787A ALA* 3.2 7.0 + - + +
788A LYS* 2.8 55.1 + - + +
826A TYR* 4.1 40.1 + - + -
828A GLU* 4.6 15.9 - - + -
829A LEU* 4.9 1.6 - - + -
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Residues in contact with GLU 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A GLU* 3.5 27.8 - - + +
742A GLY* 5.9 0.4 - - - -
783A ASN* 3.1 8.1 + - - +
784A LEU* 1.3 83.0 - - + +
786A ALA* 1.3 60.6 + - - +
788A LYS* 3.4 35.8 + - - +
789A LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A LYS 5.1 0.4 + - - -
742A GLY* 4.1 20.2 - - - -
746A ILE* 4.0 6.0 - - + +
779A VAL* 3.6 17.9 - - + +
780A ILE* 3.9 12.0 - - + +
783A ASN* 2.9 32.8 + - - +
785A GLU* 1.3 76.6 - - - +
787A ALA* 1.3 58.7 + - - +
789A LYS* 3.1 5.1 + - - +
790A LEU* 2.9 28.6 + - - +
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Residues in contact with ALA 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A ILE* 3.8 17.8 - - + +
783A ASN 3.0 8.2 + - - +
784A LEU 3.4 8.5 - - - +
786A ALA* 1.3 75.0 - - - +
788A LYS* 1.3 56.4 + - - +
790A LEU* 3.2 8.6 - - - +
791A ARG* 3.0 21.7 + - - +
796A ILE* 5.4 0.3 - - - +
823A ILE* 5.2 1.1 - - + -
826A TYR* 3.8 26.7 - - + -
829A LEU* 3.0 34.5 - - + +
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Residues in contact with LYS 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784A LEU* 2.8 40.3 + - + +
785A GLU* 3.5 41.3 + - - +
786A ALA 3.1 0.2 - - - -
787A ALA* 1.3 75.6 - - - +
789A LYS* 1.3 60.6 + - - +
791A ARG* 3.1 9.0 + - - +
792A GLU* 2.8 29.6 + - - +
828A GLU* 4.8 12.9 - - + +
829A LEU* 4.5 9.0 - - + -
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Residues in contact with LYS 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A GLY 4.7 6.3 - - - +
743A LYS* 5.4 6.3 - - - +
746A ILE* 3.8 11.2 - - + -
747A PRO* 3.7 27.0 - - + +
785A GLU 2.9 16.7 + - - +
786A ALA* 3.1 6.7 + - - +
788A LYS* 1.3 73.6 - - - +
790A LEU* 1.3 62.4 - - - +
792A GLU* 2.4 36.7 + - - +
793A THR* 2.8 52.1 + - - +
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Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ILE* 3.6 10.7 - - + +
750A VAL* 3.3 29.8 - - + -
753A LEU* 5.9 0.2 - - + -
776A ILE* 4.0 31.2 - - + -
780A ILE* 4.0 12.6 - - + -
786A ALA 2.9 11.7 + - - +
787A ALA* 3.2 10.3 - - - +
789A LYS* 1.3 77.2 - - - +
791A ARG* 1.3 62.6 + - - +
793A THR* 2.7 19.3 + - - -
795A GLY* 3.3 24.0 + - - +
796A ILE* 4.6 4.7 - - + -
799A LEU* 4.1 7.0 - - + -
819A VAL* 4.2 0.2 - - + -
823A ILE* 3.3 37.0 - - + -
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Residues in contact with ARG 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A ALA 3.0 7.1 + - - -
788A LYS* 3.1 9.5 + - - +
790A LEU* 1.3 75.8 - - - +
792A GLU* 1.3 63.9 + - - +
793A THR 3.3 0.7 + - - -
794A GLN* 3.5 15.8 + - - -
796A ILE* 3.9 23.3 - - + +
828A GLU 5.4 1.2 + - - -
829A LEU* 3.2 39.0 - - + +
832A PRO* 4.3 28.7 - - - +
833A LEU* 6.4 1.6 - - - -
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Residues in contact with GLU 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A LYS 2.8 19.4 + - - +
789A LYS* 2.4 52.3 - - - +
790A LEU 3.1 0.6 - - - -
791A ARG* 1.3 77.5 - - - +
793A THR* 1.3 57.9 + - + +
794A GLN* 3.3 14.0 + - - +
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Residues in contact with THR 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ILE* 4.2 0.7 - - - +
747A PRO* 4.1 22.0 - - + +
750A VAL* 3.6 28.6 - - - +
789A LYS* 2.8 38.5 + - - +
790A LEU* 2.7 22.5 + - - -
792A GLU* 1.3 78.8 - - - +
794A GLN* 1.3 71.0 + - - +
795A GLY 3.2 0.7 + - - -
798A LYS* 5.4 1.7 - - - -
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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