Contacts of the helix formed by residues 780 - 787 (chain A) in PDB entry 4EJX
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 LYS 780 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A GLN* 5.7 1.0 - - - +
777A VAL* 4.5 13.4 - - - +
778A GLU* 3.3 15.6 + - + +
779A ARG* 1.3 75.6 - - - +
781A ALA* 1.3 60.7 + - - +
782A GLU* 3.2 21.5 - - - +
783A GLU* 2.9 54.3 + - + +
784A GLU* 3.0 11.4 + - - -
890A ASN* 5.4 12.5 + - - +
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Residues in contact with ALA 781 (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 LYS* 1.3 75.0 - - - +
782A GLU* 1.3 64.1 + - - +
784A GLU* 3.3 30.1 + - - +
952A GLY* 4.2 12.3 - - - +
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Residues in contact with GLU 782 (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 LYS* 3.2 27.2 - - - +
781A ALA* 1.3 78.2 + - - +
783A GLU* 1.3 61.0 + - + +
784A GLU 3.3 0.7 - - - -
785A HIS* 2.8 31.0 + - - -
890A ASN* 5.3 6.2 + - - -
891A PRO* 5.7 6.2 - - - +
895A LEU* 5.1 14.4 - - + -
896A GLU 4.7 1.2 - - - +
897A PHE* 3.9 10.9 - - - -
952A GLY 5.0 1.7 - - - +
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Residues in contact with GLU 783 (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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777A VAL* 5.1 2.6 - - - +
778A GLU 3.6 5.2 - - - +
779A ARG* 3.2 21.1 - - + +
780A LYS* 3.2 70.3 + - + +
782A GLU* 1.3 81.7 - - + +
784A GLU* 1.3 61.9 + - - +
785A HIS* 3.2 10.3 - - + -
786A LEU* 3.3 29.5 - - + +
792A GLN* 5.9 4.7 - - + +
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Residues in contact with GLU 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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779A ARG* 4.2 15.9 + - + +
780A LYS 3.0 9.2 + - - +
781A ALA* 3.3 26.3 - - - +
782A GLU 3.3 1.6 - - - -
783A GLU* 1.3 76.5 - - - +
785A HIS* 1.3 59.8 + - - +
786A LEU 3.2 4.2 + - - -
787A GLY* 3.9 8.1 + - - -
950A LEU* 5.5 1.0 - - - +
951A GLN* 3.8 21.1 + - - +
952A GLY* 4.4 14.9 + - - -
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Residues in contact with HIS 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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782A GLU 2.8 29.4 + - - -
783A GLU* 4.0 1.3 - - - -
784A GLU* 1.3 77.2 - - - +
786A LEU* 1.3 79.3 + - + +
787A GLY 3.3 0.8 + - - -
792A GLN* 5.1 3.5 + - - -
896A GLU 3.5 10.0 + - - -
897A PHE* 3.3 25.6 - + + -
898A ALA* 3.1 42.5 + - - +
899A LEU* 4.9 1.1 - - + -
943A ASN* 2.8 25.7 + - - -
950A LEU* 3.4 15.1 - - + +
951A GLN 3.9 21.3 - - - +
952A GLY* 4.3 7.1 - - - -
953A LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 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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779A ARG* 3.5 26.7 - - + +
783A GLU* 3.3 33.9 - - + +
784A GLU 3.2 0.4 - - - -
785A HIS* 1.3 104.5 - - + +
787A GLY* 1.3 63.7 + - - +
788A ILE 3.3 1.4 + - - -
789A LEU* 3.3 18.7 + - + +
790A GLY 3.7 24.5 - - - +
791A PRO* 4.3 8.1 - - + -
792A GLN* 4.5 15.7 - - + +
877A PRO* 5.5 3.6 - - + -
898A ALA* 5.0 6.3 - - + -
943A ASN* 3.3 26.2 - - - +
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Residues in contact with GLY 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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724A TRP* 3.7 16.3 - - - -
766A ARG* 2.7 27.7 + - - -
779A ARG* 2.8 16.7 + - - +
784A GLU 3.9 5.8 + - - -
785A HIS 3.3 4.7 - - - -
786A LEU* 1.3 75.7 - - - +
788A ILE* 1.3 53.8 + - - -
789A LEU 3.1 2.0 + - - +
943A ASN 3.6 5.6 - - - -
945A ARG* 5.1 6.3 - - - -
950A LEU* 4.6 8.5 - - - -
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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