Contacts of the helix formed by residues 716 - 723 (chain A) in PDB entry 1EJ9
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 LEU 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A ASN* 3.5 24.2 - - + +
623A ASN* 3.5 34.0 + - + +
624A ARG* 3.5 30.5 - - + +
627A ALA* 3.4 26.2 - - + -
714A ILE* 4.3 7.2 - - + +
715A ALA* 1.3 75.0 - - - +
717A GLY* 1.3 65.3 + - - +
718A THR 3.6 0.7 - - - -
719A SER* 3.2 4.4 + - - -
720A LYS* 3.0 26.5 + - + +
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Residues in contact with GLY 717 (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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715A ALA* 3.3 6.5 - - - +
716A LEU* 1.3 77.6 - - - +
718A THR* 1.3 52.0 + - - +
720A LYS* 3.5 5.3 - - - +
721A LEU* 2.7 40.4 + - - +
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Residues in contact with THR 718 (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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632A HIS* 3.4 34.9 - - + +
715A ALA* 4.7 3.6 + - - +
716A LEU 3.6 0.6 - - - -
717A GLY* 1.3 73.2 - - - +
719A SER* 1.3 54.3 + - - +
721A LEU* 4.5 0.9 - - - -
722A ASN* 2.6 49.7 + - - +
723A PHE* 3.5 2.6 - - + -
10C C 3.5 22.7 - - + +
11C A 3.5 13.3 - - + +
12C G 2.7 26.7 + - - -
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Residues in contact with SER 719 (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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623A ASN* 3.4 16.7 + - - -
626A VAL* 4.0 23.6 - - - -
627A ALA* 4.2 8.8 - - - -
630A CYS* 4.6 1.1 - - - -
632A HIS* 3.7 17.6 + - - -
716A LEU* 3.2 11.1 + - - -
718A THR* 1.3 76.3 - - - +
720A LYS* 1.3 66.5 + - - +
723A PHE* 2.7 37.9 + - - -
724A LEU* 3.0 11.9 + - - -
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Residues in contact with LYS 720 (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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619A TYR* 4.3 12.9 - - - +
620A ASN* 5.6 1.6 + - - -
623A ASN* 4.0 15.3 - - - +
716A LEU* 3.0 18.4 + - + +
717A GLY* 3.5 5.2 - - - +
719A SER* 1.3 82.6 + - - +
721A LEU* 1.3 61.9 + - + +
724A LEU* 4.0 21.1 - - - +
743A ILE* 2.6 37.3 + - - +
744A TYR* 3.6 21.6 + - + +
748A GLN* 3.2 29.9 + - - +
752A PHE* 3.8 15.3 - - + -
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Residues in contact with LEU 721 (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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440A ASP* 5.2 0.9 - - - +
444A TYR* 4.8 1.1 + - - -
717A GLY 2.7 18.9 + - - +
718A THR* 4.5 0.7 - - - -
720A LYS* 1.3 81.3 - - + +
722A ASN* 1.3 71.8 + - - +
747A THR* 6.3 2.9 - - + -
748A GLN* 5.1 15.3 - - + +
751A LYS* 2.7 59.4 + - + +
752A PHE* 3.8 17.3 - - + -
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Residues in contact with ASN 722 (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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443A LYS* 2.8 27.3 + - - +
444A TYR* 3.2 8.1 - - - -
591A THR* 5.1 0.7 + - - +
718A THR* 2.6 39.5 + - - +
721A LEU* 1.3 95.7 + - - +
723A PHE* 1.3 65.2 + - + +
751A LYS* 4.0 10.3 - - - +
9C T 5.4 1.2 - - - +
10C C 3.6 54.3 + - + +
11C A 5.7 1.6 + - - +
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Residues in contact with PHE 723 (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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444A TYR* 3.0 15.3 - - - -
590A ARG* 3.5 57.4 - - + -
591A THR* 3.4 17.2 - - - +
594A ALA* 3.6 13.9 - - + -
595A SER* 2.7 23.9 + - - -
630A CYS* 4.2 8.3 - - - -
632A HIS* 3.4 12.6 - + - -
718A THR* 3.5 6.1 - - + -
719A SER* 2.7 36.5 + - - +
722A ASN* 1.3 75.7 - - + +
724A LEU* 1.3 51.7 + - - +
10C C 3.8 26.2 - - - -
11C A 2.9 30.5 - - - -
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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