Contacts of the helix formed by residues 802 - 812 (chain A) in PDB entry 1E3K
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 TRP 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A GLY 3.1 23.7 + - - -
774A GLN* 3.5 24.2 - - - -
775A MET* 3.6 12.9 - - - +
776A LEU* 4.0 18.6 - - + +
784A LEU 4.6 0.9 - - - -
786A GLU* 2.7 37.9 - - - -
789A MET* 3.4 32.3 - - + -
798A CYS 3.1 19.2 + - - +
799A LEU* 2.7 28.0 + - + +
801A MET* 1.4 71.1 - - - +
803A GLN* 1.3 60.6 + - - +
804A ILE 3.2 1.0 + - - -
805A PRO* 3.4 15.7 - - + +
806A GLN* 3.2 24.8 - - + +
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Residues in contact with GLN 803 (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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799A LEU 4.1 3.1 - - - +
800A THR* 3.4 43.4 + - - +
801A MET 2.8 3.4 + - - -
802A TRP* 1.3 75.4 - - - +
804A ILE* 1.3 61.9 + - - +
806A GLN* 3.5 9.1 + - - +
807A GLU* 3.1 24.3 + - - +
883A LEU* 4.1 16.1 - - + +
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Residues in contact with ILE 804 (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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760A VAL* 3.3 37.9 - - + +
761A PHE* 3.6 15.5 - - + +
763A LEU* 6.1 0.2 - - + -
764A GLY* 4.2 7.6 - - - -
801A MET 3.2 7.1 + - - +
803A GLN* 1.3 75.8 - - - +
805A PRO* 1.3 66.8 - - + +
807A GLU* 3.0 19.9 + - - +
808A PHE* 3.3 41.2 + - + -
876A LEU* 4.7 4.3 - - + -
880A LEU* 3.2 37.2 - - + -
883A LEU* 3.9 11.9 - - + -
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Residues in contact with PRO 805 (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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763A LEU* 5.5 0.2 - - + -
764A GLY* 3.5 30.5 - - - +
767A SER* 3.8 24.9 - - - -
768A TYR* 3.9 6.8 - - - +
773A GLY* 4.1 7.6 - - - -
776A LEU* 4.4 4.3 - - + -
801A MET 3.5 11.0 - - - +
802A TRP* 3.4 27.8 - - + +
804A ILE* 1.3 91.9 - - + +
806A GLN* 1.3 59.5 + - - -
808A PHE* 3.5 6.8 + - + +
809A VAL* 3.3 26.7 + - - +
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Residues in contact with GLN 806 (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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773A GLY* 3.3 22.2 + - - +
774A GLN* 3.8 23.8 + - - +
802A TRP* 3.2 26.0 + - + +
803A GLN* 3.5 10.3 + - - +
804A ILE 3.2 0.6 - - - -
805A PRO* 1.3 76.8 - - - +
807A GLU* 1.3 56.0 + - - +
809A VAL* 3.4 12.1 - - - +
810A LYS* 2.7 39.3 + - - +
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Residues in contact with GLU 807 (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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803A GLN 3.1 13.3 + - - +
804A ILE* 3.0 8.3 + - - +
806A GLN* 1.3 80.1 - - - +
808A PHE* 1.3 55.2 + - - +
810A LYS* 2.6 46.3 + - - +
811A LEU* 2.8 59.7 + - + +
876A LEU* 4.4 18.6 - - + -
879A ASN* 6.4 0.4 - - - +
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Residues in contact with PHE 808 (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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761A PHE* 3.3 46.0 - + - -
764A GLY 3.8 6.7 - - - -
765A TRP* 3.4 51.8 - + + -
768A TYR* 3.2 33.3 - + + -
804A ILE* 3.3 22.8 + - + +
805A PRO 3.7 6.3 - - - +
806A GLN 3.2 0.2 - - - -
807A GLU* 1.3 76.0 - - - +
809A VAL* 1.3 54.8 + - - +
811A LEU 4.1 0.4 - - - +
812A GLN* 2.8 27.9 + - - -
813A VAL* 3.2 22.6 + - + -
818A PHE* 4.3 2.9 - + - -
821A MET* 5.7 0.7 - - - -
876A LEU* 3.9 23.6 - - + -
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Residues in contact with VAL 809 (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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768A TYR* 3.3 27.8 - - + -
772A SER 3.7 26.7 - - - +
773A GLY* 4.4 2.7 - - - -
774A GLN* 5.3 3.8 - - - +
805A PRO 3.3 9.6 + - - +
806A GLN* 3.4 16.6 - - - +
808A PHE* 1.3 72.7 - - - +
810A LYS* 1.3 71.8 + - + +
811A LEU 3.4 0.2 + - - -
812A GLN* 3.4 15.6 + - - +
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Residues in contact with LYS 810 (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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806A GLN* 2.7 22.5 + - - +
807A GLU* 2.6 43.6 + - - +
809A VAL* 1.3 82.0 - - + +
811A LEU* 1.3 62.3 + - + +
812A GLN* 3.4 1.9 + - - +
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Residues in contact with LEU 811 (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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807A GLU* 2.8 50.5 + - + +
808A PHE 3.4 0.4 + - - -
809A VAL 3.2 0.2 - - - -
810A LYS* 1.3 75.6 - - + +
812A GLN* 1.3 61.7 + - - +
813A VAL* 3.8 12.8 - - + -
869A ARG* 2.2 45.6 + - - +
872A GLN* 3.5 52.9 - - + +
873A LEU* 4.5 5.2 - - + -
876A LEU* 4.0 18.8 - - + -
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Residues in contact with GLN 812 (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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768A TYR* 3.3 12.1 - - + +
808A PHE 2.8 9.9 + - - -
809A VAL 3.4 10.0 + - - +
810A LYS 3.3 4.1 - - - +
811A LEU* 1.3 81.6 - - - +
813A VAL* 1.3 59.8 + - - +
814A SER* 3.8 1.6 + - - -
859A ARG* 5.7 1.7 + - - -
869A ARG* 3.0 11.6 + - - -
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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