Contacts of the helix formed by residues 847 - 861 (chain A) in PDB entry 6C90
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 GLN 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A PHE* 3.6 37.9 + - - -
564A HIS* 3.8 10.3 - - - +
565A LEU* 3.8 10.2 - - + +
585A LEU* 3.0 34.5 - - + +
588A SER* 4.1 5.4 + - - -
590A TYR* 3.8 32.4 - - + +
591A GLN* 5.3 1.4 + - - +
846A LEU* 1.3 75.7 - - + +
848A MET* 1.3 59.1 + - - +
849A ASP* 3.4 2.7 - - - +
850A GLU* 3.3 20.5 + - - +
851A LEU* 3.0 26.3 + - - +
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Residues in contact with MET 848 (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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91A SER* 3.8 31.6 - - - +
582A GLU* 3.6 38.4 - - + -
585A LEU* 4.2 4.7 - - + -
586A GLU* 4.3 11.4 - - + +
845A VAL* 3.7 39.2 + - + +
846A LEU 3.1 4.6 + - - +
847A GLN* 1.3 74.3 - - - +
849A ASP* 1.3 68.8 + - - +
851A LEU* 2.9 26.5 + - - +
852A LYS* 3.0 25.6 + - + +
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Residues in contact with ASP 849 (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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847A GLN* 3.4 0.8 - - - +
848A MET* 1.3 77.7 - - - +
850A GLU* 1.3 62.5 + - - +
852A LYS* 3.3 8.6 + - - +
853A CYS* 3.1 35.8 + - - -
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Residues in contact with GLU 850 (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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564A HIS* 5.4 3.9 - - - +
565A LEU* 4.0 19.6 + - + +
847A GLN* 3.3 25.6 + - - +
848A MET 3.1 0.8 - - - -
849A ASP* 1.3 79.3 - - - +
851A LEU* 1.3 62.8 + - - +
853A CYS* 3.3 6.3 + - - +
854A ARG* 2.9 66.3 + - + +
951A LEU* 4.3 10.1 - - + -
1104A MLI 5.4 0.7 - - - +
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Residues in contact with LEU 851 (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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565A LEU* 3.7 16.1 - - + +
570A VAL* 4.0 26.5 - - + -
581A PRO* 3.7 25.1 - - + -
582A GLU* 3.4 37.9 - - + +
585A LEU* 3.8 19.3 - - + -
847A GLN 3.0 12.6 + - - +
848A MET* 2.9 16.2 + - - +
850A GLU* 1.3 76.8 - - - +
852A LYS* 1.3 66.5 + - + +
854A ARG* 3.4 3.4 + - + +
855A LYS* 3.0 38.2 + - + +
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Residues in contact with LYS 852 (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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582A GLU* 4.2 6.8 + - - +
848A MET* 3.0 24.8 + - + +
849A ASP* 3.7 9.4 - - - +
851A LEU* 1.3 85.4 - - + +
853A CYS* 1.3 63.5 + - - +
855A LYS* 3.1 36.3 + - - +
856A ARG* 3.0 37.4 + - + +
859A ARG* 5.1 6.3 + - - +
868A ASP* 5.0 0.4 + - - -
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Residues in contact with CYS 853 (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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849A ASP* 3.1 32.6 + - - +
850A GLU* 3.8 1.1 - - - +
852A LYS* 1.3 79.0 - - - +
854A ARG* 1.3 63.0 + - - +
856A ARG* 3.3 22.7 + - - +
857A VAL* 3.2 23.9 + - - +
949A ALA* 3.3 26.5 - - - +
950A LYS* 3.8 17.0 - - - -
951A LEU* 3.4 24.0 - - + -
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Residues in contact with ARG 854 (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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565A LEU* 3.5 40.4 + - - +
566A THR* 3.8 13.1 - - - +
567A TYR* 3.5 44.0 - - + -
570A VAL* 5.1 8.9 - - + +
850A GLU* 2.9 51.6 + - - +
851A LEU* 3.8 4.7 - - - +
853A CYS* 1.3 76.8 - - - +
855A LYS* 1.3 62.4 + - - +
857A VAL* 3.3 5.1 + - - +
858A LEU* 3.1 26.7 + - + +
951A LEU* 4.0 16.8 - - + +
1104A MLI 2.8 37.3 + - - -
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Residues in contact with LYS 855 (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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570A VAL* 4.2 11.9 - - + -
574A LEU* 4.6 19.5 - - + +
581A PRO* 5.2 1.9 - - + +
582A GLU* 3.5 18.2 + - - -
851A LEU* 3.0 34.0 + - + +
852A LYS* 3.1 38.1 + - - +
854A ARG* 1.3 72.8 - - - +
856A ARG* 1.3 61.4 + - - +
858A LEU* 3.0 10.3 + - + +
859A ARG* 2.8 43.2 + - - +
868A ASP* 3.0 43.0 + - - +
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Residues in contact with ARG 856 (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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852A LYS* 3.0 26.1 + - + +
853A CYS* 3.3 26.4 + - - +
855A LYS* 1.3 76.8 - - - +
857A VAL* 1.3 56.2 + - - +
859A ARG* 3.3 21.5 + - - +
860A ARG* 2.9 66.6 + - - +
949A ALA* 3.1 31.0 + - + +
950A LYS* 3.8 13.9 - - - +
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Residues in contact with VAL 857 (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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567A TYR* 3.7 24.5 - - + +
853A CYS 3.2 8.1 + - - +
854A ARG 3.5 8.1 - - - +
855A LYS 3.2 0.2 - - - -
856A ARG* 1.3 75.9 - - - +
858A LEU* 1.3 62.5 + - - +
860A ARG* 3.9 0.6 - - - +
861A LEU* 3.1 36.1 + - + +
886A LEU* 3.7 24.5 - - + -
942A ILE 5.7 0.2 - - - +
945A VAL* 4.2 13.0 - - + +
946A SER* 4.0 19.7 - - - +
949A ALA* 3.4 26.5 - - + -
951A LEU* 4.0 3.4 - - + -
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Residues in contact with LEU 858 (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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567A TYR* 3.7 25.4 - - + -
570A VAL* 4.0 24.5 - - + -
571A LEU* 3.8 30.7 - - + -
574A LEU* 4.7 5.2 - - + -
854A ARG* 3.1 15.1 + - + +
855A LYS* 3.0 12.4 + - - +
857A VAL* 1.3 76.4 - - - +
859A ARG* 1.3 59.8 + - - +
861A LEU 3.6 0.5 + - - -
862A GLY 3.2 2.4 + - - -
863A PHE* 2.7 56.3 + - + -
864A ALA* 3.3 10.2 + - + +
886A LEU* 3.7 17.3 - - + -
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Residues in contact with ARG 859 (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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852A LYS* 5.1 6.1 + - - +
855A LYS* 2.8 34.2 + - + +
856A ARG* 3.7 21.4 - - - +
858A LEU* 1.3 71.8 - - - +
860A ARG* 1.3 68.3 + - + +
861A LEU 3.0 1.8 - - - -
862A GLY* 2.9 15.1 + - - -
864A ALA* 3.3 15.2 - - + +
865A THR 3.5 19.7 + - - +
866A SER* 3.5 27.2 + - - +
868A ASP* 2.7 39.6 + - - +
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Residues in contact with ARG 860 (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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856A ARG* 2.9 58.9 + - - +
857A VAL 4.1 2.7 - - - +
859A ARG* 1.3 73.5 - - + +
861A LEU* 1.3 61.1 + - - +
862A GLY 3.5 0.4 + - - -
945A VAL* 4.3 19.9 + - + +
948A GLU* 3.3 45.4 + - - +
949A ALA* 3.4 7.4 - - - +
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Residues in contact with LEU 861 (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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857A VAL* 3.1 36.8 + - + +
859A ARG 3.0 1.0 - - - -
860A ARG* 1.3 81.3 - - - +
862A GLY* 1.3 60.6 + - - +
863A PHE* 3.4 23.6 + - + -
873A LYS* 2.7 30.3 + - - +
886A LEU* 4.3 10.1 - - + -
890A GLU* 4.0 11.2 - - + +
941A ARG* 3.9 24.7 - - + +
942A ILE* 4.3 16.6 - - + -
945A VAL* 4.1 27.1 - - + -
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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