Contacts of the helix formed by residues 884 - 894 (chain B) in PDB entry 6IEH
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 ASP 884 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567B TYR* 5.4 1.7 - - - -
883B ALA* 1.3 73.4 - - - +
885B GLU* 1.3 63.4 + - - +
886B LEU* 3.2 18.4 + - - +
887B LEU* 3.3 12.8 + - + +
888B LEU* 1.8 33.2 - - + +
912B PHE* 4.6 1.8 + - + -
958B TYR* 2.3 41.3 + - - -
962B PHE* 4.1 17.3 - - + -
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Residues in contact with GLU 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B THR* 5.1 2.3 + - - -
567B TYR* 3.6 26.4 + - + +
568B ASN* 3.2 36.0 + - + +
571B LEU* 5.7 0.9 - - + -
877B ALA* 3.7 23.1 - - + +
880B ILE* 3.2 29.0 - - + +
881B SER* 4.6 1.7 - - - -
883B ALA 2.8 14.5 + - - +
884B ASP* 1.3 77.6 - - - +
886B LEU* 1.3 68.3 + - + +
888B LEU* 3.4 9.6 - - - -
889B THR* 3.2 27.6 + - - +
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Residues in contact with LEU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B TYR* 3.8 48.9 - - + -
571B LEU* 5.6 2.5 - - + -
857B VAL* 4.4 8.5 - - + -
858B LEU* 4.2 10.1 - - + -
861B LEU* 3.9 20.9 - - + -
863B PHE* 3.5 38.6 - - + -
877B ALA* 5.7 0.2 - - + -
884B ASP* 3.2 10.8 + - - +
885B GLU* 1.3 83.4 - - + +
887B LEU* 1.3 62.1 + - - +
890B GLU* 3.3 23.6 + - - +
942B ILE* 4.5 17.9 - - + +
946B SER* 5.9 0.4 - - - +
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Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884B ASP* 3.3 17.2 + - - +
885B GLU 3.2 0.4 - - - -
886B LEU* 1.3 78.4 - - - +
888B LEU* 1.3 54.7 - - - +
890B GLU* 3.2 4.5 + - + +
891B MET* 2.6 62.7 + - + +
912B PHE* 4.1 8.1 - - + -
935B MET* 4.3 6.3 - - + +
938B CYS* 4.1 22.0 - - + +
939B ALA* 3.8 26.0 - - + +
942B ILE* 4.8 6.7 - - + +
958B TYR* 3.8 9.2 + - - +
962B PHE* 3.5 32.3 - - + -
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Residues in contact with LEU 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B ILE* 2.8 44.6 - - + -
883B ALA* 4.6 0.7 - - + -
884B ASP* 1.8 46.4 - - - +
885B GLU* 3.5 7.4 - - - -
887B LEU* 1.3 78.3 - - - +
889B THR* 1.3 56.3 + - - +
891B MET* 3.2 8.2 + - - +
892B MET* 2.7 31.3 + - - +
897B PHE* 4.5 0.2 - - - -
912B PHE* 2.6 48.2 - - + -
1003B LEU* 4.3 3.1 - - + -
1007B MET* 3.1 29.6 - - + +
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Residues in contact with THR 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B PHE* 2.8 30.2 - - - -
873B LYS* 4.1 9.8 + - - +
876B VAL* 4.2 8.7 - - + -
877B ALA* 3.4 35.2 - - + +
880B ILE* 4.0 11.7 - - + -
885B GLU 3.2 16.6 + - - +
888B LEU* 1.3 75.6 - - - +
890B GLU* 1.3 56.4 + - - +
892B MET* 3.3 8.5 - - - +
893B PHE* 2.7 37.4 + - - -
1010B ALA* 6.1 0.2 - - + -
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Residues in contact with GLU 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B LEU* 5.6 2.7 - - + -
863B PHE* 4.7 7.9 - - + -
873B LYS* 4.6 10.3 - - - +
886B LEU 3.3 16.8 + - - +
887B LEU* 3.2 6.1 + - - +
889B THR* 1.3 78.7 + - - +
891B MET* 1.3 57.8 + - - +
893B PHE* 3.0 8.0 + - - +
894B ASN* 2.8 29.4 + - - +
938B CYS* 4.7 8.5 - - - -
942B ILE* 4.7 16.8 - - + -
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Residues in contact with MET 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B LEU* 2.6 38.9 + - + +
888B LEU* 3.3 4.7 - - - +
890B GLU* 1.3 73.0 - - - +
892B MET* 1.3 62.5 + - - +
894B ASN* 3.2 11.1 + - - +
895B GLY 3.3 8.0 + - - -
896B LEU* 3.3 31.4 + - + +
897B PHE* 3.7 22.4 - - + -
908B LEU* 4.7 14.4 - - + -
912B PHE* 3.6 17.7 - - + -
935B MET* 3.1 52.3 - - + -
938B CYS* 4.1 12.5 - - + -
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Residues in contact with MET 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B VAL* 5.4 2.9 - - - -
880B ILE* 5.7 1.1 - - - -
888B LEU 2.7 19.7 + - - +
889B THR* 3.1 17.0 + - - +
891B MET* 1.3 73.0 - - - +
893B PHE* 1.3 65.3 + - + +
895B GLY* 3.0 19.3 + - - -
897B PHE* 4.2 22.2 - - + +
1007B MET* 4.5 12.8 - - + +
1010B ALA* 4.7 13.5 - - + -
1011B ALA* 4.0 31.9 - - + +
1014B ILE* 5.0 10.5 - - + -
1019B LEU* 4.2 23.9 - - + +
1023B PHE* 3.9 23.8 - - + -
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Residues in contact with PHE 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B MET* 4.9 4.7 - - - -
873B LYS* 3.6 57.0 - - + +
876B VAL* 4.7 8.5 - - + -
889B THR* 2.7 26.6 + - - +
890B GLU 3.0 4.9 + - - +
892B MET* 1.3 80.9 - - + +
894B ASN* 1.3 57.9 + - - +
895B GLY 3.2 0.9 - - - -
1014B ILE* 3.8 35.0 - - + -
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Residues in contact with ASN 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890B GLU 2.8 14.6 + - - +
891B MET* 3.2 7.8 + - - +
893B PHE* 1.3 76.1 - - - +
895B GLY* 1.3 59.3 + - - +
896B LEU* 3.2 21.4 + - - +
934B GLN* 5.5 2.3 - - - +
938B CYS* 4.7 13.0 - - - +
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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