Contacts of the helix formed by residues 878 - 889 (chain B) in PDB entry 4Z2M
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 SER 878 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805B GLY 4.7 2.8 + - - -
806B PHE* 3.9 16.4 - - - +
807B ASN 5.3 0.3 + - - -
874B ILE* 4.1 15.3 - - - -
875B PRO* 2.8 19.3 + - - +
877B ALA* 1.3 80.7 - - - +
879B LEU* 1.3 62.9 + - - +
880B ASP 3.3 1.6 - - - -
881B PRO* 3.3 10.8 - - - +
882B ILE* 3.1 34.5 + - - +
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Residues in contact with LEU 879 (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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845B PHE* 3.8 30.1 - - + -
848B VAL* 3.8 33.9 - - + -
855B PHE* 3.6 31.2 - - + -
875B PRO 3.8 1.6 + - - -
876B VAL* 2.8 28.4 + - + +
878B SER* 1.3 77.7 - - - +
880B ASP* 1.3 65.0 + - - +
882B ILE* 3.6 1.5 + - - +
883B LYS* 3.1 43.3 + - + +
895B GLU* 4.0 10.1 - - - +
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Residues in contact with ASP 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876B VAL 4.3 1.2 + - - -
877B ALA 4.3 1.7 + - - +
879B LEU* 1.3 82.0 - - - +
881B PRO* 1.3 75.3 - - + +
882B ILE 3.0 0.2 + - - -
883B LYS* 3.1 25.5 + - - +
884B GLU* 3.0 22.5 + - - +
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Residues in contact with PRO 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B LEU* 5.5 5.7 - - + +
877B ALA 3.2 22.9 - - - +
878B SER* 3.3 14.4 - - - +
880B ASP* 1.3 93.4 - - + +
882B ILE* 1.3 61.9 + - + +
884B GLU* 3.3 11.0 + - + +
885B TRP* 3.2 20.1 + - - +
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Residues in contact with ILE 882 (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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804B LEU 5.7 0.7 - - - +
806B PHE* 3.5 56.8 - - + -
845B PHE* 3.5 29.6 - - + -
855B PHE* 4.4 7.0 - - + -
857B MET* 4.6 9.2 - - + -
874B ILE* 4.2 9.9 - - + -
878B SER* 3.1 29.0 + - - +
879B LEU* 3.8 2.5 - - - +
881B PRO* 1.3 75.3 - - + +
883B LYS* 1.3 68.2 + - - +
885B TRP* 2.8 22.8 + - + +
886B LEU* 2.8 21.0 + - + +
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Residues in contact with LYS 883 (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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845B PHE* 4.0 14.6 - - + -
879B LEU* 3.1 32.5 + - - +
880B ASP* 3.1 23.7 + - - +
882B ILE* 1.3 78.3 - - - +
884B GLU* 1.3 62.6 + - - +
886B LEU* 3.1 7.7 + - - +
887B ASN* 3.0 28.7 + - - +
893B TYR* 3.6 43.9 + - + +
895B GLU* 2.3 34.9 + - - -
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Residues in contact with GLU 884 (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 ASP 3.0 11.8 + - - +
881B PRO* 3.5 12.0 - - - +
883B LYS* 1.3 77.5 - - - +
885B TRP* 1.3 62.1 + - - +
887B ASN* 3.4 11.7 + - - +
888B SER* 3.2 19.9 + - - -
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Residues in contact with TRP 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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801B PHE* 6.0 0.2 - - - -
804B LEU* 4.2 28.7 - - + +
806B PHE* 4.7 9.0 - + - -
819B PRO* 3.3 41.7 - - + +
820B THR 5.0 2.4 + - - -
824B LEU* 3.9 33.4 - - + -
837B LEU* 4.0 33.7 - - + -
857B MET* 4.7 5.4 - - + -
881B PRO 3.2 10.9 + - - +
882B ILE* 2.8 19.2 + - + +
884B GLU* 1.3 75.3 - - - +
886B LEU* 1.3 96.0 + - + +
888B SER* 2.7 27.0 + - - -
889B CYS* 3.1 24.8 + - - -
891B LEU* 5.0 1.6 - - + -
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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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843B ILE* 3.7 31.9 - - + -
845B PHE* 3.6 31.4 - - + -
857B MET* 4.8 3.1 - - + -
882B ILE* 2.8 18.3 + - + +
883B LYS* 3.1 7.8 + - - +
885B TRP* 1.3 104.0 - - + +
887B ASN* 1.3 63.5 + - - +
889B CYS* 3.0 7.8 + - - +
891B LEU* 3.0 55.4 + - + +
893B TYR* 3.8 15.7 - - + -
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Residues in contact with ASN 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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883B LYS 3.0 16.8 + - - -
884B GLU* 3.7 10.0 - - - +
885B TRP 3.2 0.2 - - - -
886B LEU* 1.3 72.6 - - - +
888B SER* 1.3 57.1 + - - +
889B CYS 2.9 5.4 - - - -
890B ASP* 2.9 26.8 + - - +
891B LEU 4.3 4.3 - - - +
892B LYS* 5.1 10.3 + - - +
893B TYR* 3.4 30.1 + - - -
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Residues in contact with SER 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B GLU* 3.2 7.3 + - - -
885B TRP* 2.7 35.6 + - - -
887B ASN* 1.3 77.8 - - - +
889B CYS* 1.3 60.3 + - - +
890B ASP* 3.5 2.1 - - - -
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Residues in contact with CYS 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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821B SER 5.6 1.6 - - - -
837B LEU* 4.2 18.6 - - + -
885B TRP* 3.1 38.8 + - - +
886B LEU 3.0 5.1 + - - +
887B ASN 2.9 1.4 - - - -
888B SER* 1.3 82.2 - - - +
890B ASP* 1.3 68.7 + - - +
891B LEU* 3.0 29.6 + - + +
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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