Contacts of the helix formed by residues 886 - 898 (chain A) in PDB entry 4Z7I
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 886 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A THR* 5.4 5.0 + - - -
884A ILE* 3.7 6.3 - - - +
885A GLY* 1.3 71.4 - - - +
887A GLU* 1.3 53.6 + - - +
888A ALA* 4.4 2.8 + - - +
889A GLU* 3.2 35.3 + - - +
890A LYS* 2.6 36.4 + - - +
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Residues in contact with GLU 887 (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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425A PHE* 3.9 19.1 - - + -
441A GLU* 3.5 30.1 - - + +
881A TYR* 5.0 2.6 + - - -
885A GLY 2.9 9.9 + - - +
886A SER* 1.3 70.7 + - - +
888A ALA* 1.3 60.4 + - - +
890A LYS* 3.5 31.8 + - - +
891A ASN* 3.0 48.9 + - - +
920A ARG* 3.3 25.1 + - - -
923A LYS* 4.7 0.5 - - - -
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Residues in contact with ALA 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER* 5.9 1.3 - - - +
454A ASP* 3.3 34.8 - - - +
886A SER* 3.4 3.1 + - - +
887A GLU* 1.3 78.3 - - - +
889A GLU* 1.3 60.1 + - - +
891A ASN* 3.5 6.5 + - - +
892A LYS* 3.2 31.8 + - - +
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Residues in contact with GLU 889 (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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846A TRP* 4.5 12.6 + - - -
851A GLY 5.8 0.2 - - - +
860A MET* 3.9 33.4 - - - +
864A PHE* 4.1 15.3 - - + -
884A ILE* 3.4 25.3 - - + +
886A SER* 3.2 27.9 + - - +
888A ALA* 1.3 77.2 - - - +
890A LYS* 1.3 64.3 + - - +
891A ASN 3.1 0.4 - - - -
892A LYS* 3.2 6.4 + - - +
893A ILE* 3.0 29.8 + - + +
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Residues in contact with LYS 890 (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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880A LYS 4.9 0.7 - - - +
881A TYR* 3.0 76.4 + - + +
884A ILE* 3.4 32.2 + - + +
885A GLY* 4.2 5.4 - - - +
886A SER 2.6 24.8 + - - +
887A GLU* 3.4 35.7 + - - +
889A GLU* 1.3 72.9 - - - +
891A ASN* 1.3 58.6 + - - +
893A ILE* 3.4 4.3 + - - +
894A LEU* 3.1 16.5 + - - +
920A ARG* 5.9 5.3 - - - +
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Residues in contact with ASN 891 (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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441A GLU* 5.3 1.6 + - - -
881A TYR* 5.1 1.6 + - - -
887A GLU* 3.0 42.0 + - - +
888A ALA* 3.8 7.0 - - - +
889A GLU 3.1 0.4 - - - -
890A LYS* 1.3 77.7 - - - +
892A LYS* 1.3 63.6 + - + +
894A LEU* 4.1 4.2 - - - +
895A GLU* 3.5 17.7 + - - +
923A LYS* 2.5 44.6 + - - +
926A PHE* 3.8 20.0 - - + -
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Residues in contact with LYS 892 (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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451A SER* 4.2 12.5 + - - -
453A ALA* 6.3 2.2 - - - -
454A ASP* 5.4 2.2 - - - -
857A THR* 2.5 46.9 + - - +
860A MET* 3.6 24.1 - - + +
861A THR* 3.2 31.1 + - + +
864A PHE* 3.8 20.2 - - + +
888A ALA* 3.2 16.6 + - - +
889A GLU 3.2 8.4 + - - +
891A ASN* 1.3 75.0 - - - +
893A ILE* 1.3 64.4 + - - +
895A GLU* 3.7 9.8 + - - +
896A ALA* 3.4 16.6 + - - +
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Residues in contact with ILE 893 (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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846A TRP* 4.8 2.0 - - + -
864A PHE* 3.4 28.9 - - + -
877A LEU* 3.2 39.7 - - + +
880A LYS* 3.6 34.5 - - + +
881A TYR* 4.2 12.6 - - + -
884A ILE* 4.4 11.7 - - + -
889A GLU* 3.0 22.0 + - + +
890A LYS* 3.6 7.9 - - - +
891A ASN 3.3 0.2 - - - -
892A LYS* 1.3 76.5 - - - +
894A LEU* 1.3 65.1 + - - +
896A ALA* 3.2 7.6 + - - +
897A LEU* 3.0 23.6 + - + +
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Residues in contact with LEU 894 (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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881A TYR* 4.3 9.0 - - + +
890A LYS 3.1 16.1 + - - +
891A ASN* 4.1 7.0 - - - +
892A LYS 3.4 0.2 - - - -
893A ILE* 1.3 76.9 - - - +
895A GLU* 1.3 64.2 + - - +
897A LEU* 3.1 15.2 + - + +
898A ALA* 3.0 21.1 + - - +
909A LEU* 4.7 2.9 - - + -
919A PHE* 3.6 35.2 - - + -
923A LYS* 3.6 35.9 - - + -
926A PHE* 3.8 14.1 - - + -
927A ILE* 3.7 33.0 - - + -
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Residues in contact with GLU 895 (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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825A GLU* 4.2 6.2 - - - +
861A THR* 4.0 18.6 + - + +
865A LYS* 3.4 23.0 + - + +
891A ASN 3.5 8.2 + - - +
892A LYS* 3.7 12.1 - - - +
893A ILE 3.3 0.2 - - - -
894A LEU* 1.3 77.8 - - - +
896A ALA* 1.3 60.7 - - - +
898A ALA* 3.3 4.0 + - - -
899A SER* 2.9 28.6 + - - +
926A PHE* 3.8 32.7 - - + -
930A THR* 3.8 17.0 - - + +
933A ARG* 5.0 9.9 + - - -
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Residues in contact with ALA 896 (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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864A PHE* 3.4 46.4 - - + +
865A LYS* 3.6 15.0 - - + +
868A ALA* 3.3 18.2 - - + +
877A LEU* 4.3 4.9 - - + -
892A LYS 3.4 3.6 + - - +
893A ILE 3.2 10.2 + - - +
895A GLU* 1.3 79.0 - - - +
897A LEU* 1.3 62.2 + - - +
899A SER* 2.9 15.9 + - - -
900A SER 3.6 1.2 + - - -
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Residues in contact with LEU 897 (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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874A TRP* 2.9 63.8 + - + +
877A LEU* 3.9 17.5 - - + +
878A LEU* 3.9 32.3 - - + +
881A TYR* 4.9 2.5 - - + -
893A ILE* 3.0 20.8 + - + +
894A LEU* 3.1 14.6 + - + +
896A ALA* 1.3 76.0 - - - +
898A ALA* 1.3 56.6 + - - +
899A SER 3.2 2.3 + - - -
900A SER* 3.6 7.8 - - - -
906A LEU* 4.1 0.3 - - - +
909A LEU* 3.3 20.7 - - + +
919A PHE* 4.0 19.7 - - + -
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Residues in contact with ALA 898 (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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894A LEU* 3.0 14.8 + - + +
895A GLU 3.6 2.5 - - - -
897A LEU* 1.3 74.3 - - - +
899A SER* 1.3 56.4 + - - +
900A SER 3.4 3.8 - - - +
906A LEU* 3.6 14.2 - - - +
909A LEU* 3.6 13.9 - - + -
927A ILE* 4.4 12.1 - - + +
930A THR* 3.5 31.3 - - + +
931A VAL* 3.8 27.0 - - + -
934A HIS* 4.8 1.2 + - - -
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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