Contacts of the helix formed by residues 910 - 926 (chain H) in PDB entry 3AOH
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 LYS 910 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551H GLU* 4.2 12.5 + - - +
552H HIS* 6.0 3.4 - - + +
886H LEU* 6.1 0.7 - - - -
906H PHE 3.9 18.6 + - - -
907H ASP* 4.6 4.1 + - - +
908H GLY 3.9 17.4 + - - -
909H ALA* 1.3 76.0 - - - +
911H GLU* 1.3 70.1 + - + +
912H PRO* 3.2 12.9 - - + -
913H GLU* 2.6 25.4 + - + +
914H ILE* 3.2 25.2 + - - +
1063I GLU* 4.8 16.6 + - - +
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Residues in contact with GLU 911 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886H LEU* 5.6 7.0 - - + +
910H LYS* 1.3 74.9 - - + +
912H PRO* 1.3 74.3 - - + +
914H ILE* 3.4 11.4 + - + +
915H LYS* 3.3 45.9 + - - +
951I ILE* 3.8 21.1 - - + +
952I ASP* 4.3 2.1 - - - +
1062I ARG* 2.4 52.0 + - - +
1063I GLU* 5.4 5.5 - - - +
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Residues in contact with PRO 912 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910H LYS* 3.6 15.3 - - + -
911H GLU* 1.3 95.2 - - + +
913H GLU* 1.3 60.2 + - + +
915H LYS* 2.9 27.5 + - + +
916H GLU* 3.0 11.6 + - - +
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Residues in contact with GLU 913 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LYS* 5.8 3.9 + - - +
6H PHE* 4.2 25.2 - - + +
8H ARG* 4.1 27.5 + - - +
908H GLY 4.4 1.0 - - - +
909H ALA* 3.4 8.7 - - - -
910H LYS* 2.6 43.7 + - + +
912H PRO* 1.3 77.3 - - + +
914H ILE* 1.3 59.5 + - + +
916H GLU* 3.0 26.4 - - - +
917H LEU* 3.2 16.8 + - + +
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Residues in contact with ILE 914 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H PHE* 6.2 0.2 - - + -
549H PHE* 4.7 0.4 - - + -
886H LEU* 4.1 35.4 - - + -
889H HIS* 4.4 7.4 - - + -
890H LEU* 4.2 42.8 - - + +
893H ALA* 6.1 0.4 - - + -
909H ALA* 4.4 14.6 - - + -
910H LYS 3.2 19.7 + - - +
911H GLU* 3.6 9.4 - - + +
912H PRO 3.1 0.8 + - - -
913H GLU* 1.3 72.1 - - - +
915H LYS* 1.3 62.9 + - + +
916H GLU 2.9 1.9 + - - -
917H LEU* 3.0 10.2 + - + +
918H LEU* 2.7 46.0 + - + +
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Residues in contact with LYS 915 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889H HIS* 6.5 1.1 - - - -
911H GLU* 3.3 34.6 + - - +
912H PRO* 2.9 10.6 + - + +
914H ILE* 1.3 81.4 - - - +
916H GLU* 1.3 52.7 + - - +
918H LEU* 3.9 7.4 - - + -
919H ALA* 2.8 34.4 + - - +
968H LEU* 3.1 48.2 - - + +
969H GLN* 4.6 3.1 - - - +
951I ILE* 5.3 3.6 - - - -
952I ASP* 3.0 33.8 + - - -
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Residues in contact with GLU 916 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LYS* 6.1 2.5 - - - +
912H PRO 3.0 9.5 + - - +
913H GLU* 3.0 23.5 - - - +
915H LYS* 1.3 77.7 - - - +
917H LEU* 1.3 64.4 + - + +
919H ALA* 3.3 10.7 - - - +
920H GLN* 3.2 17.8 + - - +
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Residues in contact with LEU 917 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LYS* 4.4 23.3 - - + +
6H PHE* 3.7 22.9 - - + -
890H LEU* 5.8 2.7 - - + -
893H ALA* 4.1 5.4 - - + -
897H LEU* 3.4 26.7 - - + +
899H GLN* 4.9 7.0 - - - +
901H TYR* 3.6 25.8 - - + -
913H GLU 3.2 15.0 + - - +
914H ILE* 3.0 9.7 + - + +
916H GLU* 1.3 77.5 - - + +
918H LEU* 1.3 67.1 + - - +
920H GLN* 3.1 14.7 + - + +
921H ALA 2.8 17.3 + - - -
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Residues in contact with LEU 918 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889H HIS* 3.5 31.4 - - + +
892H LEU* 4.4 4.9 - - + -
893H ALA* 3.8 18.2 - - + +
914H ILE* 2.7 25.8 + - + +
915H LYS* 3.4 9.9 - - + +
917H LEU* 1.3 78.2 - - - +
919H ALA* 1.3 63.7 + - - +
921H ALA* 2.8 16.6 + - - +
922H PHE 3.0 9.9 + - - -
967H PHE* 3.1 37.3 - - + +
968H LEU* 3.1 34.1 - - + +
970H GLY* 4.0 10.3 - - - +
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Residues in contact with ALA 919 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915H LYS 2.8 14.7 + - - +
916H GLU* 3.3 15.7 - - - +
917H LEU 3.1 0.2 - - - -
918H LEU* 1.3 75.2 - - - +
920H GLN* 1.3 63.4 + - - +
922H PHE* 2.9 22.3 + - - +
923H GLU* 3.6 4.0 + - - +
964H LYS* 3.7 22.5 + - - +
968H LEU* 3.9 14.6 - - + +
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Residues in contact with GLN 920 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897H LEU* 3.8 16.3 - - + +
899H GLN* 4.2 11.6 + - - -
916H GLU 3.2 8.4 + - - +
917H LEU* 3.1 19.4 - - + +
919H ALA* 1.3 78.4 - - - +
921H ALA* 1.3 63.0 + - - +
923H GLU* 3.0 22.7 + - - +
924H VAL* 3.6 11.7 - - - +
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Residues in contact with ALA 921 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893H ALA* 3.9 12.1 - - - -
896H PHE* 4.0 8.0 - - + +
897H LEU* 3.1 27.5 - - + +
917H LEU 2.8 9.5 + - - +
918H LEU 2.8 13.3 + - - +
920H GLN* 1.3 78.0 - - - +
922H PHE* 1.3 60.3 + - - +
924H VAL* 3.2 5.6 + - - +
925H TYR* 3.0 25.1 + - - +
967H PHE* 3.5 18.2 - - + -
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Residues in contact with PHE 922 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918H LEU 3.0 4.4 + - - +
919H ALA* 2.9 14.7 + - - +
921H ALA* 1.3 76.7 - - - +
923H GLU* 1.3 65.4 + - - +
924H VAL 3.1 0.4 - - - -
925H TYR* 4.6 7.0 - + - +
926H PHE* 2.9 65.6 + + + +
927H GLY 3.5 0.3 + - - -
960H GLU* 4.0 11.9 - - - -
963H LEU* 3.5 26.2 - - + -
964H LYS* 3.4 53.4 - - + +
967H PHE* 3.3 39.5 - + + -
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Residues in contact with GLU 923 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919H ALA 3.9 1.8 - - - +
920H GLN* 3.0 15.9 + - - +
922H PHE* 1.3 82.7 - - - +
924H VAL* 1.3 60.2 + - + +
927H GLY* 3.1 27.2 - - - +
928H LYS 4.1 0.3 + - - -
930H LYS* 4.5 14.9 + - - +
960H GLU* 5.6 0.2 - - - +
964H LYS* 3.4 23.5 + - - -
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Residues in contact with VAL 924 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896H PHE* 2.9 38.6 - - + +
897H LEU* 4.1 11.2 - - + -
920H GLN* 3.6 23.1 - - - +
921H ALA 3.4 6.3 - - - +
922H PHE 3.1 0.2 - - - -
923H GLU* 1.3 80.7 - - + +
925H TYR* 1.3 66.2 + - - +
928H LYS* 3.6 22.2 + - - +
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Residues in contact with TYR 925 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H LEU* 3.3 26.8 - - + +
862H PRO* 3.2 33.9 - - + +
863H ASP* 4.4 11.7 - - + -
896H PHE* 3.0 39.0 - + + -
921H ALA 3.0 9.9 + - - +
922H PHE* 4.3 7.4 - + - +
924H VAL* 1.3 84.6 - - - +
926H PHE* 1.3 72.9 + + + +
928H LYS* 4.6 2.3 - - - +
929H ARG* 3.7 24.1 + - + +
940H GLU* 4.5 4.0 + - - -
963H LEU* 5.6 7.6 - - + -
967H PHE* 3.7 30.3 - + + -
972H VAL* 4.7 13.2 - - + +
973H VAL* 5.7 0.7 + - - +
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Residues in contact with PHE 926 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922H PHE* 2.9 43.7 + + + +
925H TYR* 1.3 85.6 - + + +
927H GLY* 1.3 61.5 + - - +
928H LYS 3.3 2.0 - - - -
929H ARG* 2.9 47.6 - - + +
930H LYS* 2.9 28.0 + - + +
934H PHE 5.5 1.1 - - - -
935H GLY* 4.3 12.8 - - - -
936H VAL* 4.2 22.7 - - + -
940H GLU* 4.7 8.7 - - - -
960H GLU* 3.2 47.1 - - - -
963H LEU* 5.2 11.0 - - + -
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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
------------------------------------------------------------
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