Contacts of the helix formed by residues 881 - 898 (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 ASN 881 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553H ASP* 3.2 22.7 - - + +
557H ARG* 3.0 38.7 - - + +
843H HIS* 3.7 17.1 + - + +
844H GLY 4.7 4.8 - - - -
845H ASN* 4.8 1.2 - - - +
875H GLY 4.7 0.3 - - - +
876H VAL* 3.9 15.4 + - - +
879H ARG* 3.6 11.8 + - - +
880H MET* 1.3 75.2 - - - +
882H LEU* 1.3 67.0 + - - +
883H GLY 3.1 2.2 - - - -
884H GLN* 2.9 38.7 + - - +
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Residues in contact with LEU 882 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H HIS* 3.2 16.5 + - + +
876H VAL* 4.9 9.2 - - + +
881H ASN* 1.3 73.2 - - - +
883H GLY* 1.3 55.6 + - - +
885H ILE* 2.6 45.8 + - + +
886H LEU* 3.0 8.6 + - - +
949I ILE* 5.1 7.2 - - + -
951I ILE* 3.8 28.9 - - + -
954I ALA* 5.1 6.7 - - + -
1020I LEU* 6.2 1.3 - - + -
1038I LEU* 4.0 26.0 - - + -
1061I PHE* 3.4 41.5 - - + +
1062I ARG* 3.7 7.9 - - + +
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Residues in contact with GLY 883 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549H PHE* 3.5 19.7 - - - -
552H HIS* 3.8 4.3 - - - +
553H ASP* 2.6 25.0 + - - -
843H HIS* 3.1 21.0 + - - -
882H LEU* 1.3 71.1 - - - +
884H GLN* 1.3 50.0 + - - +
886H LEU* 3.0 6.7 + - - +
887H GLU 2.7 31.7 + - - -
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Residues in contact with GLN 884 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841H ASN* 3.2 18.9 + - - +
843H HIS* 3.0 34.6 - - + -
845H ASN* 2.9 30.0 + - - +
871H LEU* 4.7 0.9 - - - +
875H GLY 5.0 0.6 + - - -
876H VAL* 3.5 31.3 - - - +
881H ASN* 2.9 39.4 + - - +
882H LEU 2.7 4.0 + - - -
883H GLY* 1.3 66.5 - - - +
885H ILE* 1.3 68.8 + - - +
886H LEU 2.9 1.5 + - - -
887H GLU* 3.1 4.0 + - - +
888H THR* 2.9 28.3 + - - -
992H MET* 3.7 11.3 - - + +
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Residues in contact with ILE 885 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676H ILE* 4.9 11.7 - - + -
876H VAL* 3.9 28.5 - - + -
881H ASN 4.7 0.7 - - - +
882H LEU* 2.6 28.3 + - + +
884H GLN* 1.3 75.1 - - + +
886H LEU* 1.3 59.6 + - - +
888H THR* 3.5 7.4 + - - -
889H HIS* 2.7 35.0 + - + -
988H VAL* 5.5 2.0 - - + -
949I ILE* 3.4 37.2 - - + +
950I GLY* 3.6 9.6 - - - -
951I ILE* 3.3 33.2 - - + +
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Residues in contact with LEU 886 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549H PHE* 3.1 37.7 - - + -
552H HIS* 3.8 22.9 - - + +
882H LEU 3.0 5.8 + - - +
883H GLY* 3.0 13.2 + - - +
884H GLN 2.9 1.6 - - - -
885H ILE* 1.3 74.2 - - - +
887H GLU* 1.3 57.3 + - - +
888H THR 2.9 1.6 - - - -
889H HIS* 2.5 34.8 + - + +
890H LEU* 3.1 8.7 + - - +
909H ALA 5.6 2.7 - - - +
910H LYS* 6.3 0.2 - - - -
911H GLU* 5.6 8.1 - - + +
914H ILE* 4.1 21.8 - - + -
951I ILE* 3.8 40.2 - - + -
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Residues in contact with GLU 887 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H PRO* 4.9 1.8 - - + -
549H PHE* 3.4 14.6 - - + -
578H VAL* 4.6 0.3 - - - +
579H VAL* 3.4 22.9 - - + +
841H ASN* 5.0 1.4 - - - +
842H ARG* 3.0 26.1 + - - -
843H HIS* 3.6 23.5 + - - +
883H GLY 2.7 15.4 + - - +
884H GLN 3.5 7.0 - - - +
886H LEU* 1.3 72.3 - - - +
888H THR* 1.3 51.6 + - - +
890H LEU* 3.4 2.1 + - - +
891H GLY* 2.6 34.5 + - - -
991H GLN 4.0 6.3 - - - +
992H MET* 3.0 14.7 - - + +
993H PHE* 2.3 39.5 + - - +
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Residues in contact with THR 888 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674H VAL* 4.3 9.3 - - + +
676H ILE* 6.0 2.9 - - + -
884H GLN 2.9 16.8 + - - -
885H ILE* 3.6 8.4 - - - -
886H LEU 2.7 3.6 + - - -
887H GLU* 1.3 73.0 - - - +
889H HIS* 1.3 64.0 + - - -
892H LEU* 3.0 17.2 + - - +
988H VAL* 4.1 14.8 - - + -
989H VAL* 3.7 7.1 - - - +
990H GLY* 3.4 34.3 - - - +
991H GLN 4.4 7.0 - - - -
992H MET* 3.7 22.0 - - - +
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Residues in contact with HIS 889 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885H ILE* 2.7 29.4 + - + -
886H LEU* 2.5 24.2 + - + +
888H THR* 1.3 70.6 - - - +
890H LEU* 1.3 67.2 + - - +
892H LEU* 2.7 23.4 + - + +
893H ALA 3.3 2.6 + - - -
914H ILE* 4.4 13.2 - - + -
915H LYS* 6.5 1.3 - - - -
918H LEU* 3.5 12.8 - - + +
969H GLN 3.5 12.4 + - - -
970H GLY* 3.2 35.8 + - - -
971H LYS* 5.5 0.2 - - - +
988H VAL* 3.8 16.8 - - + +
950I GLY* 3.8 5.0 - - - -
951I ILE* 3.3 36.8 - - + +
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Residues in contact with LEU 890 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H PHE* 4.3 14.6 - - + -
549H PHE* 3.8 24.9 - - + -
578H VAL 4.6 0.7 - - - +
579H VAL* 3.9 20.0 - - + -
886H LEU 3.1 6.2 + - - +
887H GLU* 3.7 9.0 - - - +
889H HIS* 1.3 77.4 - - - +
891H GLY* 1.3 58.1 + - - +
893H ALA* 2.7 31.4 + - + +
894H GLY 3.0 8.3 + - - -
901H TYR* 3.1 46.0 - - + -
903H SER* 5.3 0.2 - - - -
909H ALA* 4.2 16.6 - - + -
914H ILE* 4.2 24.0 - - + +
917H LEU* 5.8 2.2 - - + -
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Residues in contact with GLY 891 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H VAL* 4.3 11.2 - - - -
887H GLU 2.6 22.9 + - - -
888H THR 3.7 1.1 - - - -
890H LEU* 1.3 76.2 - - - +
892H LEU* 1.3 58.2 + - - +
894H GLY* 3.4 2.1 + - - -
895H TYR* 3.2 3.1 + - - +
991H GLN* 3.0 54.6 - - - +
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Residues in contact with LEU 892 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673H LEU* 6.2 0.9 - - + -
861H LEU* 6.3 1.1 - - + -
888H THR 3.0 5.8 + - - +
889H HIS* 2.7 21.4 + - - +
891H GLY* 1.3 69.4 - - - +
893H ALA* 1.3 65.3 + - - +
895H TYR* 3.4 15.1 + - + +
896H PHE* 3.7 20.9 + - + +
918H LEU* 4.4 6.1 - - + -
921H ALA* 4.8 0.7 - - - +
967H PHE* 4.2 34.3 - - + +
970H GLY* 3.9 28.5 - - - +
972H VAL* 4.7 3.8 - - + -
989H VAL* 3.5 43.1 - - + +
990H GLY* 4.1 5.4 - - - -
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Residues in contact with ALA 893 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889H HIS 3.3 1.2 + - - -
890H LEU* 2.7 14.4 + - - +
892H LEU* 1.3 74.3 - - - +
894H GLY* 1.3 56.2 + - - +
895H TYR 2.9 0.9 + - - -
896H PHE* 3.1 2.9 + - - -
897H LEU* 2.7 63.5 + - + +
901H TYR* 3.8 5.2 - - + +
914H ILE* 6.1 0.2 - - + -
917H LEU* 4.0 13.7 - - + +
918H LEU* 3.8 18.6 - - + +
921H ALA* 3.9 8.3 - - - -
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Residues in contact with GLY 894 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H VAL* 6.0 2.7 - - - -
890H LEU 3.0 10.7 + - - -
891H GLY* 3.4 6.0 + - - -
892H LEU 3.3 0.2 - - - -
893H ALA* 1.3 76.6 - - - +
895H TYR* 1.3 53.0 + - - +
897H LEU* 4.3 0.4 - - - -
898H GLY* 2.6 32.2 + - - -
899H GLN 3.1 25.4 + - - -
901H TYR* 3.4 11.5 + - - -
991H GLN* 3.1 6.9 + - - +
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Residues in contact with TYR 895 (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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175F ARG* 5.9 0.7 + - - -
673H LEU* 4.0 31.2 - - + +
865H THR* 3.6 23.4 + - + -
891H GLY 3.2 3.2 + - - +
892H LEU* 3.6 12.8 - - + +
893H ALA 2.9 2.6 + - - -
894H GLY* 1.3 80.8 - - - +
896H PHE* 1.3 91.0 + + + +
898H GLY* 3.1 8.7 + - - -
990H GLY 6.3 0.2 - - - -
991H GLN* 2.6 40.4 + - + +
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Residues in contact with PHE 896 (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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673H LEU* 6.3 0.7 - - + -
861H LEU* 4.5 17.0 - - + -
863H ASP* 4.6 9.0 - - - -
865H THR* 5.4 0.7 - - + -
892H LEU* 3.7 24.9 + - + -
893H ALA 3.1 4.5 + - - +
895H TYR* 1.3 106.0 - + + +
897H LEU* 1.3 60.2 + - - +
898H GLY 3.7 0.2 + - - -
921H ALA* 4.0 17.5 - - + +
924H VAL* 2.9 35.7 - - + +
925H TYR* 3.0 64.2 - + + -
967H PHE* 4.9 4.0 - + - -
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Residues in contact with LEU 897 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893H ALA* 2.7 52.7 + - + +
896H PHE* 1.3 74.9 - - - +
898H GLY* 1.3 67.6 + - - +
899H GLN* 3.1 31.0 + - + +
901H TYR* 3.2 11.4 - - - +
917H LEU* 3.4 19.5 - - + +
920H GLN* 3.7 19.7 - - - +
921H ALA* 3.1 36.1 - - + +
924H VAL* 4.1 6.1 - - + -
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Residues in contact with GLY 898 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.3 26.3 - - - +
2H GLU 3.8 0.7 + - - -
894H GLY 2.6 17.8 + - - -
895H TYR 3.1 9.6 + - - -
896H PHE 3.3 0.6 - - - -
897H LEU* 1.3 77.7 - - - +
899H GLN* 1.3 58.1 + - - +
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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
------------------------------------------------------------
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