Contacts of the helix formed by residues 872 - 891 (chain A) in PDB entry 3OPY
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 872 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.7 16.4 - - - -
381A ILE* 5.7 0.7 - - - -
742A ASP* 2.9 29.9 + - - +
743A THR* 2.8 18.1 + - - -
746A ASN* 3.9 12.8 - - - -
870A SER 3.5 1.4 + - - -
871A PRO* 1.3 76.0 - - - +
873A SER* 1.3 58.9 + - - +
874A ILE 3.4 1.0 + - - -
875A ASP* 3.1 21.2 + - - +
876A ARG* 2.9 27.1 + - - +
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Residues in contact with SER 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 4.1 8.6 + - - -
377A LEU* 3.6 37.7 - - - +
378A GLU* 2.7 27.9 + - - +
381A ILE* 4.6 8.3 - - - +
417A ALA* 4.4 11.0 - - - -
872A SER* 1.3 67.7 - - - +
874A ILE* 1.4 58.3 + - - +
876A ARG* 3.2 11.3 + - - +
877A VAL* 2.8 41.3 + - - +
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Residues in contact with ILE 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 3.5 38.8 - - + -
501A CYS* 5.8 0.7 - - - -
503A PHE* 3.8 33.9 - - + -
737A TYR* 3.7 22.9 - - + +
742A ASP* 3.6 27.1 - - + +
872A SER* 3.4 1.4 + - - -
873A SER* 1.4 80.3 + - - +
875A ASP* 1.3 57.8 + - - +
877A VAL* 4.0 3.9 - - - +
878A ASN* 3.0 45.3 + - - +
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Residues in contact with ASP 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA* 4.4 6.0 - - + +
615A PRO* 5.9 0.2 - - - -
737A TYR* 2.4 30.7 + - - -
739A LEU* 3.7 6.5 - - - +
740A GLY* 2.9 30.0 + - - -
743A THR* 2.6 39.6 + - - +
871A PRO* 4.1 9.6 - - + -
872A SER* 3.1 19.3 + - - +
874A ILE* 1.3 77.2 - - - +
876A ARG* 1.4 52.0 + - - +
879A ALA* 2.9 36.9 + - - +
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Residues in contact with ARG 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ILE* 4.0 15.4 - - - +
385A ASP* 2.8 42.1 + - - -
416A ILE* 4.4 2.8 - - - +
417A ALA* 2.8 48.1 + - - +
418A THR* 4.6 1.6 - - - +
615A PRO* 4.9 8.2 - - + +
659A HIS* 3.9 21.7 + - + +
660A ASN* 3.6 16.2 + - - +
870A SER* 3.8 12.7 - - - -
871A PRO* 2.8 32.9 + - + +
872A SER 2.9 21.0 + - - +
873A SER* 3.5 5.2 - - - +
875A ASP* 1.4 70.4 - - - +
877A VAL* 1.3 63.5 + - - +
879A ALA* 3.8 5.7 - - - +
880A CYS* 3.3 22.5 + - - +
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A MET* 3.7 53.6 - - + +
416A ILE* 4.0 24.7 - - + +
417A ALA* 4.5 4.5 - - + +
576A SER* 4.6 8.1 - - - +
873A SER* 2.8 26.6 + - - +
874A ILE* 4.1 4.7 - - - +
876A ARG* 1.3 72.8 - - - +
878A ASN* 1.3 67.4 + - - +
880A CYS* 3.3 5.9 + - - +
881A ARG* 3.1 23.3 + - + +
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Residues in contact with ASN 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A TYR* 3.9 15.7 - - + -
739A LEU* 3.8 16.2 - - + -
874A ILE* 3.0 37.9 + - - +
877A VAL* 1.3 74.6 - - - +
879A ALA* 1.3 60.7 + - - +
880A CYS 3.1 1.6 - - - -
881A ARG* 3.2 20.3 + - - +
882A LEU* 2.9 40.7 + - + +
940A ILE* 4.4 15.5 - - - +
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Residues in contact with ALA 879 (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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612A ALA* 4.3 5.4 - - + +
615A PRO* 4.3 7.6 - - + -
616A ALA* 3.8 33.6 - - + +
619A VAL* 5.1 0.4 - - - -
724A LEU* 4.9 0.3 - - - +
739A LEU* 3.5 20.5 - - + +
875A ASP 2.9 24.4 + - - +
876A ARG 3.8 5.4 - - - +
877A VAL 3.4 0.2 - - - -
878A ASN* 1.3 70.9 - - - +
880A CYS* 1.3 56.4 - - - +
882A LEU* 4.5 0.2 - - - +
883A ALA* 3.0 31.9 + - - +
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Residues in contact with CYS 880 (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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416A ILE* 4.1 22.0 - - + -
579A ASN* 4.1 11.7 - - - -
583A VAL* 4.2 10.5 - - - -
619A VAL* 3.6 29.2 - - + +
876A ARG 3.3 10.4 + - - +
877A VAL 3.3 9.6 + - - +
878A ASN 3.1 0.6 - - - -
879A ALA* 1.3 78.1 - - - +
881A ARG* 1.4 64.3 + - - +
884A ILE* 3.2 47.6 + - - +
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Residues in contact with ARG 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A THR* 3.8 35.4 - - - +
579A ASN* 3.3 22.0 + - - +
877A VAL* 3.1 16.4 + - + +
878A ASN* 3.2 23.0 + - - +
880A CYS* 1.4 75.8 - - - +
882A LEU* 1.3 60.2 + - + +
884A ILE* 3.5 4.9 + - - +
885A LYS* 3.1 39.2 + - + +
940A ILE* 5.4 3.6 - - - +
943A SER* 2.9 31.7 + - - -
944A GLU* 3.9 2.4 - - - +
945A VAL* 3.6 35.5 - - + +
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Residues in contact with LEU 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A LEU* 3.5 27.1 - - + -
725A PRO* 5.6 1.6 - - + +
737A TYR 5.3 3.6 - - - +
739A LEU* 4.2 17.0 - - + -
878A ASN* 2.9 20.9 + - + +
879A ALA 4.5 0.9 - - - +
881A ARG* 1.3 77.0 - - + +
883A ALA* 1.4 59.4 + - - +
884A ILE 3.2 0.2 - - - -
885A LYS* 3.1 4.8 + - - +
886A CYS* 2.8 32.6 + - - -
938A ILE* 3.8 32.2 - - + +
939A GLY* 4.3 2.7 - - - +
940A ILE* 3.7 33.2 - - + -
945A VAL* 4.1 20.6 - - + -
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Residues in contact with ALA 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ALA* 3.3 25.4 - - - +
619A VAL* 3.9 8.7 - - + -
620A ALA* 3.7 17.7 - - + +
724A LEU* 4.0 12.7 - - + +
879A ALA 3.0 23.1 + - - +
882A LEU* 1.4 73.7 - - - +
884A ILE* 1.4 62.3 + - - +
886A CYS* 3.1 6.9 + - - +
887A CYS* 3.1 29.5 + - - -
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Residues in contact with ILE 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ASN* 3.4 34.5 - - + +
582A SER* 5.1 3.1 - - - -
583A VAL* 3.9 11.0 - - + -
586A TYR* 3.3 25.6 - - - +
619A VAL* 3.8 7.2 - - + -
623A ASN* 3.7 13.0 + - - +
880A CYS* 3.2 33.8 + - - +
881A ARG 3.5 6.3 - - - +
883A ALA* 1.4 77.8 - - - +
885A LYS* 1.3 62.7 + - + +
887A CYS* 3.5 1.7 + - - +
888A ASN* 3.0 47.7 + - - +
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Residues in contact with LYS 885 (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 ARG* 3.1 26.9 + - + +
882A LEU* 3.1 6.5 + - - +
884A ILE* 1.3 78.8 - - + +
886A CYS* 1.3 62.7 + - - +
888A ASN* 3.5 16.4 + - + +
889A PHE* 3.1 23.0 + - - +
938A ILE* 4.4 2.5 - - + -
945A VAL* 4.0 41.8 + - + +
947A PHE* 3.7 30.6 - - + -
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Residues in contact with CYS 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ILE* 3.9 14.1 - - + -
722A CYS* 3.5 25.1 - - - -
724A LEU* 3.8 32.3 - - - -
882A LEU 2.8 22.2 + - - -
883A ALA* 3.1 11.0 + - - +
885A LYS* 1.3 72.5 - - - +
887A CYS* 1.3 56.9 + - - +
889A PHE* 3.0 18.4 + - - +
890A ILE* 3.0 20.9 + - - +
938A ILE* 3.8 22.7 - - - -
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Residues in contact with CYS 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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620A ALA* 3.3 41.7 - - - -
623A ASN* 3.2 28.5 - - - +
624A SER* 3.5 9.0 - - - -
627A LYS* 4.0 0.7 - - - -
693A ILE* 4.0 8.1 - - - -
883A ALA 3.1 16.1 + - - +
884A ILE 3.8 0.9 - - - +
886A CYS* 1.3 74.8 - - - +
888A ASN* 1.3 66.0 + - - +
890A ILE* 4.1 4.3 - - - -
891A GLU* 3.0 43.5 + - - +
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Residues in contact with ASN 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ASN* 4.1 10.6 + - - -
627A LYS* 3.8 17.6 + - - +
884A ILE* 3.0 34.5 + - - +
885A LYS* 3.7 16.5 - - + +
887A CYS* 1.3 74.8 - - - +
889A PHE* 1.3 60.3 + - - +
891A GLU 4.1 0.3 - - - -
892A ASP* 3.4 26.0 + - - +
947A PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 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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720A PRO* 4.5 7.2 - - + -
721A MET 4.3 3.4 - - - -
722A CYS* 4.6 1.3 - - + -
885A LYS 3.1 12.3 + - - +
886A CYS 3.0 10.4 + - - +
888A ASN* 1.3 74.5 - - - +
890A ILE* 1.3 75.8 + - + +
892A ASP* 3.1 20.6 - - - +
895A PHE* 3.2 41.1 - + - -
933A ASN 3.3 25.4 - - - -
934A THR* 3.3 23.6 - - - -
936A VAL* 3.8 26.5 - - + -
938A ILE* 4.1 6.3 - - + -
947A PHE* 3.7 28.9 - + + -
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Residues in contact with ILE 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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599A LEU* 5.2 0.2 - - - -
601A ILE* 3.5 40.6 - - + -
690A ASP 4.7 0.2 - - - +
691A GLY* 4.4 2.0 - - - -
692A LEU 3.9 21.1 - - - +
693A ILE* 3.7 19.3 - - + -
720A PRO* 3.4 45.5 - - + +
721A MET* 4.0 2.0 - - - +
722A CYS* 4.0 17.3 - - - -
886A CYS 3.0 16.0 + - - +
887A CYS* 4.0 6.1 - - - +
889A PHE* 1.3 76.8 - - + +
891A GLU* 1.4 63.6 + - + +
892A ASP 3.2 5.1 + - - +
896A GLN* 3.2 23.6 + - - -
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Residues in contact with GLU 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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599A LEU* 3.9 13.2 - - + +
601A ILE* 3.4 30.6 - - + +
623A ASN* 3.7 1.2 - - - +
624A SER* 2.6 28.5 + - - -
627A LYS* 2.7 43.8 + - - +
629A HIS* 3.6 28.1 + - + +
887A CYS* 3.0 30.8 + - - +
888A ASN 4.1 2.0 - - - -
890A ILE* 1.4 75.2 - - + +
892A ASP* 1.3 64.1 + - - +
893A ALA* 3.4 2.9 + - - +
896A GLN* 4.7 1.1 - - - +
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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
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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) + - + + + + + -
------------------------------------------------------------
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