Contacts of the helix formed by residues 740 - 759 (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 GLY 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A THR* 4.2 12.1 - - - -
611A SER* 4.9 1.3 - - - -
612A ALA* 3.5 10.9 - - - +
727A THR 4.3 2.7 - - - -
728A VAL* 3.8 9.1 - - - +
739A LEU* 1.3 73.4 - - - +
741A SER* 1.4 61.4 + - - +
743A THR* 3.6 6.5 + - - +
744A CYS* 3.2 21.5 + - - +
866A GLN 5.0 0.2 - - - +
867A GLN 5.2 1.2 - - - +
875A ASP* 2.9 26.6 + - - -
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Residues in contact with SER 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A THR 3.7 7.5 + - - -
728A VAL* 3.7 23.1 - - - +
730A ASN* 3.8 10.6 + - - -
737A TYR* 3.0 27.9 - - - -
738A SER* 3.3 16.1 + - - -
739A LEU 3.4 1.2 + - - -
740A GLY* 1.4 74.1 - - - +
742A ASP* 1.3 58.5 + - - +
744A CYS* 3.2 5.0 + - - +
745A LEU* 3.0 33.4 + - - +
778A TYR* 4.4 11.7 + - - -
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Residues in contact with ASP 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 5.2 0.9 - - - +
501A CYS* 6.0 1.2 - - - -
502A ALA* 4.0 12.5 - - - +
503A PHE* 4.2 7.0 + - - +
737A TYR* 3.1 26.0 + - + +
741A SER* 1.3 72.7 + - - +
743A THR* 1.3 62.2 + - - +
745A LEU* 3.3 7.2 + - - +
746A ASN* 2.8 50.4 + - - -
782A TYR* 5.2 4.2 + - - -
872A SER* 2.9 23.1 + - - +
874A ILE* 3.6 34.0 - - + +
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Residues in contact with THR 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A SER* 3.2 21.5 + - - +
740A GLY 3.6 5.8 - - - -
742A ASP* 1.3 74.9 - - - +
744A CYS* 1.3 56.6 + - - +
746A ASN* 3.2 6.5 + - - +
747A THR* 2.9 33.6 + - - +
867A GLN 3.4 15.0 - - - +
868A GLY* 4.0 10.8 - - - -
870A SER 3.7 14.8 - - - +
871A PRO* 3.4 4.9 - - - +
872A SER* 2.8 26.6 + - - +
875A ASP* 2.6 25.0 + - - -
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Residues in contact with CYS 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A VAL* 3.5 33.2 - - + -
740A GLY 3.2 3.3 + - - +
741A SER* 3.2 11.1 + - - +
743A THR* 1.3 78.6 - - - +
745A LEU* 1.4 56.6 + - - +
747A THR* 3.1 2.9 + - - -
748A LEU* 2.8 37.3 + - - +
779A LEU* 3.7 17.3 - - + -
866A GLN* 3.2 49.1 + - - +
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Residues in contact with LEU 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA* 3.7 17.7 - - + -
741A SER* 3.0 29.1 + - - +
742A ASP* 3.3 9.1 + - - +
744A CYS* 1.4 73.7 - - - +
746A ASN* 1.3 50.7 + - - +
748A LEU* 3.3 3.9 + - + +
749A SER* 2.7 38.5 + - - -
778A TYR* 4.5 11.4 - - + +
779A LEU* 3.6 30.3 - - + +
782A TYR* 3.7 35.7 - - + -
783A ALA* 3.7 35.9 - - + +
786A ILE* 3.7 6.4 - - + +
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Residues in contact with ASN 746 (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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378A GLU* 5.1 7.1 + - - +
501A CYS* 3.4 15.0 - - - +
502A ALA* 2.8 28.4 + - - +
503A PHE 5.4 0.2 - - - +
742A ASP* 2.8 47.9 + - - -
743A THR* 3.4 7.6 - - - +
745A LEU* 1.3 72.9 - - - +
747A THR* 1.3 63.2 + - - +
749A SER* 3.3 6.2 + - - -
750A GLY* 3.2 21.0 + - - -
872A SER* 3.9 11.8 - - - -
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Residues in contact with THR 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A THR* 2.9 21.0 + - - +
744A CYS* 3.5 8.5 - - - -
746A ASN* 1.3 74.6 - - - +
748A LEU* 1.4 58.4 + - + +
750A GLY* 3.9 1.1 - - - -
751A TYR* 3.0 30.2 + - + +
865A VAL* 3.3 40.6 - - + +
866A GLN* 4.2 5.4 - - - -
868A GLY* 3.8 18.3 - - - -
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Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A CYS* 2.8 35.2 + - - +
745A LEU* 3.8 5.8 - - + +
747A THR* 1.4 75.0 - - + +
749A SER* 1.3 55.3 + - - +
751A TYR* 3.1 4.7 + - + +
752A CYS* 2.8 43.4 + - - -
769A VAL* 5.3 2.7 - - + -
771A VAL* 3.8 27.8 - - + -
779A LEU* 4.2 18.2 - - + -
783A ALA* 4.4 15.3 - - + -
787A THR* 4.8 0.4 - - - -
862A PRO* 3.8 27.6 - - + -
866A GLN* 3.6 27.6 - - + +
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Residues in contact with SER 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA* 4.2 6.6 + - - +
505A ARG* 3.8 26.5 + - - -
745A LEU 2.7 26.7 + - - -
746A ASN* 3.3 13.9 + - - -
748A LEU* 1.3 70.4 - - - +
750A GLY* 1.3 53.5 + - - +
752A CYS* 3.3 4.0 + - - +
753A ASP* 2.8 38.0 + - - +
786A ILE* 3.6 19.6 - - - +
787A THR* 3.9 14.5 - - - +
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Residues in contact with GLY 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ARG* 5.3 0.6 - - - +
746A ASN 3.2 14.1 + - - -
747A THR 4.0 0.9 - - - -
749A SER* 1.3 73.3 - - - +
751A TYR* 1.3 64.6 + - - +
753A ASP* 3.1 22.9 + - - +
754A ALA* 3.3 12.5 + - - +
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Residues in contact with TYR 751 (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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747A THR* 3.0 21.2 + - + +
748A LEU* 3.1 9.2 + - - +
750A GLY* 1.3 74.3 - - - +
752A CYS* 1.3 61.8 + - - +
754A ALA* 3.2 10.6 + - - +
755A VAL* 3.1 46.5 + - + +
769A VAL* 4.8 1.3 - - + -
860A ALA* 4.0 12.2 - - + +
861A VAL 3.9 10.7 + - - -
862A PRO* 3.6 55.0 - - + +
865A VAL* 4.5 10.5 - - + -
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Residues in contact with CYS 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A LEU* 2.8 26.5 + - - +
749A SER 3.7 4.9 - - - +
751A TYR* 1.3 72.6 - - - +
753A ASP* 1.4 61.7 + - - +
755A VAL* 3.3 10.3 - - + +
756A LYS* 2.9 34.8 + - + +
769A VAL* 3.9 33.9 - - - -
787A THR* 3.8 28.0 - - + -
827A ILE* 4.2 13.7 - - + -
829A ILE* 4.7 3.8 - - - -
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Residues in contact with ASP 753 (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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273A SER* 3.4 19.0 - - - +
499A ALA* 4.4 7.1 - - - +
505A ARG* 2.7 39.5 + - - -
749A SER 2.8 21.7 + - - +
750A GLY* 3.1 14.0 + - - +
752A CYS* 1.4 77.1 - - - +
754A ALA* 1.3 60.3 + - - +
756A LYS* 3.7 6.1 + - - +
757A GLN* 3.3 23.4 + - - +
787A THR* 5.5 1.6 - - - +
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Residues in contact with ALA 754 (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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750A GLY 3.3 7.4 + - - +
751A TYR* 3.2 12.5 + - - +
752A CYS 3.2 0.2 - - - -
753A ASP* 1.3 78.7 - - - +
755A VAL* 1.4 59.7 + - - +
757A GLN* 3.3 14.0 + - + +
758A SER* 3.1 26.0 + - - -
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Residues in contact with VAL 755 (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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751A TYR* 3.1 40.4 + - + +
752A CYS* 3.1 12.1 + - - +
754A ALA* 1.4 75.3 - - + +
756A LYS* 1.4 57.7 + - - +
758A SER* 2.8 21.9 + - - -
759A ALA* 3.0 17.3 + - - +
767A PHE* 3.4 44.4 - - + -
769A VAL* 4.2 10.3 - - + -
827A ILE* 3.7 14.4 - - + -
860A ALA* 4.6 5.2 - - + -
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Residues in contact with LYS 756 (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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270A GLY* 5.6 7.6 - - - -
272A LEU* 5.1 6.5 - - - +
752A CYS* 2.9 19.7 + - + +
753A ASP* 4.2 6.1 - - - +
755A VAL* 1.4 75.6 - - - +
757A GLN* 1.4 57.6 + - - +
759A ALA* 3.4 14.4 + - - +
760A SER* 3.1 16.3 + - - -
787A THR 3.0 26.4 + - - +
788A GLY* 3.3 15.0 + - - -
824A SER 3.4 10.6 - - - +
825A GLY 3.4 24.7 + - - +
826A LYS* 3.5 19.1 - - - +
827A ILE* 3.8 22.9 - - + -
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Residues in contact with GLN 757 (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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753A ASP 3.3 13.3 + - - +
754A ALA* 3.3 23.3 + - + +
755A VAL 3.2 0.4 - - - -
756A LYS* 1.4 72.9 - - - +
758A SER* 1.4 69.2 + - - +
759A ALA 3.2 4.5 - - - -
760A SER* 3.4 22.9 + - - -
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Residues in contact with SER 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ALA 3.1 14.9 + - - -
755A VAL* 2.8 21.9 + - - -
757A GLN* 1.4 83.6 - - - +
759A ALA* 1.4 54.4 + - - +
760A SER 3.3 7.6 + - - +
763A ARG* 4.4 13.4 - - - +
764A ARG* 4.2 15.2 + - - +
767A PHE* 4.2 13.5 - - - -
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Residues in contact with ALA 759 (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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755A VAL 3.0 14.8 + - - +
756A LYS* 3.5 15.5 - - - +
757A GLN 3.2 0.4 - - - -
758A SER* 1.4 76.2 - - - +
760A SER* 1.4 54.3 + - - +
764A ARG 3.4 18.0 - - - +
765A ARG* 3.6 24.3 - - - +
767A PHE* 3.7 16.2 - - + -
824A SER 4.1 0.3 - - - -
825A GLY* 3.4 24.3 + - - -
826A LYS 5.2 0.2 - - - +
827A ILE* 6.2 0.2 - - + -
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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
------------------------------------------------------------
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