Contacts of the helix formed by residues 748 - 768 (chain A) in PDB entry 4MS0
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 THR 748 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A PHE* 4.0 10.3 - - + -
540A ILE* 4.1 21.1 - - + -
544A ASN* 3.9 20.9 - - - +
741A LEU* 3.4 38.5 + - + +
742A THR* 3.5 11.0 + - - -
745A LEU* 2.7 29.1 + - + +
747A PRO* 1.3 74.9 - - - +
749A GLU* 1.3 64.8 + - - +
750A PRO* 3.2 4.0 - - - -
751A LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A THR* 3.5 28.1 + - + +
746A PRO* 3.0 15.7 + - - +
748A THR* 1.3 78.8 + - - +
750A PRO* 1.4 67.1 - - + +
752A LEU* 3.0 18.6 + - + +
753A LYS* 3.1 15.5 + - + +
756A ARG* 5.6 3.2 + - - +
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Residues in contact with PRO 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 3.9 26.9 - - + -
747A PRO 3.2 16.4 - - - +
748A THR 3.3 2.7 - - - -
749A GLU* 1.4 92.3 - - + +
751A LEU* 1.3 61.0 + - - +
753A LYS* 4.1 7.0 - - + +
754A ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 3.7 46.9 - - + +
536A CYS* 3.9 23.6 - - - -
540A ILE* 4.2 5.4 - - + -
672A ALA* 4.7 0.4 - - + -
679A THR* 3.5 33.8 - - + +
738A TYR* 3.7 26.5 - - + -
741A LEU* 4.2 19.7 - - + -
748A THR* 3.0 16.6 + - - +
750A PRO* 1.3 77.3 - - - +
752A LEU* 1.3 62.4 + - - +
754A ALA* 3.5 0.9 + - - +
755A CYS* 3.1 24.3 + - - +
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Residues in contact with LEU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ILE* 4.1 10.5 - - + +
738A TYR* 3.8 15.1 - - + +
739A THR* 3.6 40.2 - - + +
742A THR* 3.5 31.2 - - + +
748A THR 3.8 0.8 + - - -
749A GLU* 3.0 15.0 + - + +
751A LEU* 1.3 80.6 - - - +
753A LYS* 1.3 58.3 + - - +
755A CYS* 3.3 1.9 + - + +
756A ARG* 2.9 72.3 + - + +
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Residues in contact with LYS 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A GLU* 3.1 19.9 + - + +
750A PRO* 4.1 7.2 - - + +
752A LEU* 1.3 76.7 - - - +
754A ALA* 1.3 62.8 + - - +
756A ARG* 3.3 12.1 + - - +
757A ASP* 3.0 31.5 + - - +
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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
----------------------------------------------------------
476A HIS* 6.1 1.8 - - + -
678A VAL 4.0 2.2 - - - -
679A THR* 2.8 36.6 - - - +
680A LYS 4.6 3.5 - - - +
750A PRO 3.1 17.9 + - - +
751A LEU* 3.8 0.9 - - - +
753A LYS* 1.3 74.5 - - - +
755A CYS* 1.3 58.7 + - - +
757A ASP* 3.1 12.4 + - - +
758A ASN* 3.0 31.0 + - - -
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Residues in contact with CYS 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A VAL* 3.3 19.9 + - - +
679A THR* 4.4 1.8 - - + -
730A TYR* 3.8 12.1 - - - -
734A ALA* 3.7 29.6 - - - -
735A ILE* 3.7 19.3 - - + -
738A TYR* 3.8 19.1 - - + -
751A LEU 3.1 17.9 + - - +
752A LEU* 3.7 4.7 - - - +
754A ALA* 1.3 73.6 - - - +
756A ARG* 1.3 65.1 + - - +
758A ASN* 3.2 1.4 + - - -
759A LEU* 2.9 22.3 + - - +
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Residues in contact with ARG 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ILE* 3.9 23.9 - - + +
739A THR* 4.8 9.3 + - - +
749A GLU* 5.6 3.2 + - - -
752A LEU* 2.9 56.0 + - + +
753A LYS* 3.7 10.4 - - - +
755A CYS* 1.3 76.9 - - - +
757A ASP* 1.3 63.8 + - - +
759A LEU* 3.4 9.0 - - + +
760A SER* 3.2 21.1 + - - -
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Residues in contact with ASP 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LYS* 3.0 24.0 + - - +
754A ALA* 3.1 11.9 + - - +
756A ARG* 1.3 78.4 - - - +
758A ASN* 1.3 61.9 + - - +
760A SER* 3.4 8.7 + - - -
761A GLN* 3.1 32.0 + - + +
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Residues in contact with ASN 758 (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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678A VAL 3.0 18.3 + - - +
680A LYS 2.9 16.1 + - - +
682A TRP* 3.3 35.0 + - + +
685A THR* 2.8 31.1 + - + -
730A TYR* 3.7 23.6 - - + +
754A ALA 3.0 13.9 + - - +
755A CYS 3.2 0.6 + - - +
757A ASP* 1.3 77.0 - - - +
759A LEU* 1.3 65.0 + - - +
761A GLN* 3.1 5.9 + - - +
762A TRP* 2.9 26.5 + - - -
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Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LEU* 3.5 28.5 - - + -
730A TYR* 3.5 34.0 - - + -
731A ASN* 3.8 17.0 - - - +
735A ILE* 4.4 17.3 - - + -
755A CYS 2.9 14.2 + - - +
756A ARG* 3.4 13.7 - - + +
758A ASN* 1.3 74.2 - - - +
760A SER* 1.3 57.7 + - - +
762A TRP* 3.1 8.3 + - + +
763A GLU* 2.9 40.9 + - - +
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Residues in contact with SER 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A ARG 3.2 10.1 + - - -
757A ASP* 3.4 13.5 - - - -
759A LEU* 1.3 79.8 - - - +
761A GLN* 1.3 58.6 + - - +
763A GLU* 3.3 16.9 + - - +
764A LYS* 2.9 37.0 + - - +
767A ARG* 4.8 3.5 + - - -
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Residues in contact with GLN 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A TRP* 3.5 54.1 + - + +
757A ASP* 3.1 21.9 + - + +
758A ASN* 3.1 10.6 + - - +
760A SER* 1.3 73.5 + - - +
762A TRP* 1.3 60.2 + - - +
764A LYS* 3.3 21.3 + - - +
765A VAL* 3.0 30.0 + - - +
721B GLU* 3.2 24.1 + - - +
724B GLN* 4.0 15.0 + - - +
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Residues in contact with TRP 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A TRP* 3.5 27.6 - + - -
685A THR* 4.6 2.2 - - + +
686A LYS* 3.8 29.4 - - + -
689A ALA* 4.2 20.9 - - + -
722A VAL* 4.7 8.7 - - + -
723A PRO* 3.8 42.8 - - + +
726A GLN* 3.7 27.1 + - + -
727A LEU* 4.8 9.9 - - + +
730A TYR* 3.3 42.4 + + - -
758A ASN 2.9 25.9 + - - -
759A LEU* 3.5 7.2 - - - +
761A GLN* 1.3 72.4 - - - +
763A GLU* 1.3 66.1 + - - +
765A VAL* 3.2 12.9 + - + +
766A ILE* 3.0 27.9 + - + +
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Residues in contact with GLU 763 (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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727A LEU* 3.6 30.8 - - + +
731A ASN* 5.6 0.3 - - - +
759A LEU* 2.9 33.7 + - - +
760A SER* 3.6 18.3 + - - +
761A GLN 3.3 0.2 - - - -
762A TRP* 1.3 76.2 - - - +
764A LYS* 1.3 61.7 + - - +
766A ILE* 3.3 10.9 + - - +
767A ARG* 3.1 44.1 + - - +
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Residues in contact with LYS 764 (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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760A SER* 2.9 22.0 + - - +
761A GLN* 3.4 26.4 + - - +
762A TRP 3.2 0.2 - - - -
763A GLU* 1.3 73.2 - - - +
765A VAL* 1.3 66.7 + - + +
767A ARG* 3.2 26.1 + - - +
768A GLY 3.2 4.7 + - - -
769A GLU* 3.0 52.2 + - + +
770A GLU* 4.5 1.8 - - - +
721B GLU* 2.8 35.7 + - - +
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Residues in contact with VAL 765 (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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682A TRP* 4.1 17.3 - - + -
686A LYS* 5.4 0.9 - - - -
723A PRO* 3.6 28.0 - - + -
761A GLN 3.0 19.2 + - - +
762A TRP* 3.2 19.7 + - + +
764A LYS* 1.3 76.5 - - + +
766A ILE* 1.3 57.8 + - - +
768A GLY* 2.9 21.7 + - - -
770A GLU* 3.9 46.3 + - + +
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Residues in contact with ILE 766 (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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723A PRO* 3.6 37.5 - - + +
724A GLN* 3.9 16.6 - - + +
727A LEU* 3.7 32.1 - - + -
762A TRP 3.0 21.9 + - - +
763A GLU* 3.6 9.4 - - - +
764A LYS 3.2 0.2 - - - -
765A VAL* 1.3 76.2 - - - +
767A ARG* 1.3 62.9 + - + +
768A GLY* 3.2 1.9 + - - -
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Residues in contact with ARG 767 (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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760A SER* 4.8 4.9 + - - -
763A GLU* 3.1 32.9 + - - +
764A LYS* 3.2 36.6 + - - +
766A ILE* 1.3 76.3 - - + +
768A GLY* 1.3 58.9 + - - +
769A GLU* 3.0 34.6 + - - +
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Residues in contact with GLY 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A VAL 2.9 15.2 + - - -
766A ILE 3.1 2.5 + - - -
767A ARG* 1.3 77.9 - - - +
769A GLU* 1.3 59.9 + - - +
770A GLU* 3.5 5.3 + - - +
711B ILE* 5.0 5.4 - - - +
712B PRO* 3.6 18.9 - - - +
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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