Contacts of the helix formed by residues 728 - 744 (chain A) in PDB entry 1M14
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 728 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A LEU* 4.0 4.7 - - - +
726A ALA 3.5 5.9 + - - -
727A THR* 1.3 74.4 - - - +
729A PRO* 1.3 58.6 - - - +
730A LYS* 4.6 9.5 + - - +
731A ALA* 2.8 42.4 + - - +
732A ASN* 3.0 11.5 + - - +
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Residues in contact with PRO 729 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A THR* 3.6 13.2 - - + +
728A SER* 1.3 83.5 - - - +
730A LYS* 1.3 58.9 + - + +
732A ASN* 3.0 12.7 + - + +
733A LYS* 2.9 24.7 + - - +
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Residues in contact with LYS 730 (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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728A SER* 3.2 8.4 + - - +
729A PRO* 1.3 77.8 - - - +
731A ALA* 1.3 58.9 + - - +
733A LYS* 3.7 17.7 - - + +
734A GLU* 3.1 33.7 + - - +
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Residues in contact with ALA 731 (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 LEU* 3.4 29.3 - - + +
728A SER* 2.8 24.8 + - - +
730A LYS* 1.3 77.9 - - - +
732A ASN* 1.3 59.9 + - - +
733A LYS 3.3 0.2 - - - -
734A GLU* 3.4 11.9 + - - +
735A ILE* 3.0 33.4 + - - +
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Residues in contact with ASN 732 (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 LEU* 4.0 6.6 - - - +
727A THR* 3.0 30.9 - - - +
728A SER 3.0 23.3 + - - +
729A PRO* 3.0 10.0 + - + +
731A ALA* 1.3 76.7 - - - +
733A LYS* 1.3 62.6 + - - +
735A ILE* 3.4 7.8 + - - +
736A LEU* 3.0 36.0 + - + +
760A SER 4.8 1.2 + - - -
761A THR* 4.3 8.9 - - - +
762A VAL* 3.8 28.5 - - + +
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Residues in contact with LYS 733 (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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729A PRO 2.9 12.5 + - - +
730A LYS* 3.7 18.2 - - + +
732A ASN* 1.3 77.3 - - - +
734A GLU* 1.3 60.1 + - + +
736A LEU* 3.3 6.9 + - - +
737A ASP* 2.8 53.7 + - - +
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Residues in contact with GLU 734 (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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730A LYS* 3.1 23.7 + - + +
731A ALA* 3.6 10.6 - - - +
732A ASN 3.2 0.6 - - - -
733A LYS* 1.3 81.5 - - + +
735A ILE* 1.3 64.9 + - + +
737A ASP* 3.3 12.3 + - - +
738A GLU* 3.1 24.9 + - - +
833A GLY* 5.9 1.0 - - - -
851A LYS* 3.6 23.3 + - - -
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Residues in contact with ILE 735 (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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721A LYS* 6.0 7.4 - - + -
722A GLU* 4.9 3.1 - - - -
723A LEU* 3.9 33.7 - - + +
731A ALA 3.0 18.5 + - - +
732A ASN* 3.9 5.6 - - - +
733A LYS 3.3 0.2 - - - -
734A GLU* 1.3 75.6 - - + +
736A LEU* 1.3 59.8 + - - +
738A GLU* 3.1 11.0 + - - +
739A ALA* 3.0 26.5 + - - +
762A VAL* 3.6 49.8 - - + +
764A LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 736 (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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680A LEU* 5.8 1.1 - - + -
732A ASN* 3.0 32.9 + - + +
733A LYS* 3.8 5.6 - - - +
735A ILE* 1.3 78.3 - - - +
737A ASP* 1.3 57.7 + - - +
739A ALA* 3.7 9.5 - - + +
740A TYR* 3.0 26.2 + - - +
756A ILE* 3.9 28.3 - - + -
758A LEU* 5.2 3.6 - - + -
762A VAL* 3.8 28.3 - - + -
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Residues in contact with ASP 737 (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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733A LYS* 2.8 53.4 + - - +
734A GLU* 3.6 11.5 - - - +
735A ILE 3.2 0.4 - - - -
736A LEU* 1.3 75.1 - - - +
738A GLU* 1.3 65.5 + - - +
740A TYR* 3.3 9.8 - - - +
741A VAL* 3.3 25.8 + - - +
832A PHE 5.8 0.2 - - - -
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Residues in contact with GLU 738 (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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721A LYS* 3.8 24.5 + - - +
734A GLU 3.1 12.9 + - - +
735A ILE* 3.4 11.6 - - - +
737A ASP* 1.3 76.0 - - - +
739A ALA* 1.3 55.5 + - - +
741A VAL* 2.9 10.3 - - - +
742A MET* 2.8 47.9 + - + +
764A LEU* 4.1 20.0 - - + +
831A ASP* 4.6 6.7 + - - -
832A PHE* 3.9 33.1 + - + -
833A GLY* 4.0 19.1 + - - +
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Residues in contact with ALA 739 (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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680A LEU* 4.7 8.1 - - + -
735A ILE* 3.0 12.8 + - + +
736A LEU* 3.7 16.4 - - + +
738A GLU* 1.3 75.9 - - - +
740A TYR* 1.3 57.5 + - - +
742A MET* 4.5 0.9 - - - -
743A ALA* 2.8 35.4 + - - +
753A LEU* 3.5 8.2 - - + +
756A ILE* 3.8 28.5 - - + -
764A LEU* 3.9 14.7 - - + +
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Residues in contact with TYR 740 (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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676A ASN* 3.1 33.2 + - + +
680A LEU* 6.3 0.9 - - - -
736A LEU 3.0 14.7 + - - +
737A ASP* 3.3 13.0 - - - +
738A GLU 3.1 0.2 - - - -
739A ALA* 1.3 79.6 - - - +
741A VAL* 1.3 67.4 + - + +
743A ALA* 3.3 7.9 + - - +
744A SER* 2.6 28.0 + - - -
837A LEU* 3.7 28.5 - - + +
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Residues in contact with VAL 741 (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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737A ASP 3.3 10.7 + - - +
738A GLU* 2.9 27.8 + - - +
740A TYR* 1.3 87.6 - - + +
742A MET* 1.3 63.0 + - - +
744A SER* 3.0 20.5 + - - -
745A VAL* 3.6 14.6 + - - +
809A LEU* 4.7 20.8 - - + +
832A PHE* 3.4 36.8 - - + +
835A ALA* 4.6 19.7 - - + +
837A LEU* 5.1 7.9 - - + +
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Residues in contact with MET 742 (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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738A GLU* 2.8 41.1 + - + +
739A ALA* 4.5 0.2 - - - -
741A VAL* 1.3 73.2 - - + +
743A ALA* 1.3 58.6 + - - +
744A SER 3.1 0.7 - - - -
745A VAL* 3.2 27.5 + - - +
751A CYS* 3.7 36.3 - - + +
753A LEU* 3.7 36.8 + - + +
764A LEU* 4.8 7.6 - - - -
766A THR* 3.9 29.8 - - + -
830A THR* 5.4 2.5 - - - +
831A ASP 6.1 0.4 - - - -
832A PHE* 3.8 26.5 - - + -
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Residues in contact with ALA 743 (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 ALA* 3.2 20.6 - - + +
679A LEU 4.3 17.8 + - - +
680A LEU* 4.6 13.2 - - + -
739A ALA 2.8 20.3 + - - +
740A TYR* 3.8 4.5 - - - +
742A MET* 1.3 76.1 - - - +
744A SER* 1.3 60.3 + - - +
745A VAL 3.5 2.7 - - - +
753A LEU* 3.5 16.5 - - + +
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Residues in contact with SER 744 (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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676A ASN* 3.1 23.9 + - - +
678A ALA* 4.1 7.4 - - - +
740A TYR* 2.6 27.6 + - - -
741A VAL* 3.0 10.7 + - - -
743A ALA* 1.3 80.2 - - - +
745A VAL* 1.3 60.1 + - - +
803A TYR* 4.2 0.7 + - - -
807A ARG* 2.7 46.9 + - - +
837A LEU* 5.4 5.6 - - - -
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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
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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