Contacts of the helix formed by residues 717 - 738 (chain B) in PDB entry 5MJA
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 717 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLY 5.0 0.6 + - - +
715B GLN 5.9 0.4 - - - +
716B PHE* 1.3 74.5 - - - +
718B VAL* 1.3 64.3 + - - +
719B ILE* 3.3 16.6 - - + +
720B GLN* 3.0 37.4 + - - +
721B LEU* 3.0 23.7 + - - +
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Residues in contact with VAL 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B THR* 1.3 71.7 - - - +
719B ILE* 1.3 57.6 + - - +
721B LEU* 3.2 11.6 + - + +
722B VAL* 2.8 44.8 + - + +
818B MET* 4.4 11.2 - - + -
848B ASP* 3.7 28.3 - - + +
850B PRO* 3.7 26.5 - - + -
888B LEU* 4.4 16.6 - - + +
890B THR* 6.6 0.2 - - + -
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Residues in contact with ILE 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PRO* 3.6 21.1 - - + +
642A GLY* 3.2 31.6 - - - +
643A LYS* 3.9 22.6 - - + +
644A ARG* 5.5 0.7 - - - +
717B THR* 3.3 18.4 - - + +
718B VAL* 1.3 78.6 - - - +
720B GLN* 1.4 58.0 + - + +
722B VAL* 3.8 4.5 - - - +
723B GLY* 2.9 26.2 + - - -
882B ILE* 3.9 40.0 - - + +
888B LEU* 4.3 14.1 - - + -
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Residues in contact with GLN 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLY 5.5 2.7 + - - +
644A ARG* 4.6 23.2 - - - +
715B GLN 4.2 1.7 - - - +
716B PHE* 3.2 29.4 - - + +
717B THR* 3.0 42.6 + - - +
719B ILE* 1.4 77.4 - - + +
721B LEU* 1.3 63.2 + - - +
723B GLY* 3.2 4.1 + - - -
724B MET* 3.1 29.8 + - + +
756B LEU* 5.4 10.4 - - + +
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Residues in contact with LEU 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B LEU* 3.9 27.6 - - + -
716B PHE* 4.0 17.9 - - + +
717B THR 3.0 20.6 + - - +
718B VAL* 3.7 7.4 - - + +
720B GLN* 1.3 76.6 - - - +
722B VAL* 1.4 56.0 + - - +
724B MET* 3.2 12.9 + - + +
725B LEU* 3.0 31.7 + - - +
817B VAL* 3.9 24.2 - - + +
818B MET* 3.8 33.2 - - + +
820B PHE* 3.9 27.8 - - + -
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Residues in contact with VAL 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B VAL* 2.8 29.1 + - + +
719B ILE* 3.8 7.0 - - - +
721B LEU* 1.4 70.9 - - - +
723B GLY* 1.3 58.8 + - - +
725B LEU* 3.2 9.1 + - - +
726B ARG* 2.8 28.5 + - - +
818B MET* 4.9 0.7 - - + -
853B LEU* 3.7 32.5 - - + -
878B LEU* 4.2 20.8 - - + +
881B MET* 4.8 2.9 - - + -
882B ILE* 3.7 26.9 - - + -
888B LEU* 4.3 17.9 - - + -
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Residues in contact with GLY 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LYS* 6.3 1.8 - - - -
719B ILE 2.9 15.0 + - - -
720B GLN* 3.2 5.3 + - - -
722B VAL* 1.3 75.8 - - - +
724B MET* 1.3 58.9 + - - +
726B ARG* 3.4 9.2 + - - +
727B GLY* 3.2 18.2 + - - -
882B ILE* 4.5 7.9 - - - -
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Residues in contact with MET 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B LEU* 4.1 22.9 - - + -
708B PHE* 4.9 3.1 - - + -
709B LEU* 4.2 9.0 - - + -
716B PHE* 3.9 41.1 - - + -
720B GLN* 3.1 18.0 + - + +
721B LEU* 3.2 19.7 + - + +
723B GLY* 1.3 75.5 - - - +
725B LEU* 1.4 56.5 + - - +
727B GLY* 3.4 2.6 + - - -
728B ILE* 3.2 34.1 + - + +
752B VAL* 5.9 0.2 - - - -
756B LEU* 4.1 27.1 - - + +
758B CYS* 3.7 25.2 - - - +
817B VAL* 4.7 6.1 - - + -
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Residues in contact with LEU 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B LEU 3.0 13.9 + - - +
722B VAL* 3.5 12.8 - - - +
724B MET* 1.4 71.5 - - - +
726B ARG* 1.3 59.7 + - - +
728B ILE* 3.4 9.3 + - + -
729B ALA 3.0 18.0 + - - -
810B TYR* 2.6 30.2 + - + +
813B VAL* 4.3 3.1 - - + -
814B MET* 3.6 53.4 - - + +
817B VAL* 3.6 24.7 - - + -
818B MET* 3.9 28.7 - - + -
853B LEU* 4.7 5.8 - - + -
878B LEU* 3.8 5.4 - - + -
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Residues in contact with ARG 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LYS* 3.9 17.6 - - - +
676A ASP* 2.8 35.5 + - - +
679B ASN* 5.2 1.8 + - - -
722B VAL 2.8 17.2 + - - +
723B GLY* 3.7 5.8 - - - +
725B LEU* 1.3 71.9 - - - +
727B GLY* 1.3 61.2 + - - +
729B ALA* 3.4 2.6 + - - +
730B ALA* 2.9 36.2 + - - +
875B VAL* 3.5 20.6 - - + +
878B LEU* 3.5 25.1 - - + +
879B ASP* 2.8 44.1 + - - +
882B ILE* 4.0 16.4 - - + -
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Residues in contact with GLY 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ASN* 3.0 37.9 - - - +
723B GLY 3.2 13.8 + - - -
724B MET* 3.4 3.8 + - - -
725B LEU 3.3 0.4 - - - -
726B ARG* 1.3 76.3 - - - +
728B ILE* 1.3 63.8 + - - +
730B ALA* 3.2 2.7 + - - -
731B GLY 3.0 18.9 + - - -
758B CYS* 4.3 2.7 - - - -
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Residues in contact with ILE 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ASN* 5.0 0.2 - - - -
705B LEU* 3.7 30.1 - - + -
724B MET 3.2 21.7 + - - +
725B LEU* 3.8 13.2 - - + +
726B ARG 3.4 0.2 - - - -
727B GLY* 1.3 75.4 - - - +
729B ALA* 1.3 56.0 + - - +
731B GLY* 3.2 2.8 + - - -
732B MET* 2.9 30.1 + - + +
745B LEU* 4.3 11.2 - - + -
750B ILE* 3.9 33.7 - - + -
758B CYS* 3.8 16.4 - - + +
760B VAL* 4.2 8.9 - - + +
810B TYR* 3.8 20.0 - - + -
813B VAL* 4.1 11.0 - - + -
817B VAL* 4.7 0.2 - - + -
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Residues in contact with ALA 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B LEU 3.0 18.1 + - - +
726B ARG 3.6 4.7 - - - +
728B ILE* 1.3 74.5 - - - +
730B ALA* 1.4 52.5 + - - +
732B MET* 3.3 5.8 + - - +
733B LYS* 2.8 34.7 + - - +
810B TYR* 3.6 19.0 - - + +
871B PHE* 4.1 5.4 - - + -
874B ILE* 3.7 23.6 - - + -
875B VAL* 3.6 14.2 - - + +
878B LEU* 4.1 5.2 - - + -
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Residues in contact with ALA 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A ASP* 3.4 25.8 - - - +
677B HIS* 3.6 13.5 + - + +
679B ASN* 3.8 10.1 - - - +
726B ARG* 2.9 29.7 + - - +
727B GLY 3.5 5.4 - - - +
729B ALA* 1.4 71.2 - - - +
731B GLY* 1.3 63.7 + - - +
733B LYS* 3.4 5.8 + - - +
734B TYR* 3.1 19.1 + - - +
875B VAL* 3.7 11.2 - - + +
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Residues in contact with GLY 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B HIS* 3.9 8.7 - - - -
679B ASN* 3.7 28.0 - - - +
680B ILE* 3.4 14.4 - - - +
727B GLY 3.0 10.7 + - - -
728B ILE 3.7 3.4 - - - -
730B ALA* 1.3 75.4 - - - +
732B MET* 1.4 57.3 + - - +
734B TYR 3.4 1.2 + - - -
735B LEU* 2.9 25.2 + - - +
760B VAL* 4.4 4.5 - - - -
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Residues in contact with MET 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ILE* 2.9 23.2 + - + +
729B ALA 3.7 0.2 - - - +
731B GLY* 1.4 73.7 - - - +
733B LYS* 1.3 58.4 + - - +
735B LEU* 4.0 21.2 - - + +
736B SER* 2.9 34.6 + - - +
742B HIS* 4.1 6.5 - - + -
745B LEU* 3.8 31.6 - - + -
760B VAL* 4.0 26.9 - - + -
806B ASP* 3.4 30.7 - - + +
871B PHE* 3.5 41.3 - - + -
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Residues in contact with LYS 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A GLN* 4.1 18.3 + - - +
676A ASP* 6.0 6.7 - - + +
734A TYR* 4.9 5.1 + - - -
738A MET* 4.4 8.1 - - - +
729B ALA 2.8 20.3 + - - +
730B ALA* 3.4 8.9 + - - +
732B MET* 1.3 71.1 - - - +
734B TYR* 1.3 57.2 + - - +
736B SER* 3.2 3.0 + - - -
737B GLU* 2.8 67.5 + - - +
871B PHE* 3.6 16.1 - - + +
872B ALA* 3.7 35.4 - - - +
875B VAL* 4.2 17.5 - - + -
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Residues in contact with TYR 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A HIS* 5.1 0.2 - + - -
733A LYS* 4.9 5.0 + - - -
734A TYR* 4.0 31.2 - + - -
674B GLN 3.9 5.9 + - - -
675B PHE* 3.6 34.3 - + + -
676B ASP* 2.9 35.3 + - - +
677B HIS* 3.5 32.3 - + + -
680B ILE* 3.2 21.3 - - + -
730B ALA 3.1 5.5 + - - +
731B GLY 3.5 7.2 - - - +
733B LYS* 1.3 81.4 - - - +
735B LEU* 1.3 61.4 + - - +
737B GLU* 3.8 4.9 - - - +
738B MET* 3.1 45.6 + - + +
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Residues in contact with LEU 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B PHE* 4.0 14.4 - - + -
680B ILE* 4.3 5.8 - - + -
731B GLY 2.9 17.6 + - - +
732B MET* 4.0 26.0 - - + +
734B TYR* 1.3 80.7 - - - +
736B SER* 1.3 62.1 + - - +
738B MET* 3.1 18.4 + - - +
740B TYR* 3.3 46.6 + - + +
742B HIS* 4.0 20.2 - - + +
760B VAL* 4.7 5.2 - - + -
763B PHE* 3.4 37.7 - - + -
766B SER* 4.6 2.7 - - - +
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Residues in contact with SER 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B MET* 2.9 27.2 + - - -
733B LYS* 3.2 9.5 + - - -
735B LEU* 1.3 74.1 - - - +
737B GLU* 1.3 62.9 + - - +
739B ASN* 3.0 22.5 + - - +
740B TYR 3.6 12.1 + - - -
769B LEU* 5.5 0.9 - - - +
803B SER* 3.2 27.3 + - - -
806B ASP* 5.8 0.7 - - - -
871B PHE* 3.7 19.4 - - - +
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Residues in contact with GLU 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A MET* 4.6 13.3 - - - +
733B LYS* 2.8 64.4 + - - +
734B TYR* 3.8 4.9 - - - +
736B SER* 1.3 75.3 - - - +
738B MET* 1.4 56.6 + - - +
739B ASN* 3.1 15.8 + - - +
872B ALA* 4.0 12.0 + - - +
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Residues in contact with MET 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS* 4.7 8.3 - - - +
737A GLU* 4.6 14.4 - - - +
674B GLN* 3.4 35.7 - - + +
675B PHE* 4.0 21.8 - - + -
734B TYR* 3.1 46.7 + - + +
735B LEU 3.1 11.0 + - - +
737B GLU* 1.4 74.6 - - - +
739B ASN* 1.3 66.6 + - - +
740B TYR* 3.4 11.5 - - + -
768B TYR* 3.6 10.6 - - - -
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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
------------------------------------------------------------
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