Contacts of the helix formed by residues 743 - 762 (chain D) in PDB entry 5ON2
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 743 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D ASP* 1.3 80.5 - - - +
744D GLU* 1.3 64.1 + - - -
745D GLN* 3.3 2.9 - - - -
746D ASP* 3.3 26.5 + - - +
747D ARG* 3.3 10.4 + - - +
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Residues in contact with GLU 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D ASP 5.4 3.8 - - - +
686D VAL* 5.6 1.5 - - - +
687D ALA* 4.9 24.1 + - + +
742D ASP 4.7 5.4 - - - +
743D GLY* 1.3 69.3 - - - -
745D GLN* 1.3 58.8 + - - +
747D ARG* 3.5 21.8 + - + +
748D ALA* 3.0 25.5 + - - +
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Residues in contact with GLN 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687D ALA* 6.0 0.9 - - - +
688D ALA 4.0 9.2 - - - +
689D LEU* 4.0 10.5 - - - +
690D ASN* 3.6 30.5 + - - +
693D ALA 3.4 14.1 + - - +
694D LEU* 3.4 30.2 - - - +
698D GLN* 4.8 14.2 + - - +
743D GLY 3.3 1.0 - - - -
744D GLU* 1.3 75.9 - - - +
746D ASP* 1.3 63.8 + - - +
748D ALA* 3.5 6.2 + - - +
749D LEU* 3.3 19.9 + - - +
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Residues in contact with ASP 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D GLN* 2.7 38.7 + - - +
740D PRO* 3.3 50.0 - - - +
741D THR* 4.8 0.7 - - - -
743D GLY* 3.3 20.0 + - - +
745D GLN* 1.3 76.4 - - - +
747D ARG* 1.3 58.7 + - - +
749D LEU* 3.3 11.1 + - - +
750D MET* 2.8 29.3 + - - +
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Residues in contact with ARG 747 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D HIS* 2.8 44.1 + - + -
683D LYS* 3.6 31.2 + - - +
684D GLY 3.3 17.4 + - - -
685D ASP 3.2 22.2 + - - -
686D VAL* 3.2 24.5 - - + +
741D THR* 3.7 32.3 - - + +
742D ASP 4.2 11.9 - - - -
743D GLY 3.3 10.4 + - - +
744D GLU* 3.8 21.5 - - - +
745D GLN 3.3 0.4 - - - -
746D ASP* 1.3 73.3 - - - +
748D ALA* 1.3 59.4 + - - +
749D LEU 3.4 0.2 - - - -
750D MET* 3.9 7.2 - - - -
751D GLN* 3.1 24.6 + - - +
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Residues in contact with ALA 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D VAL* 4.7 2.0 - - - +
687D ALA* 3.6 25.6 - - + +
688D ALA 4.3 0.9 - - - +
689D LEU* 3.8 34.5 - - + +
744D GLU 3.0 15.3 + - - +
745D GLN* 3.5 15.3 - - - +
746D ASP 3.3 0.4 - - - -
747D ARG* 1.3 76.1 - - - +
749D LEU* 1.3 60.8 + - - +
751D GLN* 3.5 8.4 + - - +
752D GLU* 3.4 15.2 + - - +
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Residues in contact with LEU 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689D LEU* 3.9 14.0 - - + +
694D LEU* 5.8 4.5 - - + -
698D GLN* 3.7 39.3 - - + +
701D LEU* 3.9 26.2 - - + -
702D ARG* 3.8 37.5 - - + -
705D VAL* 5.3 6.5 - - + -
736D LEU* 6.3 0.2 - - - -
745D GLN 3.3 10.0 + - - +
746D ASP* 3.3 13.3 + - - +
748D ALA* 1.3 77.8 - - - +
750D MET* 1.3 58.2 + - - +
752D GLU* 3.3 11.4 + - - +
753D ALA* 3.1 26.8 + - + +
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Residues in contact with MET 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D LEU* 4.5 13.9 - - + -
680D HIS* 3.4 31.4 - - + +
701D LEU* 5.4 2.7 - - + -
736D LEU* 3.5 45.3 - - + +
739D ALA* 4.5 11.7 - - + -
740D PRO 4.9 2.7 - - - +
741D THR* 4.0 24.0 - - + +
746D ASP 2.8 18.0 + - - +
747D ARG* 3.7 3.8 - - - +
748D ALA 3.4 0.2 - - - -
749D LEU* 1.3 70.8 - - - +
751D GLN* 1.3 59.7 + - - +
753D ALA* 4.6 2.0 - - - -
754D LEU* 3.1 47.5 + - + +
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Residues in contact with GLN 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D HIS* 2.9 27.5 + - - -
681D THR* 5.9 0.3 - - - +
686D VAL* 3.8 26.1 - - + +
687D ALA 5.9 0.2 - - - +
747D ARG 3.1 16.7 + - - +
748D ALA* 3.6 7.6 - - - +
749D LEU 3.3 0.4 - - - -
750D MET* 1.3 74.5 - - - +
752D GLU* 1.3 63.4 + - - +
754D LEU* 4.0 1.0 - - - +
755D LEU* 3.1 53.9 + - + +
776D LEU* 3.1 37.0 + - - +
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Residues in contact with GLU 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689D LEU* 3.2 15.8 - - + +
702D ARG* 2.9 35.0 + - - -
705D VAL* 5.0 5.2 - - + +
706D HIS* 2.7 33.8 + - - -
748D ALA 3.4 9.3 + - - +
749D LEU* 3.3 13.4 + - + +
751D GLN* 1.3 80.6 - - - +
753D ALA* 1.3 57.5 + - - +
755D LEU* 3.6 9.6 + - - +
756D ALA* 3.1 26.8 + - + +
759D ARG* 5.1 1.4 + - - -
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Residues in contact with ALA 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705D VAL* 3.9 28.0 - - + +
736D LEU* 3.5 35.0 - - + -
749D LEU* 3.1 14.4 + - + +
750D MET* 4.1 4.0 - - - +
752D GLU* 1.3 76.8 - - - +
754D LEU* 1.3 55.4 + - - +
756D ALA* 3.1 3.1 + - - +
757D VAL* 2.7 40.6 + - + +
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Residues in contact with LEU 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D VAL* 6.2 1.1 - - + -
676D LEU* 3.8 31.9 - - + +
677D VAL* 3.9 23.1 - - + -
680D HIS* 3.6 39.3 - - + -
733D MET* 4.9 9.2 - - - -
736D LEU* 5.1 2.9 - - + -
750D MET* 3.1 36.3 + - + +
751D GLN 4.3 1.1 - - - +
753D ALA* 1.3 73.8 - - + +
755D LEU* 1.3 64.6 + - - +
757D VAL* 4.4 5.4 - - + +
758D VAL* 3.2 31.9 + - + +
776D LEU* 3.8 17.4 - - + +
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Residues in contact with LEU 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751D GLN* 3.1 49.4 + - + +
752D GLU* 3.7 8.1 - - - +
753D ALA 3.3 0.2 - - - -
754D LEU* 1.3 77.8 - - - +
756D ALA* 1.3 60.5 + - - +
758D VAL* 4.3 0.7 - - - +
759D ARG* 3.1 43.7 + - - +
773D TRP* 3.5 33.3 - - + -
776D LEU* 4.2 24.0 - - + +
778D GLY* 4.8 7.2 - - - -
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Residues in contact with ALA 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705D VAL* 4.6 4.9 - - + -
709D ILE* 3.7 32.3 - - + -
732D LEU* 6.1 0.2 - - + -
752D GLU* 3.1 14.4 + - + +
753D ALA* 3.1 12.2 + - - +
755D LEU* 1.3 75.4 - - - +
757D VAL* 1.3 64.6 - - + +
759D ARG* 3.5 16.4 + - - +
760D MET* 3.1 31.2 + - + +
788D PRO* 4.3 4.1 - - + +
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Residues in contact with VAL 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D VAL* 5.1 8.5 - - + -
729D ILE* 3.9 11.4 - - + -
732D LEU* 3.7 28.5 - - + -
733D MET* 4.0 20.2 - - + -
736D LEU* 3.9 16.6 - - + -
753D ALA 2.7 22.8 + - - +
754D LEU* 4.2 9.4 - - + +
756D ALA* 1.3 71.1 - - - +
758D VAL* 1.3 59.9 + - + +
760D MET* 3.2 11.7 + - + +
761D LEU* 3.0 52.1 + - + +
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Residues in contact with VAL 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D VAL* 5.1 7.2 - - + -
677D VAL* 4.7 8.7 - - + -
754D LEU* 3.2 20.6 + - + +
755D LEU 4.3 2.5 - - - +
757D VAL* 1.3 77.6 - - + +
759D ARG* 1.3 58.0 + - - +
761D LEU* 3.3 1.9 + - - -
762D ASN* 3.0 23.0 + - - +
769D CYS* 3.2 47.0 - - + +
772D LEU* 4.2 23.8 - - + -
773D TRP* 4.3 10.3 - - + +
776D LEU* 3.9 16.2 - - + -
782D ILE* 3.7 7.6 - - + -
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Residues in contact with ARG 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D MET* 3.5 25.3 - - + +
752D GLU 5.1 1.4 + - - -
755D LEU* 3.1 30.9 + - - +
756D ALA* 3.8 13.2 - - - +
757D VAL 3.3 0.6 - - - -
758D VAL* 1.3 76.9 - - - +
760D MET* 1.3 61.6 + - - +
762D ASN* 3.5 11.0 + - - +
763D PRO* 3.6 0.2 - - - +
773D TRP* 3.5 34.9 - - + -
782D ILE* 4.3 5.2 - - + -
785D ALA* 4.8 2.9 - - - -
786D PRO* 3.2 37.5 + - - +
787D TRP* 3.3 18.3 - - - -
788D PRO* 3.7 36.4 - - + +
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Residues in contact with MET 760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708D THR* 3.8 26.7 - - + +
709D ILE* 3.8 21.5 - - + +
712D VAL* 3.7 35.8 - - + +
729D ILE* 3.8 20.6 - - + +
732D LEU* 4.4 4.3 - - + -
756D ALA* 3.1 26.1 + - + +
757D VAL* 3.2 24.4 + - + +
759D ARG* 1.3 78.1 - - - +
761D LEU* 1.3 59.6 + - - +
763D PRO* 3.5 10.2 - - - +
764D PHE* 3.6 17.7 - - - -
787D TRP* 3.9 18.0 - - + -
788D PRO* 4.5 8.5 - - + -
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Residues in contact with LEU 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644D LEU* 4.1 26.9 - - + -
669D PHE* 4.2 21.5 - - + -
670D LEU* 5.3 4.7 - - + -
673D VAL* 5.3 8.1 - - + -
726D ILE* 5.5 2.5 - - + -
729D ILE* 3.5 37.2 - - + -
757D VAL* 3.0 37.3 + - + +
758D VAL* 3.3 1.3 + - - -
760D MET* 1.3 74.4 - - - +
762D ASN* 1.3 56.0 + - - +
763D PRO* 3.4 1.6 - - - -
764D PHE* 3.0 10.7 + - + +
765D THR* 2.8 40.5 + - - +
769D CYS* 3.4 20.4 - - - -
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Residues in contact with ASN 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 4.1 9.6 - - - +
68D MET* 3.2 25.2 - - - +
758D VAL 3.0 11.5 + - - +
759D ARG 3.5 10.5 - - - +
760D MET 3.4 0.4 - - - -
761D LEU* 1.3 75.6 - - - +
763D PRO* 1.4 67.1 - - + +
766D PRO* 3.2 37.9 - - - +
769D CYS* 3.7 10.8 - - - +
782D ILE* 3.4 46.1 + - + +
783D ASP* 4.2 11.0 + - - +
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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