Contacts of the helix formed by residues 662 - 684 (chain A) 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 662 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A PHE* 3.5 24.9 - - - -
660A GLU 3.1 0.2 + - - -
661A SER* 1.3 73.2 - - - +
663A VAL* 1.3 64.7 + - - +
664A GLU* 3.2 4.3 - - - +
665A GLY* 3.3 15.0 + - - -
666A ALA 3.9 3.5 + - - -
24B A 4.9 3.4 + - - -
25B C 3.5 24.8 + - - +
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A MET* 3.4 33.7 - - + -
637A TYR* 4.0 29.0 - - + +
641A THR* 3.7 9.8 - - + +
642A VAL* 6.1 0.7 - - - -
645A PHE* 3.4 30.9 - - + -
660A GLU* 3.4 32.7 + - + +
662A GLY* 1.3 77.8 - - - +
664A GLU* 1.3 65.4 + - + +
666A ALA* 3.4 13.3 + - - +
667A ASN* 3.5 9.5 + - - +
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A TYR* 2.9 37.8 + - - -
662A GLY 3.2 1.6 - - - +
663A VAL* 1.3 83.5 - - + +
665A GLY* 1.3 56.7 + - - +
667A ASN* 3.5 7.7 + - + +
668A ARG* 3.0 58.5 + - + +
25B C 4.3 5.6 - - - +
26B A 4.1 19.7 - - - +
38B A 5.0 7.3 + - - -
605D LYS* 5.0 5.2 + - - -
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Residues in contact with GLY 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLY 3.3 6.7 + - - -
663A VAL 3.3 1.0 - - - -
664A GLU* 1.3 76.0 - - - +
666A ALA* 1.3 58.0 + - - +
668A ARG* 3.9 2.4 - - - +
669A PHE* 3.1 27.4 + - - +
672A ARG* 5.3 1.2 + - - -
730A MET* 4.8 6.4 - - - +
24B A 3.9 10.1 - - - +
25B C 3.5 36.9 + - - -
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A THR* 3.6 28.3 - - + +
644A LEU* 4.0 22.1 - - + +
645A PHE* 4.3 14.4 - - + +
648A PHE* 6.5 0.2 - - + -
662A GLY 3.9 3.7 + - - +
663A VAL 3.4 9.5 + - - +
664A GLU 3.3 0.4 - - - -
665A GLY* 1.3 73.9 - - - +
667A ASN* 1.3 58.4 + - - +
669A PHE* 3.3 3.9 + - - +
670A LEU* 3.1 33.5 + - - +
730A MET* 5.6 2.0 - - - -
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Residues in contact with ASN 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.5 16.0 - - - -
7A PRO* 5.2 1.8 - - - +
637A TYR* 3.8 31.9 + - + +
641A THR* 3.4 30.9 + - + +
663A VAL 3.5 4.2 + - - +
664A GLU* 3.5 11.7 + - + +
665A GLY 3.4 0.4 - - - -
666A ALA* 1.3 76.4 - - - +
668A ARG* 1.3 64.9 + - + +
670A LEU* 3.5 3.2 + - - +
671A LYS* 3.2 44.9 + - - +
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Residues in contact with ARG 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLU* 3.0 43.1 + - + +
665A GLY 3.9 4.3 - - - +
667A ASN* 1.3 78.3 - - + +
669A PHE* 1.3 60.8 + - - +
671A LYS* 3.4 10.3 + - + +
672A ARG* 3.1 40.2 + - + +
25B C 3.0 38.5 + - - +
26B A 2.8 30.3 + - - -
39B U 4.3 27.1 + - - +
40B C 5.6 5.6 - - - -
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Residues in contact with PHE 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU* 3.8 23.6 - - + -
665A GLY 3.1 19.7 + - - +
666A ALA* 3.3 4.5 + - - +
668A ARG* 1.3 76.9 - - - +
670A LEU* 1.3 59.6 + - + +
672A ARG* 3.2 32.6 + - + +
673A VAL* 3.0 39.2 + - + +
726A ILE* 5.1 5.2 - - + -
729A ILE* 4.4 6.7 - - + -
730A MET* 3.7 41.5 - - + -
733A MET* 3.9 31.9 - - + -
761A LEU* 3.9 28.9 - - + -
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Residues in contact with LEU 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.1 17.5 - - + +
640A ASP* 4.0 14.6 - - + +
641A THR* 3.8 37.0 - - - +
644A LEU* 4.5 9.9 - - + -
666A ALA 3.1 19.2 + - - +
667A ASN* 4.0 3.8 - - - +
668A ARG 3.4 0.2 - - - -
669A PHE* 1.3 78.1 - - + +
671A LYS* 1.3 59.4 + - - +
673A VAL* 3.4 6.2 + - + +
674A TRP* 3.0 29.1 + - - +
761A LEU* 5.0 9.2 - - + -
765A THR* 4.1 15.9 - - + +
768A ILE* 3.8 35.3 - - + +
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Residues in contact with LYS 671 (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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4A GLN* 5.5 8.5 - - - +
5A TYR* 4.3 33.2 - - + +
667A ASN* 3.2 41.9 + - - +
668A ARG* 3.6 7.6 - - + +
669A PHE 3.3 0.2 - - - -
670A LEU* 1.3 76.0 - - - +
672A ARG* 1.3 58.6 + - + +
674A TRP* 3.5 6.7 + - - +
675A LYS* 2.9 30.1 + - - +
38B A 4.6 17.2 + - - -
39B U 4.1 17.2 + - - +
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Residues in contact with ARG 672 (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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665A GLY 5.3 1.0 + - - -
668A ARG* 3.1 35.7 + - - +
669A PHE* 3.2 39.6 + - + +
671A LYS* 1.3 74.2 - - + +
673A VAL* 1.3 63.0 + - - +
675A LYS* 3.6 7.4 + - + +
676A LEU* 3.2 23.9 + - - +
730A MET* 5.2 2.6 - - - +
733A MET* 3.8 10.9 - - + +
734A ASN* 4.2 13.8 + - - -
24B A 4.0 24.2 + - - -
25B C 5.3 3.8 + - - -
40B C 4.2 24.4 + - - +
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Residues in contact with VAL 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 3.0 41.8 + - + +
670A LEU* 3.8 11.4 - - + +
671A LYS 3.4 0.2 - - - -
672A ARG* 1.3 73.7 - - - +
674A TRP* 1.3 63.4 + - - +
676A LEU* 3.5 2.6 + - - +
677A VAL* 3.3 28.3 + - + +
733A MET* 3.7 27.8 - - + +
754A LEU* 5.9 1.8 - - + -
757A VAL* 5.1 3.4 - - + -
758A VAL* 5.0 7.4 - - + -
761A LEU* 4.2 19.1 - - + -
768A ILE* 5.2 4.3 - - + -
769A CYS* 6.5 0.4 - - - -
772A LEU* 3.9 21.5 - - + -
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Residues in contact with TRP 674 (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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1A MET* 3.5 30.5 - - + +
2A GLN* 3.1 25.7 + - + -
3A GLU 3.2 20.2 + - - -
4A GLN 3.7 8.9 + - - -
5A TYR* 3.8 34.1 - + + -
6A ARG 5.6 0.2 - - - -
10A ILE* 3.9 28.3 - - + -
670A LEU 3.0 18.4 + - - +
671A LYS 3.8 4.5 - - - +
672A ARG 3.4 0.2 - - - -
673A VAL* 1.3 77.5 - - - +
675A LYS* 1.3 57.7 + - - +
677A VAL* 3.6 2.3 + - - +
678A TYR* 3.1 28.8 + - + +
768A ILE* 3.9 13.2 - - + -
771A THR* 4.0 21.3 - - + -
772A LEU* 3.7 35.0 - - + -
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Residues in contact with LYS 675 (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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3A GLU* 5.5 2.2 - - + -
671A LYS 2.9 19.5 + - - +
672A ARG* 3.9 8.7 - - + +
673A VAL 3.3 0.2 - - - -
674A TRP* 1.3 80.5 - - - +
676A LEU* 1.3 61.1 + - - +
678A TYR* 3.5 8.2 + - + +
679A GLU* 3.2 52.5 + - + +
39B U 4.5 23.6 + - - +
40B C 4.8 9.9 + - - +
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Residues in contact with LEU 676 (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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672A ARG 3.2 17.4 + - - +
673A VAL 3.9 4.5 - - - +
674A TRP 3.4 0.4 - - - -
675A LYS* 1.3 76.5 - - - +
677A VAL* 1.3 57.9 + - - +
679A GLU* 3.9 12.4 + - + +
680A HIS* 3.2 26.2 + - - +
733A MET* 3.4 28.7 - - + +
736A LEU* 4.0 28.0 - - + +
737A ALA* 4.7 11.2 - - + +
741A THR* 6.1 0.7 - - + -
750A MET* 4.3 20.9 - - + -
754A LEU* 3.7 22.0 - - + -
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Residues in contact with VAL 677 (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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1A MET* 3.9 11.7 - - + -
673A VAL* 3.3 17.1 + - + +
674A TRP 4.1 0.4 - - - +
676A LEU* 1.3 74.1 - - - +
678A TYR* 1.3 60.0 + - - +
680A HIS* 3.6 4.9 - - - +
681A THR* 2.8 37.1 + - + +
754A LEU* 3.8 28.5 - - + -
758A VAL* 4.8 4.3 - - + -
772A LEU* 3.8 35.2 - - + -
775A GLU* 4.7 2.0 - - + -
776A LEU* 3.8 31.2 - - + -
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Residues in contact with TYR 678 (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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1A MET* 3.9 28.4 - - + -
2A GLN 3.7 15.9 - - - +
3A GLU* 3.7 51.4 + - + +
674A TRP* 3.1 21.3 + - + +
675A LYS* 3.6 9.6 - - + +
676A LEU 3.5 0.2 - - - -
677A VAL* 1.3 76.0 - - - +
679A GLU* 1.3 76.6 + - + +
681A THR* 3.4 6.5 + - - -
682A ALA* 3.2 35.3 + - + +
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Residues in contact with GLU 679 (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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675A LYS* 3.2 48.5 + - + +
676A LEU* 4.2 13.7 - - + +
678A TYR* 1.3 88.8 - - + +
680A HIS* 1.3 61.2 + - - +
682A ALA* 4.2 4.5 - - - +
683A LYS* 3.4 36.2 + - - +
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A LEU* 3.2 20.7 + - + +
677A VAL 3.3 3.8 + - - +
679A GLU* 1.3 79.8 - - - +
681A THR* 1.3 65.9 + - + +
682A ALA 3.6 0.3 + - - -
683A LYS* 3.6 11.6 + - - +
684A GLY 5.4 0.9 + - - -
686A VAL* 3.9 12.6 - - + +
741A THR* 5.7 1.4 - - - +
747A ARG* 3.0 66.2 + - - +
750A MET* 3.4 17.6 - - + +
751A GLN* 2.8 38.0 + - - -
754A LEU* 3.7 19.1 - - + -
776A LEU* 4.1 11.0 - - + -
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Residues in contact with THR 681 (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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1A MET* 3.8 13.1 - - - +
677A VAL* 2.8 40.9 + - + +
678A TYR* 3.4 5.2 + - - -
680A HIS* 1.3 75.5 - - + +
682A ALA* 1.3 64.5 + - - +
684A GLY* 3.2 20.3 + - - +
775A GLU* 3.4 31.3 + - + +
776A LEU* 4.2 11.0 - - + -
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Residues in contact with ALA 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A TYR* 3.2 30.8 + - + +
679A GLU* 4.2 6.5 - - - +
680A HIS 3.4 0.4 - - - -
681A THR* 1.3 76.8 + - - +
683A LYS* 1.3 61.5 + - + +
684A GLY* 3.6 0.5 + - - -
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Residues in contact with LYS 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A GLU* 3.4 29.2 + - - +
680A HIS* 3.6 6.5 + - - +
681A THR 3.2 0.6 - - - -
682A ALA* 1.3 79.1 - - + +
684A GLY* 1.3 56.5 + - - +
741A THR* 2.8 34.1 + - - +
747A ARG* 3.6 35.0 - - - +
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Residues in contact with GLY 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A HIS* 4.1 2.1 + - - +
681A THR* 3.2 17.9 + - - +
682A ALA 4.5 0.9 - - - -
683A LYS* 1.3 80.2 - - - +
685A ASP* 1.3 64.0 + - - -
686A VAL* 4.4 2.1 - - - +
747A ARG* 2.8 18.4 + - - +
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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
------------------------------------------------------------
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