Contacts of the helix formed by residues 49 - 69 (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 HIS 49 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER* 5.4 3.7 + - - -
47D ARG 4.4 5.6 - - - -
48D LEU* 1.3 76.5 - - - +
50D MET* 1.3 63.5 + - - +
51D GLY* 3.1 12.0 + - - -
52D HIS* 2.9 57.6 + + - +
53D VAL* 3.1 14.1 + - - +
620D MET* 3.6 21.9 + - + +
621D SER* 4.3 15.1 - - - -
622D LYS 5.1 2.0 + - - -
627D GLY* 3.7 26.7 - - - -
628D ILE 3.5 9.9 - - - +
630D PRO* 4.2 0.4 - - - -
901D LSS 3.6 28.8 + + - -
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Residues in contact with MET 50 (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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49D HIS* 1.3 74.5 - - - +
51D GLY* 1.3 57.3 + - - +
53D VAL* 3.7 10.4 - - + +
54D ARG* 3.0 31.0 + - - +
569D VAL* 3.9 14.3 - - + +
620D MET* 3.8 15.1 - - + -
628D ILE* 3.4 22.4 + - + +
630D PRO* 3.9 22.4 - - + -
633D MET* 4.8 3.8 - - + +
642D VAL* 4.0 22.7 - - + -
646D MET* 3.7 26.7 - - - +
658D TRP* 3.8 41.1 - - + -
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D HIS* 3.1 8.8 + - - -
50D MET* 1.3 77.9 - - - +
52D HIS* 1.3 59.8 + - - +
54D ARG* 4.1 0.5 - - - +
55D ASN* 3.3 18.0 + - - +
566D GLN* 3.6 0.9 + - - -
569D VAL* 3.9 7.6 - - - +
620D MET* 4.1 2.6 - - - -
901D LSS 3.3 52.4 + - - -
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Residues in contact with HIS 52 (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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42D PRO* 3.8 9.9 - - + +
43D TYR 5.0 2.5 - - - -
45D SER* 5.0 4.0 - - - -
47D ARG 4.8 1.3 - - - -
48D LEU* 3.9 26.5 - - + +
49D HIS* 2.9 54.9 + + - +
51D GLY* 1.3 71.9 - - - +
53D VAL* 1.3 67.3 + - + +
55D ASN* 3.2 2.3 + - - +
56D TYR* 3.0 49.2 + + + -
108D MET* 4.7 8.1 - - + -
901D LSS 2.9 53.6 + - - -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 5.1 2.9 - - + -
49D HIS 3.1 12.8 + - - +
50D MET* 3.8 23.6 - - + +
51D GLY 3.4 0.2 - - - -
52D HIS* 1.3 75.0 - - + +
54D ARG* 1.3 56.7 + - - +
56D TYR* 5.2 0.4 - - - -
57D THR* 2.6 48.4 + - - +
115D LEU* 4.1 24.0 - - + -
117D PHE* 4.4 6.2 - - - -
630D PRO* 3.7 31.9 - - + -
642D VAL* 4.4 11.9 - - + +
643D ARG* 5.6 1.1 - - + -
646D MET* 4.2 12.1 - - + -
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Residues in contact with ARG 54 (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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50D MET 3.0 19.1 + - - +
51D GLY 4.1 1.3 - - - +
53D VAL* 1.3 76.8 - - - +
55D ASN* 1.3 61.4 + - - +
57D THR* 4.6 0.2 - - - -
58D ILE* 3.2 40.2 + - + +
566D GLN* 3.3 16.0 + - - +
567D GLY 3.3 14.5 + - - -
568D MET 4.0 1.2 + - - -
569D VAL* 3.5 15.8 - - + +
646D MET* 4.2 17.5 + - + +
647D MET* 4.1 16.3 - - + +
650D SER* 3.8 15.0 + - - -
651D PRO 2.7 32.9 + - - -
652D ALA* 3.5 10.5 + - - +
654D MET 2.8 22.3 + - - -
656D LEU* 3.3 35.7 - - - +
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Residues in contact with ASN 55 (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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39D SER* 3.8 15.9 + - - -
40D MET 4.3 0.6 - - - +
51D GLY 3.3 7.3 + - - +
52D HIS* 3.2 9.7 + - - +
54D ARG* 1.3 80.7 - - - +
56D TYR* 1.3 63.3 + - + +
58D ILE* 3.7 4.7 + - - +
59D GLY 3.3 18.7 + - - -
528D ILE* 3.3 28.4 + - - +
529D GLY* 3.5 9.9 - - - -
566D GLN* 3.1 30.2 + - - +
901D LSS 2.6 36.5 + - - +
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Residues in contact with TYR 56 (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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39D SER* 3.6 24.5 - - - -
40D MET 2.7 29.7 + - - -
42D PRO* 3.2 32.2 - - + +
48D LEU* 5.2 1.3 - - + -
52D HIS* 3.0 45.9 + + + +
55D ASN* 1.3 79.5 - - + +
57D THR* 1.3 60.5 + - - +
59D GLY* 3.8 1.7 - - - +
60D ASP* 3.0 28.8 + - - +
75D GLN* 4.4 2.3 - - - +
77D ILE* 4.4 9.0 - - + -
112D LEU* 4.1 21.5 - - + -
117D PHE* 3.8 20.8 - + + -
119D TYR* 3.2 25.9 + - - +
901D LSS 3.5 9.3 - - - -
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Residues in contact with THR 57 (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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53D VAL* 2.6 34.5 + - - +
54D ARG* 4.6 0.2 - - - -
56D TYR* 1.3 75.1 - - - +
58D ILE* 1.3 65.5 + - - +
60D ASP* 3.3 1.9 + - - +
61D VAL* 3.0 33.2 + - + +
117D PHE* 3.7 16.9 - - - -
643D ARG* 3.8 46.7 - - + +
646D MET* 5.2 0.8 - - + +
647D MET* 3.9 24.0 - - + -
764D PHE 5.3 0.4 - - - +
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Residues in contact with ILE 58 (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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54D ARG* 3.2 27.6 + - + +
55D ASN* 3.7 4.0 - - - +
57D THR* 1.3 77.9 - - - +
59D GLY* 1.3 61.9 + - - +
61D VAL* 3.4 2.9 + - - +
62D ILE* 3.2 31.3 + - + +
528D ILE* 3.9 9.9 - - + -
564D LEU* 3.9 27.1 - - + -
566D GLN* 3.8 26.9 - - + +
647D MET* 3.6 24.2 - - + -
652D ALA* 3.8 23.1 - - + -
722D PHE* 3.9 14.1 - - + -
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Residues in contact with GLY 59 (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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37D CYS* 3.4 8.0 - - - -
39D SER* 3.9 20.2 - - - -
55D ASN 3.3 7.3 + - - -
56D TYR 3.6 1.8 + - - -
57D THR 3.3 0.4 - - - -
58D ILE* 1.3 80.1 - - - +
60D ASP* 1.3 50.7 + - - +
62D ILE 3.3 1.0 + - - -
63D ALA* 2.8 34.0 + - - +
75D GLN* 3.2 9.0 - - - +
528D ILE* 4.2 16.8 - - - +
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Residues in contact with ASP 60 (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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56D TYR 3.0 18.4 + - - +
57D THR 3.3 2.0 + - - +
59D GLY* 1.3 73.0 - - - +
61D VAL* 1.3 60.9 + - - +
63D ALA* 3.9 1.1 - - - +
64D ARG* 2.8 57.1 + - - +
75D GLN* 2.9 31.8 + - - +
116D GLY 3.8 1.2 - - - +
117D PHE* 3.8 11.7 - - + -
118D GLY* 3.0 18.6 + - - -
643D ARG* 2.7 34.6 + - - +
763D PRO 4.6 0.4 - - - -
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Residues in contact with VAL 61 (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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57D THR* 3.0 29.8 + - + +
58D ILE* 3.6 5.8 - - - +
60D ASP* 1.3 77.0 - - - +
62D ILE* 1.3 56.0 + - - +
65D TYR* 3.0 30.7 + - - +
647D MET* 4.5 4.0 - - + -
716D ILE* 4.6 6.3 - - + -
722D PHE* 3.4 31.6 - - + -
763D PRO* 3.4 35.9 - - + +
764D PHE* 3.7 33.4 - - + -
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Residues in contact with ILE 62 (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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35D TYR* 4.3 4.5 - - + +
37D CYS* 3.9 14.4 - - - -
58D ILE* 3.2 33.6 + - + +
59D GLY 3.8 4.5 - - - +
61D VAL* 1.3 75.5 - - - +
63D ALA* 1.3 59.5 + - - +
65D TYR* 3.7 7.1 - - + +
66D GLN* 3.0 45.6 + - + +
526D ILE* 4.0 33.9 - - + -
528D ILE* 4.3 7.4 - - + -
564D LEU* 4.2 8.7 - - + -
716D ILE* 5.2 5.8 - - + +
720D GLN* 4.6 7.4 - - + +
722D PHE* 4.1 17.0 - - + -
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Residues in contact with ALA 63 (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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37D CYS* 4.0 7.6 - - - -
59D GLY 2.8 17.3 + - - +
60D ASP* 3.3 5.8 + - - +
62D ILE* 1.3 77.8 - - - +
64D ARG* 1.3 58.0 + - + +
66D GLN* 4.9 0.4 - - - -
67D ARG* 3.2 23.9 + - - +
73D VAL* 3.6 25.8 - - + +
75D GLN* 3.6 35.7 - - + +
118D GLY 5.5 0.2 - - - +
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Residues in contact with ARG 64 (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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18D TRP* 3.3 22.2 - - - -
24D PHE* 3.5 31.3 - - + -
60D ASP* 2.8 46.4 + - - +
63D ALA* 1.3 69.1 - - + +
65D TYR* 1.3 65.2 + - - +
67D ARG* 3.4 8.5 + - - +
68D MET* 3.1 30.3 + - - +
116D GLY 3.3 21.2 + - - -
118D GLY 3.9 4.2 - - - +
643D ARG* 4.1 0.2 - - - +
762D ASN* 4.1 12.9 + - - +
763D PRO* 3.9 30.7 - - + -
766D PRO* 3.4 19.1 - - - +
783D ASP* 2.8 29.7 + - - +
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Residues in contact with TYR 65 (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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61D VAL 3.0 21.4 + - - +
62D ILE* 3.7 6.7 - - + +
64D ARG* 1.3 76.1 - - - +
66D GLN* 1.3 85.8 + - + +
68D MET* 3.2 8.8 + - - +
69D LEU* 3.1 46.8 + - + +
713D THR* 3.4 27.7 + - + +
716D ILE* 3.6 24.0 - - + -
717D GLY* 3.9 21.3 - - - -
763D PRO* 4.3 10.4 - - + +
787D TRP* 3.7 46.0 - + - -
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Residues in contact with GLN 66 (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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35D TYR* 3.5 44.9 + - + -
62D ILE* 3.0 27.5 + - + +
63D ALA* 4.7 0.7 - - - -
65D TYR* 1.3 96.1 - - + +
67D ARG* 1.3 65.2 + - - +
69D LEU* 3.5 18.8 + - - +
71D LYS* 3.0 56.9 + - - +
73D VAL* 3.7 14.6 - - + -
717D GLY* 5.5 3.4 + - - -
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Residues in contact with ARG 67 (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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23D THR* 2.9 45.8 + - - +
24D PHE* 4.0 23.1 - - - +
25D GLU 5.2 0.2 + - - -
26D VAL* 3.7 25.7 - - - +
32D LYS* 6.1 0.8 - - - +
63D ALA 3.2 17.2 + - - +
64D ARG* 3.7 8.3 - - - +
65D TYR 3.3 0.2 - - - -
66D GLN* 1.3 76.6 - - - +
68D MET* 1.3 56.7 + - - +
70D GLY* 3.0 22.3 + - - -
71D LYS 3.7 9.6 + - - +
72D ASN* 4.9 3.4 + - - +
73D VAL* 3.3 21.4 + - + +
783D ASP* 3.3 23.7 - - - +
784D ASN* 3.0 26.8 + - - +
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Residues in contact with MET 68 (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 3.1 16.8 + - - +
65D TYR 3.2 8.5 + - - +
67D ARG* 1.3 75.4 - - - +
69D LEU* 1.3 60.6 + - - +
70D GLY* 3.4 1.2 + - - -
759D ARG* 3.5 49.6 - - + +
762D ASN* 3.2 28.3 - - + +
763D PRO* 4.7 4.0 - - - -
782D ILE* 4.2 9.0 - - + +
783D ASP 4.1 12.3 - - - +
785D ALA 3.3 25.0 - - - +
786D PRO* 3.5 7.1 - - - +
787D TRP* 3.0 50.6 + - + -
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Residues in contact with LEU 69 (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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65D TYR* 3.1 51.9 + - + +
66D GLN* 3.5 33.0 - - - +
67D ARG 3.2 0.2 - - - -
68D MET* 1.3 75.4 - - - +
70D GLY* 1.3 56.3 + - - +
71D LYS* 3.7 17.6 - - + +
713D THR* 5.5 2.0 - - + -
787D TRP* 4.2 22.7 - - + -
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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
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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