Contacts of the helix formed by residues 48 - 70 (chain Z) in PDB entry 3SDI
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 PHE 48 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951 ARG* 3.7 11.0 - - - -
1241 LEU* 3.7 19.7 - - + -
1261 VAL* 3.4 22.9 - - + -
-6Z PRO 3.4 25.8 - - - -
-5Z TYR* 4.0 9.2 - + - -
-4Z GLY* 3.3 42.1 + - - +
-2Z ASN* 3.8 4.5 - - - -
47Z GLY* 1.3 68.5 - - - +
49Z ALA* 1.3 65.9 + - - +
50Z ALA* 3.5 19.5 - - + -
51Z ASP* 3.0 31.6 + - + +
52Z GLY 2.9 18.2 + - - -
96Z TYR* 3.0 25.4 + - + +
97Z VAL* 3.7 3.0 - - - +
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Residues in contact with ALA 49 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261 VAL* 4.8 6.7 - - + -
1271 THR 5.4 4.7 - - - +
-2Z ASN* 2.8 32.6 + - + +
20Z ASN* 4.1 14.6 - - - +
47Z GLY 3.3 5.0 + - - +
48Z PHE* 1.3 71.6 - - - +
50Z ALA* 1.3 54.8 + - - +
52Z GLY* 3.7 3.5 - - - +
53Z ASP* 2.9 41.2 + - - +
97Z VAL* 5.7 0.2 - - - -
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Residues in contact with ALA 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 TYR* 3.6 17.4 - - + -
1241 LEU 3.6 15.5 - - - +
1251 GLY 3.6 23.3 - - - +
1261 VAL* 3.8 8.1 - - + +
1271 THR 5.7 0.2 - - - +
48Z PHE* 3.2 28.2 - - + -
49Z ALA* 1.3 77.8 - - - +
51Z ASP* 1.3 62.3 + - - +
53Z ASP* 3.7 6.4 - - - +
54Z ALA* 3.2 17.0 + - - +
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Residues in contact with ASP 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 TYR* 2.7 28.5 + - - -
951 ARG* 2.8 17.7 + - - -
-5Z TYR* 3.6 9.0 - - - -
48Z PHE* 3.0 22.3 + - + +
50Z ALA* 1.3 77.3 - - - +
52Z GLY* 1.3 64.2 + - - +
54Z ALA* 3.2 4.5 + - - +
55Z LEU* 3.1 20.5 + - - +
90Z LYS* 5.6 0.2 - - - -
94Z PRO 3.2 7.2 - - - +
95Z TYR* 3.0 26.0 - - + -
96Z TYR 2.8 30.8 + - - +
97Z VAL* 4.3 2.7 - - + -
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Residues in contact with GLY 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Z ALA* 3.5 30.0 - - - +
48Z PHE 2.9 11.8 + - - -
49Z ALA* 3.3 4.0 + - - -
51Z ASP* 1.3 76.6 - - - +
53Z ASP* 1.3 58.0 + - - +
55Z LEU* 3.4 2.6 + - - +
56Z VAL* 3.0 35.6 + - - +
97Z VAL* 3.6 8.4 - - - +
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Residues in contact with ASP 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191 ARG* 4.7 4.9 + - - -
1251 GLY 5.7 0.2 - - - +
1271 THR* 3.7 23.6 + - - +
31Z GLU* 5.6 0.3 - - - +
35Z PHE* 4.8 15.3 - - - -
49Z ALA* 2.9 25.3 + - - +
50Z ALA* 3.7 7.1 - - - +
52Z GLY* 1.3 74.4 - - - +
54Z ALA* 1.3 60.6 + - - +
56Z VAL* 3.9 4.3 - - - +
57Z LYS* 2.9 37.7 + - + +
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Residues in contact with ALA 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 TYR* 3.5 36.1 - - + +
50Z ALA 3.2 6.7 + - - +
51Z ASP 3.2 8.9 + - - +
53Z ASP* 1.3 78.7 - - - +
55Z LEU* 1.3 58.7 + - - +
57Z LYS* 3.3 8.5 - - - +
58Z ARG* 2.8 36.0 + - + +
95Z TYR* 3.9 11.2 - - + +
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Residues in contact with LEU 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Z MET* 4.0 17.5 - - + -
45Z ALA* 3.9 13.7 - - + -
51Z ASP 3.1 15.1 + - - +
52Z GLY* 3.7 4.3 - - - +
53Z ASP 3.3 0.2 - - - -
54Z ALA* 1.3 73.2 - - - +
56Z VAL* 1.3 60.2 + - - +
58Z ARG* 3.1 7.2 + - + +
59Z PHE* 2.8 29.3 + - - +
83Z ILE* 5.1 1.6 - - + +
86Z LEU* 3.9 28.5 - - + -
87Z LEU* 3.9 19.3 - - + -
95Z TYR* 3.9 32.4 - - + +
97Z VAL* 4.2 5.2 - - + -
99Z THR* 3.5 25.8 - - + +
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Residues in contact with VAL 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z PHE* 3.7 44.2 - - + -
37Z CYS* 4.8 4.9 - - - -
43Z MET* 4.1 25.1 - - + -
45Z ALA* 4.3 16.6 - - + +
52Z GLY 3.0 22.4 + - - +
53Z ASP* 4.0 4.3 - - - +
55Z LEU* 1.3 74.6 - - - +
57Z LYS* 1.3 57.8 + - - +
59Z PHE* 3.1 2.9 + - - +
60Z LYS* 2.9 48.6 + - + +
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Residues in contact with LYS 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 GLU* 2.9 24.8 + - - -
891 THR* 5.0 3.6 + - - -
100S SER 4.8 1.2 + - - -
101S LEU* 2.8 55.4 + - + +
53Z ASP* 2.9 25.7 + - + +
54Z ALA* 3.3 9.0 - - - +
56Z VAL* 1.3 73.5 - - - +
58Z ARG* 1.3 59.6 + - + +
60Z LYS* 3.4 8.2 + - + +
61Z ASN* 3.0 30.2 + - - +
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Residues in contact with ARG 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Z ALA* 2.8 22.9 + - + +
55Z LEU* 3.1 6.7 + - - +
57Z LYS* 1.3 76.6 - - + +
59Z PHE* 1.3 57.8 + - - +
61Z ASN* 3.8 6.6 - - - +
62Z SER* 3.0 24.8 + - - -
86Z LEU* 3.6 54.7 + - + +
90Z LYS* 5.1 3.8 - - - +
95Z TYR* 3.1 32.0 + - - -
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Residues in contact with PHE 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z CYS* 3.8 30.3 - - + -
41Z ILE* 4.2 14.1 - - + -
43Z MET* 3.6 31.4 - - + -
55Z LEU 2.8 15.6 + - - +
56Z VAL 3.7 3.1 - - - +
58Z ARG* 1.3 76.0 - - - +
60Z LYS* 1.3 65.4 + - - +
61Z ASN 3.1 0.2 - - - -
62Z SER* 3.0 6.5 + - - -
63Z VAL* 3.0 37.9 + - + +
74Z LEU* 4.1 8.5 - - + -
79Z ALA* 3.7 31.4 - - + -
82Z ASN* 3.9 19.7 - - - -
83Z ILE* 3.7 26.7 - - + -
86Z LEU* 4.0 8.3 - - + +
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Residues in contact with LYS 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z PHE* 4.2 27.4 - - - +
36Z ASP 3.5 24.6 + - - -
37Z CYS* 4.0 22.3 - - + +
56Z VAL* 2.9 27.9 + - + +
57Z LYS* 3.8 7.6 - - + +
59Z PHE* 1.3 76.7 - - - +
61Z ASN* 1.3 60.9 - - - +
63Z VAL* 3.3 10.0 + - - +
64Z LYS* 3.2 20.3 + - - +
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Residues in contact with ASN 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S ASN* 2.8 44.7 + - - +
101S LEU* 4.0 23.2 - - + +
57Z LYS 3.0 17.2 + - - +
58Z ARG* 3.8 7.4 - - - +
60Z LYS* 1.3 75.3 - - - +
62Z SER* 1.3 65.3 + - - +
64Z LYS* 3.2 11.9 + - - +
65Z TRP* 3.1 40.3 + - - -
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Residues in contact with SER 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R TYR* 4.7 8.8 + - - -
58Z ARG 3.0 17.9 + - - -
59Z PHE* 3.1 15.5 - - - -
61Z ASN* 1.3 76.2 - - - +
63Z VAL* 1.3 56.8 + - - +
65Z TRP* 3.3 5.7 + - - +
66Z TYR* 2.8 29.5 + - - +
74Z LEU* 5.8 1.3 - - - -
82Z ASN* 2.6 34.4 + - - -
86Z LEU* 5.1 5.1 - - - +
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Residues in contact with VAL 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z CYS 3.9 21.1 - - - +
38Z GLY* 4.9 2.2 - - - -
39Z ASP* 4.4 12.1 - - + +
41Z ILE* 5.3 3.1 - - + -
59Z PHE* 3.0 45.4 + - + +
60Z LYS* 3.4 8.7 - - - +
61Z ASN 3.2 0.2 - - - -
62Z SER* 1.3 73.6 - - - +
64Z LYS* 1.3 65.2 + - - +
66Z TYR* 3.2 9.6 + - - +
67Z HIS* 3.2 44.3 + - + +
74Z LEU* 3.8 14.6 - - + -
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Residues in contact with LYS 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S CYS 5.6 0.2 + - - -
71S ASP* 3.1 33.4 + - - +
72S GLU* 5.5 8.5 - - - -
96S CYS* 5.8 0.2 - - - +
97S ASN* 3.7 32.9 - - + +
100S SER* 4.6 10.7 + - - -
60Z LYS 3.2 9.8 + - - +
61Z ASN* 3.2 13.4 + - - +
63Z VAL* 1.3 79.3 - - - +
65Z TRP* 1.3 63.5 + - + +
67Z HIS* 3.1 21.1 + - - +
68Z PHE* 3.1 42.0 + - + -
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Residues in contact with TRP 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S ASN* 4.3 21.5 - - - -
93S ARG* 3.7 33.9 - - + -
94S GLN* 4.2 28.5 - - + -
97S ASN* 3.4 23.6 + - + +
61Z ASN* 3.1 39.2 + - - +
62Z SER* 3.9 5.4 - - - +
64Z LYS* 1.3 78.7 - - + +
66Z TYR* 1.3 61.5 + - - +
68Z PHE* 3.6 20.1 - + + +
69Z ASP* 2.8 60.7 + - - +
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Residues in contact with TYR 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99R HIS* 4.4 2.9 - + - -
103R TYR* 3.6 34.1 + + + +
105R GLU* 2.3 40.2 + - - -
62Z SER 2.8 15.5 + - - +
63Z VAL* 3.2 12.8 + - - +
65Z TRP* 1.3 77.0 - - - +
67Z HIS* 1.3 58.0 + - - +
70Z HIS* 3.0 53.9 + - + +
72Z LYS* 3.4 47.8 + - + +
73Z LYS 4.1 1.4 + - - -
74Z LEU* 3.7 42.5 - - + +
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Residues in contact with HIS 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S LYS* 6.1 3.6 - - - +
38Z GLY* 6.1 0.2 - - - -
39Z ASP* 2.9 41.9 + - - -
63Z VAL* 3.2 25.6 + - + +
64Z LYS* 3.1 11.3 + - - +
66Z TYR* 1.3 76.3 - + - +
68Z PHE* 1.3 69.0 + - + +
70Z ASN* 3.4 5.0 + - - -
71Z ASP* 2.9 54.3 + - - +
72Z LYS 3.0 21.9 + - - -
74Z LEU 4.6 0.2 - - - -
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Residues in contact with PHE 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S LYS* 4.1 31.0 - - + -
70S CYS 3.7 22.4 - - - -
71S ASP* 4.5 2.0 - - - -
86S ARG* 5.9 0.7 + - - -
93S ARG* 3.5 64.8 + - + +
97S ASN* 6.5 0.7 - - + -
64Z LYS* 3.1 39.0 + - + -
65Z TRP* 3.6 35.0 - + + +
67Z HIS* 1.3 83.6 - - + +
69Z ASP* 1.3 66.4 + - - +
70Z ASN* 4.3 3.3 + - - -
71Z ASP* 5.7 1.3 - - - -
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Residues in contact with ASP 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110R GLU* 5.2 3.3 - - - +
111R SER* 3.2 18.0 + - - -
114R GLN* 6.1 1.0 - - - +
86S ARG* 5.4 9.6 + - - +
90S ASN* 5.3 2.9 + - - -
93S ARG* 4.9 3.1 + - - -
65Z TRP* 2.8 46.0 + - - +
66Z TYR* 4.9 0.2 - - - -
68Z PHE* 1.3 77.3 - - - +
70Z HIS* 1.3 82.2 + - + +
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Residues in contact with HIS 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R HIS* 3.1 38.8 + + - -
103R TYR* 4.8 7.4 - + - -
107R ILE* 4.6 4.6 - - + +
108R ASN* 3.9 18.3 - - + +
110R GLU* 5.8 0.2 - - - -
111R SER* 3.1 35.5 + - - +
66Z TYR* 3.0 38.5 + + + +
67Z HIS 3.9 0.2 - - - -
68Z PHE 3.4 0.2 - - - -
69Z ASP* 1.3 98.4 + - + +
70Z ASN* 1.3 70.8 + - - +
71Z ASP 3.3 2.0 - - - -
72Z LYS* 3.1 25.1 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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