Contacts of the helix formed by residues 3 - 28 (chain C) in PDB entry 5MJ3
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 SER 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET* 1.3 77.4 - - - +
4C ILE* 1.3 62.2 + - - +
5C GLN* 2.9 20.7 + - - +
6C GLU* 3.0 31.4 + - - +
7C ILE* 3.0 27.4 + - - +
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Residues in contact with ILE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET 3.7 1.5 + - - +
3C SER* 1.3 74.2 + - - +
5C GLN* 1.3 61.7 + - - +
7C ILE* 3.3 8.9 + - + +
8C GLN* 2.9 33.4 + - + +
69C ILE* 3.9 24.5 - - + +
70C TYR* 6.4 0.4 - - + -
72C MET* 3.1 39.9 - - + -
92C ILE* 3.2 20.2 - - + -
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Residues in contact with GLN 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 2.9 12.0 + - - +
4C ILE* 1.3 79.0 - - - +
6C GLU* 1.3 57.3 + - + +
8C GLN* 3.3 6.8 + - - +
9C LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET* 3.2 34.6 - - + +
3C SER* 3.0 29.3 + - - +
4C ILE 3.3 0.4 - - - -
5C GLN* 1.3 77.5 - - + +
7C ILE* 1.3 58.7 + - - +
9C LYS* 3.2 12.9 + - + +
10C GLU* 2.9 30.8 + - - +
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET* 4.1 16.8 - - - +
3C SER 3.0 20.6 + - - +
4C ILE* 3.7 8.7 - - + +
6C GLU* 1.3 75.4 - - - +
8C GLN* 1.3 58.7 + - - +
10C GLU* 3.2 11.0 + - - +
11C ILE* 2.9 31.6 + - + +
69C ILE* 3.7 29.8 - - + -
92C ILE* 3.7 39.0 - - + -
95C ILE* 4.0 12.8 - - + -
96C GLN* 4.0 15.9 - - + -
99C ILE* 3.9 11.9 - - + -
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 2.9 24.5 + - + +
5C GLN* 3.8 5.8 - - - +
7C ILE* 1.3 76.8 - - - +
9C LYS* 1.3 58.6 + - - +
11C ILE* 3.3 10.7 + - - +
12C ALA* 2.9 28.9 + - - +
66C GLN* 2.6 36.7 + - - +
69C ILE* 4.2 16.1 - - + +
70C TYR* 2.5 39.4 + - + -
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Residues in contact with LYS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG 5.9 2.5 - - - +
58B GLU* 5.2 11.2 - - + +
5C GLN 2.9 14.4 + - - +
6C GLU* 3.2 13.0 + - + +
8C GLN* 1.3 76.8 - - - +
10C GLU* 1.3 63.0 + - + +
12C ALA* 3.2 6.7 + - + +
13C GLN* 3.0 49.0 + - + +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET* 3.7 32.9 - - - +
6C GLU 2.9 12.1 + - - +
7C ILE* 3.2 10.7 + - - +
9C LYS* 1.3 77.2 - - + +
11C ILE* 1.3 62.2 + - - +
13C GLN* 3.3 12.9 + - - +
14C ILE* 3.0 29.2 + - - +
96C GLN* 5.3 2.9 - - - +
99C ILE* 3.9 33.6 - - + +
103C GLN* 4.4 13.9 + - - +
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 2.9 23.7 + - + +
8C GLN* 3.7 11.9 - - - +
9C LYS 3.2 0.2 - - - -
10C GLU* 1.3 75.7 - - - +
12C ALA* 1.3 59.6 + - - +
14C ILE* 3.3 8.4 + - - +
15C GLN* 2.8 31.6 + - + +
62C ILE* 3.8 28.5 - - + -
65C ILE* 4.4 11.7 - - + -
66C GLN* 3.8 26.5 - - + +
69C ILE* 3.0 36.8 - - + -
99C ILE* 4.0 15.9 - - + -
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 4.5 20.6 - - - +
55B ASP* 5.6 0.2 - - - +
8C GLN 2.9 17.6 + - - +
9C LYS* 3.2 8.5 + - + +
11C ILE* 1.3 76.3 - - - +
13C GLN* 1.3 59.5 + - + +
15C GLN* 3.4 8.1 + - - +
16C ALA* 2.9 28.6 + - - +
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.3 37.2 - - + +
57B ARG 5.4 2.8 + - - -
58B GLU* 4.6 12.5 + - - +
156B TRP* 4.5 7.7 + - + +
157B GLN* 5.6 0.3 + - - -
160B LEU* 3.4 32.3 - - + +
164B LYS* 5.8 2.8 - - - +
9C LYS* 3.0 36.5 + - + +
10C GLU* 3.7 11.9 - - - +
12C ALA* 1.3 75.5 - - + +
14C ILE* 1.3 66.8 + - - +
16C ALA* 3.2 2.8 + - - +
17C VAL* 3.0 28.5 + - - +
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TRP* 4.0 26.2 - - + -
10C GLU 3.0 19.9 + - - +
11C ILE* 3.6 7.4 - - - +
13C GLN* 1.3 78.8 - - - +
15C GLN* 1.3 63.9 + - - +
17C VAL* 3.3 1.2 + - - +
18C ILE* 3.0 30.5 + - + +
62C ILE* 4.0 17.5 - - + -
99C ILE* 3.6 39.0 - - + +
102C ILE* 4.0 16.2 - - + -
103C GLN* 4.1 13.2 - - + +
106C ILE* 3.5 21.1 - - + -
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Residues in contact with GLN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 2.8 28.7 + - + +
12C ALA* 3.7 7.2 - - - +
14C ILE* 1.3 74.4 - - - +
16C ALA* 1.3 62.1 + - - +
18C ILE* 3.4 18.2 - - - +
19C ALA* 3.1 25.3 + - - +
59C GLN* 4.6 12.4 + - - +
62C ILE* 3.4 33.7 - - + +
63C ALA* 5.4 2.4 - - - +
66C GLN* 4.8 9.2 - - - +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.7 13.0 - - + +
55B ASP* 3.4 41.3 - - + +
56B LEU* 3.9 10.5 - - + -
12C ALA 2.9 18.0 + - - +
13C GLN 3.2 4.0 + - - +
15C GLN* 1.3 77.1 - - - +
17C VAL* 1.3 63.6 + - - +
19C ALA* 3.4 5.8 + - - +
20C GLY* 3.0 18.2 + - - -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 4.2 9.6 - - + -
56B LEU* 4.6 2.7 - - + -
156B TRP* 4.2 13.2 - - + -
159B LEU* 4.3 6.7 - - + -
160B LEU* 3.9 22.7 - - + -
163B PHE* 3.9 31.5 - - + -
13C GLN 3.0 21.0 + - - +
14C ILE 3.9 2.7 - - - +
16C ALA* 1.3 76.0 - - - +
18C ILE* 1.3 59.7 + - - +
20C GLY* 3.1 2.4 + - - -
21C ILE* 2.9 45.5 + - + +
106C ILE* 4.0 15.0 - - + -
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.0 20.0 + - + +
15C GLN* 3.4 20.0 - - - +
17C VAL* 1.3 77.6 - - - +
19C ALA* 1.3 60.0 + - - +
21C ILE* 3.8 7.6 - - + +
22C GLN* 2.9 30.7 + - - +
55C ILE* 4.1 16.4 - - + +
58C ILE* 4.1 18.6 - - + -
59C GLN* 3.4 38.6 - - + +
62C ILE* 4.6 1.8 - - + -
106C ILE* 3.2 42.0 - - + -
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN 3.1 19.2 + - - +
16C ALA* 3.7 6.3 - - - +
18C ILE* 1.3 77.3 - - - +
20C GLY* 1.3 57.9 + - - +
22C GLN* 3.4 14.5 + - - +
23C LYS* 3.0 27.2 + - - +
59C GLN* 4.4 7.9 - - - +
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 3.9 7.7 - - - +
50B LEU 3.0 29.2 + - - +
51B VAL* 5.2 0.9 - - - +
163B PHE* 5.6 0.2 - - - -
16C ALA 3.0 12.0 + - - -
17C VAL* 3.1 3.3 + - - -
19C ALA* 1.3 73.8 - - - +
21C ILE* 1.3 63.8 + - - +
23C LYS* 3.3 7.5 + - - +
24C TYR* 2.9 23.9 + - - +
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Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 4.2 18.1 - - + +
159B LEU* 5.5 0.4 - - + -
163B PHE* 5.2 1.6 - - + -
17C VAL* 2.9 28.3 + - + +
18C ILE* 3.8 7.4 - - + +
20C GLY* 1.3 74.9 - - - +
22C GLN* 1.3 63.6 + - - +
24C TYR* 3.1 7.8 + - + +
25C ILE* 3.0 29.8 + - + +
55C ILE* 3.7 22.0 - - + -
106C ILE* 3.9 28.9 - - + +
109C ILE* 4.3 12.6 - - + -
110C TYR* 4.4 25.4 - - + +
113C ILE* 4.8 8.7 - - + -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE 2.9 15.3 + - - +
19C ALA* 3.4 8.9 - - - +
21C ILE* 1.3 78.6 - - - +
23C LYS* 1.3 61.7 + - - +
25C ILE* 3.4 11.9 + - - +
26C TYR* 3.5 36.5 + - + +
52C GLN* 5.0 5.9 + - + +
55C ILE* 4.0 24.6 - - + +
56C ALA* 4.7 8.9 - - - +
59C GLN* 3.0 40.6 + - - -
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 5.3 15.0 - - + -
19C ALA 3.0 16.0 + - - +
20C GLY* 3.3 7.4 + - - +
22C GLN* 1.3 75.9 - - - +
24C TYR* 1.3 62.9 + - - +
26C TYR* 3.2 33.4 + - + +
27C THR* 3.4 13.7 - - + +
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP 6.0 0.2 - - - -
46B SER 3.4 23.1 + - - -
47B ALA 3.2 16.5 + - - -
48B HIS 3.6 15.9 - - - -
49B PRO* 3.5 29.2 - - + -
50B LEU* 6.3 0.4 - - + -
120B PRO* 4.3 3.3 - - - +
20C GLY 2.9 17.5 + - - +
21C ILE* 3.1 6.3 + - + +
23C LYS* 1.3 77.7 - - - +
25C ILE* 1.3 62.0 + - - +
27C THR* 2.6 37.9 + - + -
28C MET* 3.5 16.1 - - + +
113C ILE* 3.7 22.7 - - + -
114C MET* 3.7 21.7 - - + +
117C VAL* 3.7 23.5 - - + +
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.0 14.1 + - + +
22C GLN* 3.6 9.2 - - - +
23C LYS 3.3 0.2 - - - -
24C TYR* 1.3 76.6 - - + +
26C TYR* 1.3 68.3 + - + +
28C MET* 3.0 33.6 + - + +
48C ILE* 3.5 31.0 - - + +
51C ILE* 3.8 18.8 - - + -
52C GLN* 4.9 10.5 - - + +
55C ILE* 3.2 35.2 - - + -
113C ILE* 3.9 22.7 - - + -
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 3.5 36.9 + - + +
23C LYS* 3.2 21.9 + - + +
25C ILE* 1.3 84.5 - - + +
27C THR* 1.3 63.2 + - + +
28C MET 3.0 10.4 + - - +
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 5.3 1.6 + - - -
23C LYS* 3.4 20.9 - - + +
24C TYR* 2.6 35.9 + - + +
26C TYR* 1.3 75.8 - - + +
28C MET* 1.3 57.8 + - - +
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Residues in contact with MET 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.5 13.9 - - + +
25C ILE* 3.1 31.9 - - + +
26C TYR 3.0 11.8 - - - +
27C THR* 1.3 81.1 - - - +
48C ILE* 4.9 20.1 - - + +
113C ILE* 3.8 24.2 - - + -
116C MET* 3.7 37.0 - - + -
117C VAL* 3.7 33.7 - - + -
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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
------------------------------------------------------------
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