Contacts of the helix formed by residues 25 - 52 (chain B) in PDB entry 1JVM
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 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.8 37.5 + + + +
118A GLU* 5.8 4.7 - - + +
24B LEU* 1.3 78.8 + - - +
26B TRP* 1.3 96.3 + + - +
27B ARG 3.1 5.6 - - - -
28B ALA* 3.0 27.2 - - - +
29B ALA 3.5 2.6 + - - -
109B ALA* 3.7 18.7 + - + +
112B THR* 3.1 41.5 + - + +
113B TRP* 4.2 9.4 - + - +
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Residues in contact with TRP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.3 4.2 - - - -
25B HIS* 1.3 113.4 + + - +
27B ARG* 1.3 60.0 + - - +
28B ALA 2.9 6.1 - - - -
29B ALA* 3.1 29.3 + - + +
30B GLY* 3.3 6.4 + - - -
109B ALA* 4.5 11.9 - - + -
110B LEU* 5.2 8.1 - - + -
113B TRP* 3.5 56.3 - + + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.5 25.8 + - + +
26B TRP* 1.3 80.0 - - - +
28B ALA* 1.3 59.1 + - - +
30B GLY* 4.1 1.4 + - - -
31B ALA* 3.6 16.6 + - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 5.9 2.9 - - + -
114A PHE* 3.7 23.6 - - + -
24B LEU 4.5 0.6 + - - +
25B HIS* 3.0 19.4 + - - +
27B ARG* 1.3 79.5 - - - +
29B ALA* 1.3 64.6 + - - +
31B ALA* 2.9 23.1 - - - +
32B ALA 3.1 3.8 + - - -
105B LEU* 3.5 14.4 - - + +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B HIS 3.5 2.5 + - - +
26B TRP* 3.1 25.4 + - + +
28B ALA* 1.3 76.8 - - - +
30B GLY* 1.3 66.5 + - - +
31B ALA 2.9 1.6 + - - -
32B ALA* 2.9 16.3 + - - +
33B THR* 3.1 13.8 + - - -
105B LEU* 3.7 12.8 - - + +
106B VAL* 4.8 15.9 - - + +
109B ALA* 5.0 10.7 - - + +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP 3.3 8.5 + - - -
27B ARG 4.5 1.8 - - - -
29B ALA* 1.3 78.3 - - - +
31B ALA* 1.3 65.3 + - - +
33B THR* 3.1 12.5 - - - -
34B VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG 3.6 12.1 + - - +
28B ALA* 2.9 22.6 + - - +
29B ALA 2.9 1.2 + - - -
30B GLY* 1.3 74.5 - - - +
32B ALA* 1.3 62.7 + - - +
34B VAL* 2.9 16.9 + - - +
35B LEU* 2.8 30.2 + - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.1 1.0 + - - -
29B ALA 2.9 13.1 + - - +
31B ALA* 1.3 74.0 - - - +
33B THR* 1.3 67.4 + - - +
35B LEU* 2.9 16.3 + - + +
36B LEU* 2.8 25.8 + - - +
102B SER* 3.9 29.7 + - - +
105B LEU* 3.4 25.6 - - + -
106B VAL* 5.2 2.5 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA* 3.1 9.3 + - - +
30B GLY* 3.1 17.1 - - - +
32B ALA* 1.3 78.0 - - - +
34B VAL* 1.3 71.7 + - + +
36B LEU* 3.5 7.0 + - - +
37B VAL* 3.0 31.1 + - + +
102B SER* 5.2 0.6 - - - -
106B VAL* 5.6 4.7 - - - +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 3.0 18.4 - - - +
31B ALA* 2.9 8.4 + - - +
33B THR* 1.3 78.6 - - + +
35B LEU* 1.3 68.4 + - + +
37B VAL* 2.7 21.8 + - + +
38B ILE* 2.9 33.1 + - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 2.8 32.5 - - + +
32B ALA* 2.9 11.9 + - + +
34B VAL* 1.3 75.0 - - + +
36B LEU* 1.3 52.6 + - - +
38B ILE* 2.9 20.7 + - + +
39B VAL* 2.6 43.9 + - + +
102B SER* 5.5 1.3 - - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA 2.8 19.3 + - - +
33B THR* 3.6 7.0 - - - +
35B LEU* 1.3 72.4 - - - +
37B VAL* 1.3 54.1 + - + +
39B VAL* 3.0 8.4 + - + +
40B LEU* 2.7 49.6 + - + +
73B ALA* 4.6 10.5 - - + -
95B VAL* 4.6 0.4 - - + +
98B ALA* 3.5 17.3 - - + -
99B GLY* 3.3 37.2 - - - +
102B SER* 3.5 24.4 + - - +
103B PHE* 4.2 17.7 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 3.0 25.4 - - + +
34B VAL* 2.7 13.5 + - + +
36B LEU* 1.3 73.7 - - + +
38B ILE* 1.3 62.9 + - + +
40B LEU* 3.3 15.9 - - + +
41B LEU* 3.0 46.6 + - + +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 2.9 41.9 + - + +
35B LEU* 2.9 22.3 + - + +
37B VAL* 1.3 76.4 - - + +
39B VAL* 1.3 56.6 + - + +
40B LEU 3.0 0.5 + - - -
41B LEU* 3.0 9.9 + - + +
42B ALA* 2.4 45.8 + - + +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 2.6 40.7 + - + +
36B LEU* 3.3 10.8 - - + +
38B ILE* 1.3 74.1 - - + +
40B LEU* 1.3 53.2 + - + +
42B ALA* 3.6 8.5 - - + -
43B GLY* 2.4 34.3 + - - +
94B VAL* 4.1 22.7 - - + -
95B VAL* 4.1 14.7 - - + +
98B ALA* 3.9 27.1 - - + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 2.7 32.5 + - + +
37B VAL* 3.3 21.3 - - + +
39B VAL* 1.3 68.9 - - - +
41B LEU* 1.3 60.3 + - + +
43B GLY* 3.5 0.2 - - - -
44B SER* 2.3 44.3 + - - +
66B LEU* 5.9 1.6 - - + -
69B SER* 3.4 42.0 + - - +
70B VAL* 4.2 12.3 - - + +
73B ALA* 4.1 15.9 - - + -
95B VAL* 4.2 6.7 - - + -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.0 31.4 - - + +
38B ILE* 3.0 8.0 + - + +
40B LEU* 1.3 75.7 - - + +
42B ALA* 1.3 58.4 + - - +
44B SER* 3.4 5.6 - - - -
45B TYR* 2.8 36.4 + - - +
66B LEU* 4.1 21.3 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 2.4 37.1 + - + +
39B VAL* 3.5 11.9 - - + +
41B LEU* 1.3 72.6 - - - +
43B GLY* 1.3 53.2 + - - +
45B TYR* 4.1 2.6 - - - +
46B LEU* 2.6 44.7 + - + +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 2.4 23.5 + - - +
42B ALA* 1.3 72.8 - - - +
44B SER* 1.3 53.9 + - - +
46B LEU* 3.9 4.0 - - - +
47B ALA* 2.6 38.7 + - - +
68B TRP* 4.9 1.3 - - - -
69B SER* 4.3 3.1 - - - -
91B VAL* 3.6 20.4 - - - -
95B VAL* 4.4 8.7 - - - -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU 2.3 36.8 + - - -
41B LEU* 3.4 7.9 - - - -
43B GLY 1.3 71.0 - - - +
45B TYR* 1.3 64.5 + - - +
47B ALA* 5.0 0.4 - - - -
48B VAL* 3.1 27.0 + - - +
62B TYR* 4.9 2.9 - - - -
65B ALA* 3.8 8.8 - - - +
66B LEU* 3.1 39.0 - - - +
68B TRP* 5.4 0.2 - - - -
69B SER* 3.0 20.0 + - - -
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU 2.8 20.0 + - - +
42B ALA* 4.1 1.6 - - - +
44B SER* 1.3 74.9 - - - +
46B LEU* 1.3 63.4 + - - +
48B VAL* 3.8 8.3 + - + +
49B LEU* 3.4 52.6 + - + +
62B TYR* 5.6 11.2 - - + +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 2.6 28.9 + - + +
43B GLY* 3.5 5.4 - - - +
45B TYR* 1.3 80.1 - - - +
47B ALA* 1.3 63.5 + - - +
49B LEU* 3.5 6.5 + - - +
50B ALA* 3.4 17.7 + - + +
91B VAL* 4.0 26.0 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLY 2.6 21.3 + - - +
44B SER 4.0 1.3 - - - +
46B LEU* 1.3 71.8 - - - +
48B VAL* 1.3 65.5 + - - +
50B ALA* 3.0 12.6 + - - +
51B GLU* 3.0 20.9 + - + +
59B LEU* 5.3 5.4 - - + -
65B ALA* 5.3 2.2 - - + -
68B TRP* 3.7 21.1 - - + -
88B GLY* 5.1 4.7 - - - +
91B VAL* 3.4 27.1 - - + -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER 3.1 12.8 + - - +
45B TYR* 4.0 7.9 - - + +
46B LEU 3.4 0.2 - - - -
47B ALA* 1.3 75.2 - - - +
49B LEU* 1.3 72.6 + - + +
52B ARG* 2.7 46.1 + - + +
59B LEU 3.9 8.1 - - - +
60B ILE 3.4 21.5 - - - +
61B THR 3.7 2.7 - - - +
62B TYR* 3.3 30.1 - - + +
65B ALA* 3.2 31.1 - - + +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 3.4 53.2 - - + +
46B LEU* 3.5 6.2 + - - +
47B ALA 3.2 0.4 - - - -
48B VAL* 1.3 90.2 - - + +
50B ALA* 1.3 58.9 + - - +
51B GLU 3.3 0.4 + - - -
52B ARG* 4.5 26.7 - - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.4 12.5 + - + +
47B ALA* 3.0 13.7 + - - +
49B LEU* 1.3 78.1 - - - +
51B GLU* 1.3 60.0 + - - +
52B ARG 5.1 0.2 - - - -
54B ALA* 5.4 0.3 - - - +
85B THR* 3.4 18.5 + - - +
87B TRP* 4.2 14.2 - - + +
88B GLY* 4.2 20.0 - - - +
91B VAL* 4.7 4.5 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.0 16.3 + - + +
50B ALA* 1.3 80.9 - - - +
52B ARG* 1.3 71.7 + - - +
54B ALA* 3.0 24.3 + - - +
57B ALA* 4.2 16.6 - - + +
59B LEU* 3.6 35.1 - - + +
82B TYR 3.7 3.5 - - - +
83B PRO* 3.5 13.1 - - - +
84B VAL* 2.9 23.7 + - - +
85B THR* 2.7 47.8 + - - +
88B GLY* 4.5 5.8 - - - -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 2.7 30.7 + - - +
49B LEU* 4.5 23.2 - - - +
50B ALA 5.1 0.2 - - - -
51B GLU* 1.3 78.6 - - - +
53B GLY* 1.3 62.7 + - - +
54B ALA* 4.9 0.2 - - - +
57B ALA* 4.7 2.7 - - - +
59B LEU 3.9 5.9 + - - -
60B ILE* 3.9 34.7 + - + +
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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) + - + + + + + -
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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