Contacts of the helix formed by residues 38 - 64 (chain B) in PDB entry 3J41
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 PRO 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 4.2 5.2 - - + -
36B PRO* 3.4 29.2 - - + +
37B GLY* 1.3 93.0 - - - +
39B LEU* 1.3 63.9 + - + +
177B TYR* 3.6 5.3 - - - +
33C ARG* 5.7 2.5 - - - +
39C LEU* 3.3 39.0 - - + +
43C GLN* 2.3 36.7 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 3.3 45.8 - - + +
39A LEU* 3.3 36.8 - - + +
42A LEU* 4.9 5.6 - - + +
33B ARG* 5.2 4.9 - - - +
35B ALA* 5.4 4.9 - - + -
38B PRO* 1.3 82.6 - - + +
40B HIS* 1.3 74.0 - - + +
41B VAL 3.3 0.2 - - - -
42B LEU* 3.5 10.1 + - + +
43B GLN* 3.0 26.3 + - - +
39C LEU* 3.3 22.4 - - + +
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 3.8 16.6 - - - -
33B ARG* 2.7 43.0 + - + +
34B TRP* 2.8 24.6 + - - -
35B ALA* 3.3 28.7 - - + -
37B GLY* 4.3 13.5 - - - -
38B PRO* 4.6 0.2 - - - +
39B LEU* 1.3 85.1 - - + +
41B VAL* 1.3 60.6 + - + +
43B GLN 3.3 0.2 + - - -
44B VAL* 2.9 41.4 + - + +
176B MET* 3.8 20.5 - - + +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY* 2.7 39.8 + - - +
39B LEU 3.3 0.2 - - - -
40B HIS* 1.3 76.8 - - + +
42B LEU* 1.3 57.8 + - - +
45B ALA* 2.7 38.6 + - - +
172B HIS 3.8 9.2 - - - +
173B LEU* 3.8 35.0 - - + +
176B MET* 3.9 22.6 - - + +
177B TYR* 3.6 18.4 - - + -
43C GLN* 3.4 10.8 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.6 20.2 - - + -
38B PRO 4.2 1.8 - - - +
39B LEU* 3.5 11.6 + - + +
40B HIS 3.4 0.2 - - - -
41B VAL* 1.3 78.1 - - - +
43B GLN* 1.3 57.8 + - - +
45B ALA* 3.7 0.9 - - - +
46B LEU* 3.0 58.4 + - + +
169B THR* 6.2 0.2 - - + -
173B LEU* 4.0 13.5 - - + -
39C LEU* 5.0 6.1 - - + +
42C LEU* 3.6 34.5 - - + -
43C GLN* 3.3 29.6 - - + +
46C LEU* 3.7 20.9 - - + -
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Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.4 4.6 + - - -
38A PRO* 2.3 33.5 + - - +
41A VAL* 3.4 8.6 - - + +
42A LEU* 3.3 30.4 - - + +
173A LEU* 3.9 23.5 - - + +
177A TYR* 3.3 22.3 + - - -
30B ALA* 4.9 5.3 - - + +
33B ARG* 3.4 19.3 + - - +
39B LEU 3.0 17.8 + - - +
40B HIS 3.5 3.6 - - - +
42B LEU* 1.3 76.4 - - - +
44B VAL* 1.3 59.6 + - - +
46B LEU* 3.5 3.3 + - - +
47B ALA* 2.9 29.2 + - - +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 3.6 23.1 - - - +
31B SER* 3.2 29.6 - - - +
33B ARG* 4.0 2.7 - - - +
40B HIS* 2.9 33.6 + - + +
43B GLN* 1.3 73.5 - - - +
45B ALA* 1.3 65.2 + - - +
47B ALA* 3.7 5.3 - - - +
48B PHE* 3.1 39.0 + - + -
172B HIS* 4.3 1.8 - - + -
176B MET* 3.3 30.3 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL 2.7 22.8 + - - +
42B LEU 3.7 1.6 - - - +
44B VAL* 1.3 75.2 - - - +
46B LEU* 1.3 55.9 + - - +
48B PHE* 3.6 1.4 + - - +
49B GLY 3.0 15.6 + - - -
169B THR* 2.8 44.5 + - + +
172B HIS* 3.5 20.2 - - + -
173B LEU* 3.6 21.1 - - + +
176B MET* 4.3 0.4 - - - -
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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
----------------------------------------------------------
42A LEU* 3.7 24.9 - - + -
46A LEU* 5.0 9.2 - - + -
173A LEU* 4.0 11.4 - - + -
42B LEU* 3.0 41.7 + - + +
43B GLN* 3.8 4.0 - - - +
45B ALA* 1.3 76.0 - - - +
47B ALA* 1.3 56.3 + - - +
50B LEU* 2.7 49.9 + - + +
166B PHE* 4.2 21.3 - - + -
169B THR* 3.9 17.5 - - + +
46C LEU* 5.1 7.9 - - + -
50C LEU* 5.6 1.6 - - + -
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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
----------------------------------------------------------
170A LEU* 3.6 12.6 - - + +
173A LEU* 3.6 19.0 - - + +
26B PHE 4.8 2.2 - - - +
27B GLY* 5.2 2.0 - - - -
30B ALA* 3.6 30.1 - - + -
43B GLN 2.9 19.5 + - - +
44B VAL* 3.4 5.6 + - - +
46B LEU* 1.3 76.0 - - - +
48B PHE* 1.3 59.8 + - + +
51B ALA* 2.7 32.7 + - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.0 26.0 - + - -
24B VAL* 5.6 0.2 - - - -
27B GLY* 3.4 36.3 - - - -
28B LEU* 4.0 2.2 - - + -
31B SER* 3.4 21.5 - - - -
44B VAL* 3.1 33.7 + - + +
45B ALA 4.1 1.8 - - - +
47B ALA* 1.3 76.7 - - + +
49B GLY* 1.3 59.3 + - - +
51B ALA* 3.1 5.6 + - - +
52B LEU 2.9 26.0 + - - -
168B LEU* 3.5 13.5 - - + +
172B HIS* 3.4 36.1 - + + +
187B ARG* 3.8 47.3 - - + -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 3.0 10.7 + - - -
48B PHE* 1.3 77.5 - - - +
50B LEU* 1.3 59.5 + - - +
52B LEU 3.3 0.3 + - - -
53B ALA* 2.9 24.7 + - - +
165B GLY* 3.1 37.2 - - - -
168B LEU* 4.2 2.8 - - - +
169B THR* 3.2 17.3 - - - -
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 5.5 1.6 - - + -
166A PHE* 3.7 55.6 - - + +
169A THR* 3.7 29.8 - - + -
170A LEU* 4.0 9.0 - - + +
173A LEU* 4.5 6.7 - - + -
46B LEU* 2.7 35.6 + - + +
47B ALA* 4.1 1.8 - - - +
49B GLY* 1.3 73.2 - - - -
51B ALA* 1.3 56.5 + - - +
53B ALA* 4.0 3.4 - - + +
54B THR* 2.6 38.2 + - - -
162B LEU* 4.3 7.2 - - + -
166B PHE* 4.3 20.0 - - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.8 25.0 - - + +
23B TYR* 4.6 16.2 - - + +
26B PHE* 4.6 11.0 - - + -
27B GLY 5.1 0.9 - - - +
47B ALA 2.7 19.7 + - - +
48B PHE* 3.4 8.5 - - - +
50B LEU* 1.3 78.0 - - - +
52B LEU* 1.3 59.1 + - - +
54B THR* 3.5 0.9 - - - -
55B LEU* 2.9 41.8 + - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.1 17.6 - - + -
48B PHE 2.9 15.7 + - - +
49B GLY 3.6 4.3 - - - +
51B ALA* 1.3 72.7 - - - +
53B ALA* 1.3 55.0 + - - +
54B THR 3.1 1.3 - - - -
55B LEU* 3.0 6.5 + - + -
56B VAL* 2.7 53.9 + - + +
65B ALA 4.9 6.7 - - - +
66B HIS 5.2 2.9 - - - +
67B VAL* 5.1 11.9 - - + -
141B PHE* 3.3 35.9 - - + -
164B VAL* 3.6 21.5 - - + +
165B GLY* 4.2 1.1 - - - -
168B LEU* 3.5 20.9 - - + -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 6.1 2.2 - - + -
49B GLY 2.9 19.7 + - - +
50B LEU* 4.0 7.9 - - + +
52B LEU* 1.3 71.6 - - - +
54B THR* 1.3 61.8 + - - +
57B GLN* 3.2 29.9 + - - +
161B ALA* 3.1 35.1 + - + +
162B LEU* 3.8 22.9 - - + +
165B GLY* 4.1 1.3 - - - -
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 3.5 30.7 - - + +
144A CYS* 3.9 20.5 - - + -
163A ALA* 4.7 2.6 + - - +
166A PHE* 4.4 2.6 + - - +
167A SER* 3.6 27.3 + - - +
170A LEU* 4.6 3.3 - - + +
50B LEU 2.6 22.3 + - - -
51B ALA* 3.5 7.4 - - - +
53B ALA* 1.3 78.1 - - - +
55B LEU* 1.3 65.5 + - + +
57B GLN* 3.2 6.0 + - - +
58B ALA* 2.9 27.2 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 5.5 4.7 - - + -
143A LEU* 5.4 2.7 - - + -
170A LEU* 6.5 0.2 - - + -
19B ALA* 3.2 39.0 - - + +
22B PHE* 3.8 31.4 - - + -
23B TYR* 3.5 28.9 - - + +
26B PHE* 6.2 0.2 - - + -
51B ALA* 2.9 22.7 + - + +
52B LEU* 3.7 5.4 - - + +
54B THR* 1.3 79.1 - - + +
56B VAL* 1.3 60.6 + - - +
58B ALA* 3.6 10.7 - - + +
59B VAL* 2.8 35.8 + - + +
65B ALA* 4.4 2.0 - - - -
67B VAL* 5.1 6.1 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 4.3 3.3 + - - -
154A ASN* 5.5 0.7 + - - -
52B LEU* 2.7 48.1 + - + +
53B ALA 4.8 0.2 - - - +
55B LEU* 1.3 72.8 - - - +
57B GLN* 1.3 59.0 + - - +
60B GLY* 2.9 25.8 + - - -
65B ALA* 3.6 20.0 - - + +
149B TYR* 4.0 21.8 - - + +
160B VAL* 4.6 9.6 - - + +
161B ALA* 3.6 29.4 - - + +
164B VAL* 4.5 10.1 - - + -
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A CYS* 4.4 3.6 - - - -
147A ALA* 3.6 2.8 - - - +
148A THR* 3.8 14.7 - - + +
153A ARG* 2.7 35.9 + - - +
154A ASN* 4.4 3.3 + - - -
156A ARG 4.8 1.0 - - - +
157A LEU* 2.9 56.0 + - - +
159A SER 4.7 0.4 + - - -
160A VAL* 5.3 1.0 - - - +
163A ALA* 3.8 28.0 - - + +
53B ALA 3.2 18.7 + - - +
54B THR* 3.2 10.3 + - - +
56B VAL* 1.3 76.9 - - - +
58B ALA* 1.3 62.9 + - - +
61B HIS* 3.8 0.5 - - - -
159B SER* 3.6 5.6 + - - -
161B ALA* 3.4 17.7 - - + +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.7 35.7 - - + +
144A CYS* 4.6 4.2 - - + +
147A ALA* 3.4 16.6 - - - +
219A TYR* 4.0 6.9 - - - -
54B THR* 2.9 18.1 + - + +
55B LEU* 3.6 13.0 - - + +
57B GLN* 1.3 78.6 - - - +
59B VAL* 1.3 66.8 + - + +
61B HIS* 3.1 15.8 + - - -
62B ILE* 4.4 1.0 - - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 5.0 11.9 - - + -
15B ALA* 3.8 30.1 - - + +
16B GLU* 5.1 0.4 - - - +
18B PHE* 6.3 1.6 - - + -
19B ALA* 4.0 22.2 - - + +
55B LEU* 2.8 19.9 + - + +
58B ALA* 1.3 86.9 - - + +
60B GLY* 1.3 60.6 + - - +
61B HIS* 3.2 6.5 - - - -
62B ILE* 3.1 11.7 + - + -
63B SER* 3.0 34.8 + - - +
65B ALA* 3.7 13.9 + - + -
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 4.8 1.3 - - - -
154A ASN* 5.7 1.8 - - - -
56B VAL* 2.9 27.8 + - - -
59B VAL* 1.3 79.8 - - - +
61B HIS* 1.3 57.8 + - - +
64B GLY* 3.0 25.3 + - - -
65B ALA* 3.7 17.3 - - - -
149B TYR* 6.1 0.4 - - - -
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 4.0 0.6 - - - +
150A ASP* 4.6 1.1 - - - -
153A ARG* 3.5 49.3 + - + +
154A ASN* 3.4 20.9 - - - +
219A TYR* 3.1 29.9 + + - -
224A PHE* 5.9 1.8 - + - -
225A PRO* 5.5 2.3 - - - +
58B ALA 3.1 25.5 + - - -
60B GLY* 1.3 80.1 - - - +
62B ILE* 1.3 78.9 + - + +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 4.5 12.8 - - + +
222A LEU* 5.0 12.8 - - + -
224A PHE* 5.1 12.6 - - + -
225A PRO* 4.4 27.7 - - + +
11B ARG* 4.1 12.1 - - + +
12B ALA* 3.5 29.2 - - - +
15B ALA* 4.2 5.2 - - + -
58B ALA 4.4 7.9 - - - +
59B VAL* 3.1 16.0 + - + +
61B HIS* 1.3 111.9 - - + +
63B SER* 1.3 56.4 + - - +
85B ARG* 5.6 1.0 + - - -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 3.5 24.0 - - - -
15B ALA* 3.6 9.2 - - - +
16B GLU* 2.6 25.4 + - - -
59B VAL* 3.0 9.4 + - - +
62B ILE* 1.3 76.8 - - - +
64B GLY* 1.3 60.9 + - - +
65B ALA* 3.2 6.7 + - - -
66B HIS* 3.7 5.2 - - - -
89B TYR* 2.9 41.0 + - - -
----------------------------------------------------------
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY* 3.0 21.7 + - - -
63B SER* 1.3 78.9 - - - +
65B ALA* 1.3 62.3 + - - +
66B HIS* 3.5 11.3 + - - -
149B TYR* 2.7 42.3 + - - -
----------------------------------------------------------
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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