Contacts of the helix formed by residues 21 - 47 (chain C) in PDB entry 4PHZ
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 LEU 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 4.9 19.5 - - + +
29B MET* 4.3 19.3 - - + -
19C VAL* 4.9 6.5 - - + -
20C ASP* 1.3 82.8 - - - +
22C ARG* 1.3 67.2 + - - +
23C GLY 3.1 3.1 - - - -
24C MET* 3.1 14.8 + - + +
25C TRP* 3.0 56.0 + - + +
105C VAL* 4.7 6.1 - - + -
109C GLN* 3.3 40.8 + - + +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 3.0 42.2 + - - +
21C LEU* 1.3 79.6 - - - +
23C GLY* 1.3 52.2 + - - +
25C TRP* 3.3 37.2 + - - +
26C ILE* 2.8 48.2 + - + +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 5.7 1.0 - - - +
21C LEU* 3.1 1.0 - - - +
22C ARG* 1.3 75.5 - - - +
24C MET* 1.3 64.4 + - - +
26C ILE* 3.3 14.6 + - - +
27C GLY* 3.0 18.4 + - - -
109C GLN* 4.3 0.2 + - - -
302C PGT 2.6 39.9 + - - +
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Residues in contact with MET 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.8 24.0 - - + -
21C LEU* 3.1 18.7 + - + +
23C GLY* 1.3 72.9 - - - +
25C TRP* 1.3 101.0 + - + +
27C GLY* 2.9 5.0 + - - -
28C LEU* 2.8 39.1 + - + +
109C GLN* 3.4 35.1 + - + +
112C VAL* 4.0 22.9 - - + -
113C VAL* 4.2 4.0 - - + +
302C PGT 3.5 13.5 + - - +
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Residues in contact with TRP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 3.0 40.8 + - + +
22C ARG* 3.3 38.3 - - - +
24C MET* 1.3 100.1 - - + +
26C ILE* 1.3 66.2 + - + +
28C LEU* 4.2 18.6 - - + -
29C VAL* 2.8 38.4 + - + +
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 2.8 35.6 + - + +
23C GLY* 3.4 11.9 - - - +
24C MET 3.2 0.2 - - - -
25C TRP* 1.3 72.7 - - + +
27C GLY* 1.3 53.4 + - - +
29C VAL* 3.5 3.4 + - - +
30C LEU* 2.8 59.9 + - + +
302C PGT 6.1 1.8 - - + -
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY 3.0 8.9 + - - -
24C MET 2.9 11.4 + - - -
26C ILE* 1.3 70.8 - - - +
28C LEU* 1.3 62.5 + - - -
30C LEU* 3.3 5.5 + - - +
31C LEU* 3.0 28.6 + - - +
113C VAL* 4.3 5.8 - - - -
302C PGT 3.8 33.4 - - - +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET* 2.8 34.0 + - + +
25C TRP* 3.8 29.6 - - + +
27C GLY* 1.3 67.2 - - - -
29C VAL* 1.3 66.2 + - + +
31C LEU* 3.3 2.0 + - + -
32C ASN* 2.7 40.9 + - - +
112C VAL* 4.4 11.2 - - + -
113C VAL* 3.8 20.8 - - + +
116C ILE* 4.1 37.2 - - + -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TRP* 2.8 32.2 + - + +
26C ILE* 3.8 3.8 - - - +
28C LEU* 1.3 71.8 - - + +
30C LEU* 1.3 56.4 + - + +
31C LEU 2.7 12.5 + - - -
32C ASN* 4.7 2.5 - - - +
33C VAL* 3.0 42.8 + - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 2.8 44.6 + - + +
27C GLY* 3.6 8.1 - - - +
29C VAL* 1.3 71.5 - - + +
31C LEU* 1.3 56.4 + - - +
33C VAL* 4.9 3.4 - - - -
34C PHE* 3.6 10.8 - - - +
302C PGT 3.4 44.7 - - + +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.0 15.2 + - - +
28C LEU* 3.7 4.3 - - + +
29C VAL 2.7 6.9 + - - -
30C LEU* 1.3 74.6 - - - +
32C ASN* 1.3 59.0 - - - +
33C VAL 3.1 0.9 - - - -
34C PHE* 2.8 23.9 + - + +
35C TYR* 2.9 33.0 + - + +
113C VAL* 4.4 13.5 - - + +
116C ILE* 3.5 28.9 - - + -
117C ALA* 4.0 23.6 - - + +
156C ILE* 4.3 17.7 - - + -
160C ILE* 4.6 2.2 - - + -
302C PGT 3.9 35.7 - - + -
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 2.7 36.9 + - - +
29C VAL* 4.3 2.8 - - - +
31C LEU* 1.3 75.6 - - - +
33C VAL* 1.3 58.5 + - + +
35C TYR* 4.2 0.9 - - - +
36C LEU* 3.0 39.3 + - + +
116C ILE* 3.8 13.7 - - - +
120C TRP* 3.3 34.0 + - + +
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Residues in contact with VAL 33 (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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29C VAL* 3.0 36.1 + - + +
30C LEU* 4.9 3.1 - - - -
32C ASN* 1.3 76.3 - - + +
34C PHE* 1.3 67.1 + - - +
36C LEU* 3.2 7.7 + - - +
37C ILE* 3.0 38.6 + - + +
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Residues in contact with PHE 34 (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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30C LEU 3.6 16.4 + - - +
31C LEU* 2.8 15.8 + - + +
33C VAL* 1.3 77.0 - - - +
35C TYR* 1.3 89.6 + + - +
37C ILE* 3.3 20.1 - - + +
38C VAL* 3.0 38.0 + - + +
152C MET* 3.9 20.9 - - + -
156C ILE* 4.0 11.7 - - + -
302C PGT 3.9 29.4 - - + -
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Residues in contact with TYR 35 (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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31C LEU* 2.9 33.2 + - + +
34C PHE* 1.3 93.9 - + - +
36C LEU* 1.3 52.2 + - - +
38C VAL* 3.0 3.9 + - + +
39C ARG* 2.6 37.6 + - - +
117C ALA* 5.0 3.4 + - - -
120C TRP* 3.1 69.2 - + + +
125C PHE* 3.7 15.9 - + + -
152C MET* 3.3 29.6 - - + -
153C SER* 3.4 16.8 + - - -
156C ILE* 3.3 33.0 - - + +
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Residues in contact with LEU 36 (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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32C ASN* 3.0 28.5 + - + +
33C VAL* 3.3 8.1 - - - +
35C TYR* 1.3 72.1 - - - +
37C ILE* 1.3 65.4 + - - +
39C ARG* 3.9 5.4 - - + +
40C ILE* 3.0 54.1 + - + +
120C TRP* 4.6 14.3 - - + -
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Residues in contact with ILE 37 (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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33C VAL* 3.0 36.9 + - + +
34C PHE* 3.3 18.6 - - + +
36C LEU* 1.3 77.4 - - - +
38C VAL* 1.3 59.3 + - + +
40C ILE* 3.5 8.7 - - - +
41C TYR* 2.6 44.2 + - + +
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Residues in contact with VAL 38 (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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34C PHE* 3.0 43.9 + - + +
35C TYR* 3.0 11.1 + - - +
37C ILE* 1.3 80.0 - - + +
39C ARG* 1.3 64.2 + - - +
41C TYR* 3.3 9.5 + - + +
42C GLU* 2.9 23.2 + - + +
125C PHE* 4.4 6.3 - - + -
148C ILE* 3.8 42.8 - - + -
152C MET* 4.0 9.2 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 2.8 34.0 + - + +
112B ASN* 2.9 16.1 + - - -
115B GLY* 3.7 1.0 - - - -
116B TRP* 3.2 31.0 - - - +
35C TYR 2.6 19.1 + - - +
36C LEU* 3.9 6.5 - - + +
38C VAL* 1.3 73.3 - - - +
40C ILE* 1.3 61.9 + - + +
42C GLU* 3.1 24.7 - - - +
43C GLN* 3.0 51.6 + - - +
120C TRP* 5.4 1.8 - - + -
124C PHE* 3.9 22.9 - - + -
125C PHE* 4.7 1.1 - - + -
128C GLN* 3.5 5.4 - - - +
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Residues in contact with ILE 40 (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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36C LEU* 3.0 45.5 + - + +
37C ILE* 3.5 6.3 - - - +
39C ARG* 1.3 75.9 - - + +
41C TYR* 1.3 67.3 + - + +
43C GLN* 3.1 11.3 + - + +
44C VAL* 3.1 27.9 + - + +
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Residues in contact with TYR 41 (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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37C ILE* 2.6 27.0 + - + +
38C VAL* 3.6 11.4 - - + +
40C ILE* 1.3 74.7 - - + +
42C GLU* 1.3 54.0 + - - +
44C VAL* 3.2 5.8 + - - +
45C PHE* 2.8 64.9 + + + -
61C TYR* 2.6 41.7 + + - +
62C TRP* 3.9 17.9 - + - -
64C SER* 5.1 0.9 + - - -
65C ILE* 3.8 25.2 - - + +
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Residues in contact with GLU 42 (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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116B TRP* 2.9 30.4 + - + -
38C VAL 2.9 16.4 + - - +
39C ARG* 3.1 28.9 - - - +
40C ILE 3.2 0.2 - - - -
41C TYR* 1.3 73.2 - - - +
43C GLN* 1.3 59.7 + - - +
44C VAL 3.2 0.4 - - - -
46C GLY* 2.8 24.5 + - - -
62C TRP* 3.4 28.0 - - + -
125C PHE* 3.5 9.8 - - - -
128C GLN* 2.3 43.7 + - - +
144C PRO 5.3 0.3 - - - -
145C SER* 5.1 2.4 - - - -
148C ILE* 3.6 23.1 - - + +
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Residues in contact with GLN 43 (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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115B GLY 3.3 18.9 + - - +
116B TRP* 3.6 19.7 + - - +
118B TYR* 3.6 17.4 + - - -
39C ARG* 3.0 40.2 + - - +
40C ILE* 3.2 14.8 - - + +
42C GLU* 1.3 78.9 - - - +
44C VAL* 1.3 67.9 + - + +
46C GLY 4.0 1.6 + - - -
47C TRP* 4.1 18.8 + - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 3.1 18.4 + - + +
41C TYR* 3.6 9.2 - - - +
42C GLU 3.2 0.2 - - - -
43C GLN* 1.3 86.3 - - + +
45C PHE* 1.3 87.0 + - + +
46C GLY 3.3 0.2 - - - -
47C TRP* 3.1 20.8 - - - +
48C ARG 4.3 1.2 - - - +
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Residues in contact with PHE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 2.8 57.1 + + + +
44C VAL* 1.3 93.7 - - + +
46C GLY* 1.3 59.1 + - - +
48C ARG 4.3 2.0 - - - -
49C ALA* 3.2 25.7 - - + +
61C TYR* 3.3 51.6 - + + -
62C TRP* 2.5 37.8 + - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 4.3 5.6 - - - -
42C GLU 2.8 23.9 + - - -
44C VAL 3.3 0.2 - - - -
45C PHE* 1.3 77.5 - - - +
47C TRP* 1.3 57.8 + - - +
48C ARG 3.4 0.7 + - - -
50C GLY* 3.1 32.2 + - - -
51C LEU* 4.0 1.2 - - - +
62C TRP* 4.0 8.1 - - - -
132C TRP* 3.7 20.9 - - - -
144C PRO* 5.1 0.9 - - - -
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Residues in contact with TRP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 4.1 14.3 + - + +
128A ARG* 3.5 39.2 - - - +
132A TRP* 3.8 19.7 - + + -
116B TRP* 2.2 70.0 - + - -
117B THR* 3.1 29.4 - - + -
118B TYR* 4.7 0.7 - + - -
43C GLN* 4.1 18.3 + - - +
44C VAL 3.1 15.1 + - - +
46C GLY* 1.3 69.3 - - - +
48C ARG* 1.3 80.5 + - + +
51C LEU* 4.3 13.2 - - + -
132C TRP* 4.5 3.8 - + - -
135C THR* 4.2 16.4 - - + +
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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