Contacts of the helix formed by residues 40 - 64 (chain C) in PDB entry 4NEF
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 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 4.8 4.7 - - - -
42B LEU* 5.3 2.4 - - - +
38C LEU 3.6 3.3 + - - -
39C PRO* 1.3 75.4 - - - +
41C VAL* 1.4 58.3 + - - +
42C LEU* 3.7 6.9 + - - +
43C GLN* 3.2 29.6 + - - +
44C ILE* 3.0 30.5 + - - +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.7 15.7 - - + +
43A GLN* 3.3 21.4 + - - +
40C SER* 1.4 72.8 - - - +
42C LEU* 1.4 57.9 + - - +
44C ILE* 3.5 2.8 + - + +
45C ALA* 2.9 30.3 + - - +
172C HIS 4.2 0.2 - - - +
173C LEU* 4.0 20.6 - - + +
176C ILE* 3.7 36.1 - - + +
177C HIS* 3.6 37.0 - - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 5.3 2.0 - - - +
42A LEU* 3.7 37.9 - - + -
43A GLN* 3.5 26.2 + - + +
46A MET* 3.6 33.9 - - + -
42B LEU* 3.8 17.9 - - + -
40C SER* 3.3 6.4 + - - +
41C VAL* 1.4 75.0 - - - +
43C GLN* 1.3 58.2 + - - +
45C ALA* 3.4 1.8 + - + +
46C MET* 2.9 43.5 + - - +
173C LEU* 3.9 20.4 - - + -
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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
----------------------------------------------------------
40B SER* 4.7 5.1 - - - -
41B VAL* 3.4 42.2 - - - +
42B LEU* 3.4 25.3 - - + +
173B LEU* 3.6 25.2 - - + +
177B HIS* 4.5 4.5 + - - -
30C SER* 4.5 5.2 - - - +
37C ALA 5.7 0.3 - - - +
38C LEU 5.0 2.6 + - - -
39C PRO* 3.5 26.5 - - + +
40C SER* 3.2 29.9 + - - +
42C LEU* 1.3 75.6 - - - +
44C ILE* 1.4 57.2 + - - +
46C MET* 3.5 4.2 - - - +
47C ALA* 3.0 26.5 + - - +
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 5.3 0.2 - - - +
30C SER 4.1 2.7 - - - +
31C ALA* 4.0 28.3 - - + +
39C PRO* 3.8 32.3 - - + +
40C SER 3.0 22.2 + - - +
41C VAL* 4.7 3.1 - - - +
43C GLN* 1.4 71.5 - - - +
45C ALA* 1.4 65.9 + - - +
47C ALA* 3.0 15.9 + - + +
48C PHE* 3.1 40.8 + - + -
172C HIS* 4.7 0.2 - - - +
176C ILE* 3.7 28.7 - - + -
180C GLY 5.8 1.1 - - - +
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL 2.9 19.1 + - - +
42C LEU* 3.5 3.8 - - + +
44C ILE* 1.4 75.5 - - - +
46C MET* 1.3 52.8 + - - +
48C PHE* 3.6 1.7 + - - +
49C GLY 2.9 28.1 + - - -
169C ALA* 3.4 36.3 - - + +
172C HIS* 3.6 19.1 - - + -
173C LEU* 3.5 21.5 - - + +
176C ILE* 4.1 0.6 - - - +
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Residues in contact with MET 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 4.4 16.6 - - + -
50A LEU* 5.4 1.3 - - - -
42B LEU* 3.7 28.0 - - + -
46B MET* 4.4 22.0 - - + -
166B PHE* 5.1 0.4 - - + -
173B LEU* 3.9 4.0 - - + -
42C LEU* 2.9 32.6 + - - +
43C GLN 3.5 6.1 - - - +
45C ALA* 1.3 74.8 - - - +
47C ALA* 1.3 58.6 + - - +
49C GLY* 4.8 0.4 - - - -
50C LEU* 2.8 58.1 + - + +
166C PHE* 3.7 31.9 - - + -
169C ALA* 4.9 8.3 - - - -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.3 15.9 - - + +
173B LEU* 3.5 16.8 - - + +
26C PHE* 4.8 2.9 - - - +
27C GLY* 4.9 5.6 + - - +
30C SER* 3.5 35.2 - - - +
43C GLN 3.0 13.8 + - - +
44C ILE* 3.0 9.8 + - - +
46C MET* 1.3 74.7 - - - +
48C PHE* 1.3 59.7 + - + +
51C GLY* 3.1 22.2 + - - -
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.6 32.0 - + - -
24C VAL* 6.0 0.7 - - - -
27C GLY* 3.3 42.4 - - - -
28C LEU* 3.9 4.0 - - + -
31C ALA* 4.2 4.3 - - + -
44C ILE* 3.1 44.4 + - + +
45C ALA 4.1 0.2 - - - +
47C ALA* 1.3 72.8 - - + +
49C GLY* 1.3 61.0 + - - +
51C GLY* 3.3 1.4 + - - -
52C ILE 3.1 23.9 + - - -
168C VAL* 3.7 11.3 - - + +
172C HIS* 3.4 38.6 - + + +
187C ARG* 3.7 47.6 - - + -
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA 2.9 18.8 + - - -
46C MET 3.9 0.2 - - - -
48C PHE* 1.3 78.3 - - - +
50C LEU* 1.4 57.8 + - - +
51C GLY 3.2 0.3 + - - -
52C ILE* 3.3 0.9 + - - -
53C GLY 3.1 22.7 + - - -
165C GLY* 3.2 34.5 - - - -
166C PHE* 6.2 1.1 - - - -
168C VAL* 4.0 3.1 - - - +
169C ALA* 3.9 10.3 - - - -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 6.0 0.4 - - + -
46B MET* 5.5 2.9 - - - -
166B PHE* 3.7 60.5 - - + +
169B ALA* 3.9 13.9 - - + -
170B LEU* 3.8 12.7 - - + +
173B LEU* 4.6 6.5 - - + -
46C MET* 2.8 53.2 + - + +
49C GLY* 1.4 68.2 - - - -
51C GLY* 1.3 57.6 + - - +
53C GLY* 4.0 2.7 - - - +
54C THR* 2.6 37.7 + - - +
162C LEU* 5.5 3.8 - - + -
165C GLY 6.4 0.2 - - - -
166C PHE* 4.3 13.5 - - + -
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Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.7 16.6 - - - +
23C PHE* 4.6 8.1 - - - -
26C PHE* 5.8 2.0 - - - -
47C ALA 3.1 20.1 + - - -
48C PHE 3.6 2.7 - - - -
49C GLY 3.1 0.6 - - - -
50C LEU* 1.3 77.1 - - - +
52C ILE* 1.3 62.6 + - - +
54C THR* 3.8 1.7 - - - -
55C LEU* 3.1 35.4 + - - +
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.5 40.6 - - + -
48C PHE 3.1 12.9 + - - +
49C GLY 3.3 2.4 + - - +
51C GLY* 1.3 73.2 - - - +
53C GLY* 1.3 54.1 + - - +
55C LEU* 3.1 4.4 + - - +
56C VAL* 2.8 45.5 + - + +
66C HIS 5.1 3.8 - - - +
67C ILE* 3.8 33.4 - - + +
68C ASN* 6.2 0.4 - - + -
164C ILE* 3.9 23.8 - - + -
165C GLY* 4.5 1.8 - - - -
168C VAL* 3.8 31.0 - - + -
184C ASN* 5.1 1.8 - - - +
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Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B SER* 5.4 1.1 + - - -
49C GLY 3.1 15.6 + - - -
50C LEU* 4.1 2.2 - - - -
52C ILE* 1.3 75.7 - - - +
54C THR* 1.3 59.0 + - - +
56C VAL* 4.6 0.4 - - - -
57C GLN* 3.1 19.8 + - - +
161C ALA* 3.3 35.8 - - - +
162C LEU* 5.0 10.9 - - - +
165C GLY* 3.8 4.6 - - - -
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.5 28.5 - - + +
144B CYS* 3.8 15.8 - - + -
163B SER* 4.6 3.5 + - - -
166B PHE* 4.2 4.5 + - - +
167B SER* 3.7 31.7 + - - +
170B LEU* 3.8 6.8 - - + +
50C LEU 2.6 23.8 + - - -
51C GLY 3.8 3.8 - - - -
52C ILE 3.3 0.2 - - - -
53C GLY* 1.3 74.8 - - - +
55C LEU* 1.3 61.7 + - + +
57C GLN* 3.4 7.3 + - - +
58C ALA* 2.9 28.5 + - + +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 5.5 5.8 - - + -
143B LEU* 5.8 1.3 - - + -
170B LEU* 5.9 2.0 - - + -
19C ALA* 3.4 33.4 - - + +
22C LEU* 3.9 31.2 - - + -
23C PHE* 3.7 26.0 - - + +
51C GLY* 3.1 21.4 + - - +
52C ILE 3.1 0.2 + - - -
54C THR* 1.3 79.7 - - + +
56C VAL* 1.3 59.1 + - - +
58C ALA* 4.4 5.6 - - + +
59C LEU* 2.9 41.6 + - + +
65C ALA* 3.7 5.0 - - - +
67C ILE* 3.7 18.8 - - + -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 5.4 1.7 + - - -
52C ILE* 2.8 35.6 + - + +
53C GLY* 4.0 4.9 - - - +
55C LEU* 1.3 74.8 - - - +
57C GLN* 1.3 58.9 + - - +
60C GLY* 2.9 27.9 + - - -
64C GLY 5.4 3.1 - - - +
65C ALA* 3.6 30.3 - - + +
67C ILE* 4.3 2.0 - - + -
159C THR* 4.0 20.9 - - + -
161C ALA* 3.9 22.7 - - + -
164C ILE* 4.3 16.8 - - + -
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B CYS* 4.1 7.0 - - - +
147B ALA* 3.4 1.0 - - - +
148B SER* 3.4 24.3 + - - +
153B ARG* 2.8 51.1 + - - +
157B PRO* 3.2 33.9 + - - +
159B THR* 4.0 4.6 + - - -
163B SER* 3.0 33.1 + - - +
53C GLY 3.1 18.0 + - - +
54C THR* 3.4 8.1 - - - +
56C VAL* 1.3 79.7 - - - +
58C ALA* 1.3 58.1 + - - +
61C HIS* 4.1 0.7 - - - -
159C THR 5.8 0.6 - - - +
161C ALA* 3.7 14.0 - - + +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN 5.3 0.7 - - - +
143B LEU* 3.8 33.0 - - + +
144B CYS* 3.9 6.1 - - + +
147B ALA* 3.6 13.2 - - - +
219B TYR* 4.3 6.6 - - - -
54C THR* 2.9 18.2 + - + +
55C LEU* 4.2 8.7 - - + +
57C GLN* 1.3 77.3 - - - +
59C LEU* 1.3 72.5 + - + +
61C HIS* 3.0 18.9 + - - -
62C ILE* 4.6 0.5 - - - +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 5.0 6.7 - - + -
219B TYR* 5.9 1.6 - - + -
223B LEU* 3.8 38.6 - - + -
15C ALA* 3.8 19.3 - - + +
18C LEU* 4.7 9.4 - - + -
19C ALA* 3.6 35.9 - - + +
22C LEU* 5.5 0.2 - - + -
55C LEU* 2.9 29.9 + - + +
58C ALA* 1.3 89.9 - - + +
60C GLY* 1.3 61.8 + - - +
61C HIS* 3.3 3.6 - - - -
62C ILE* 3.0 20.2 + - + -
63C SER* 3.2 15.7 + - - +
65C ALA* 4.0 8.1 - - + -
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Residues in contact with GLY 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 6.1 0.2 - - - -
56C VAL* 2.9 28.5 + - - -
58C ALA 3.9 0.4 - - - -
59C LEU* 1.3 70.4 - - - +
61C HIS* 1.3 57.5 + - - +
62C ILE 3.2 1.7 + - - -
64C GLY* 2.8 29.5 + - - -
65C ALA* 3.7 18.3 - - - +
159C THR* 6.4 1.1 - - - -
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Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.7 3.8 - - - +
153B ARG* 3.3 52.5 + - + +
219B TYR* 3.0 30.0 - + - -
224B PHE* 3.8 22.2 - + + -
57C GLN 4.1 0.2 - - - -
58C ALA 3.0 26.5 + - - -
60C GLY* 1.3 76.6 - - - +
62C ILE* 1.3 76.6 + - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 5.2 1.8 - - + -
223B LEU* 3.5 37.5 - - + +
224B PHE* 4.4 18.4 - - + -
8C ALA 4.7 1.9 - - - +
11C ARG* 3.2 34.1 - - + +
12C ALA* 3.4 15.8 + - - +
15C ALA* 3.5 18.8 - - + -
58C ALA 4.6 4.0 - - - +
59C LEU* 3.0 11.2 + - + +
61C HIS* 1.3 112.8 - - + +
63C SER* 1.4 56.1 + - - +
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.3 27.6 - - - -
15C ALA* 3.8 11.2 - - - +
16C GLU* 2.9 20.7 + - - -
59C LEU* 3.2 9.1 + - - +
60C GLY 3.5 0.4 + - - -
62C ILE* 1.4 76.0 - - - +
64C GLY* 1.3 61.6 + - - +
65C ALA* 3.3 6.6 + - - -
66C HIS* 3.8 2.9 + - - -
85C ARG* 5.4 0.6 - - - +
89C TYR* 2.8 38.1 + - - -
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Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 5.4 3.3 - - - +
60C GLY* 2.8 20.1 + - - -
63C SER* 1.3 78.7 - - - +
65C ALA* 1.3 68.4 + - - +
66C HIS* 3.5 12.4 + - - -
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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