Contacts of the helix formed by residues 7 - 32 (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 ILE 7 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 1.3 77.3 - - - +
8C ALA* 1.3 66.5 + - - +
10C SER* 3.0 11.4 + - - -
11C ARG* 3.0 66.7 + - + +
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Residues in contact with ALA 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 4.2 4.2 - - - +
7C ILE* 1.3 78.9 - - - +
9C PHE* 1.3 55.6 + - - +
11C ARG* 3.4 14.0 + - - +
12C ALA* 3.0 27.8 + - - +
62C ILE 4.7 1.7 - - - +
85C ARG* 5.8 1.3 - - - +
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Residues in contact with PHE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 4.0 13.4 + - - +
7C ILE 3.2 0.8 - - - -
8C ALA* 1.3 74.5 - - - +
10C SER* 1.4 64.6 + - - +
12C ALA* 3.3 5.9 + - - +
13C VAL* 3.0 43.9 + - + +
84C LEU* 3.8 22.7 - - + -
85C ARG* 3.7 55.9 - - + +
88C PHE* 3.5 48.9 - + + -
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Residues in contact with SER 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 3.0 16.5 + - - -
7C ILE* 3.0 12.8 + - - -
9C PHE* 1.4 80.0 - - - +
11C ARG* 1.4 57.2 + - - +
13C VAL* 3.4 5.5 + - - +
14C PHE* 2.9 32.0 + - - +
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Residues in contact with ARG 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR 5.0 2.0 + - - -
222B VAL* 3.2 29.0 + - - +
223B LEU* 3.2 16.9 - - - +
225B PRO* 3.4 27.2 - - - +
7C ILE* 3.0 58.4 + - + +
8C ALA* 3.6 11.1 - - - +
10C SER* 1.4 74.7 - - - +
12C ALA* 1.3 57.1 + - - +
14C PHE* 3.9 6.4 - - - +
15C ALA 3.0 23.0 + - - -
62C ILE* 3.2 25.3 - - + +
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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
----------------------------------------------------------
8C ALA 3.0 12.8 + - - +
9C PHE 3.5 8.3 - - - +
11C ARG* 1.3 73.7 - - - +
13C VAL* 1.4 58.0 + - - +
15C ALA 3.4 0.2 + - - -
16C GLU* 3.0 26.9 + - - +
62C ILE 3.4 22.4 + - - +
63C SER* 3.3 12.7 - - - -
85C ARG* 3.6 13.7 - - - +
89C TYR* 3.2 25.4 - - + +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 3.0 53.2 + - + +
10C SER* 3.9 5.4 - - - +
12C ALA* 1.4 70.9 - - - +
14C PHE* 1.4 60.5 + - - +
16C GLU* 3.3 3.4 + - - +
17C PHE* 3.0 24.7 + - + +
88C PHE* 3.6 37.0 - - + +
89C TYR* 4.1 11.9 - - + -
92C ALA* 3.5 13.1 - - + +
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Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.2 27.1 - - + -
222B VAL* 4.0 26.2 - - + -
223B LEU* 3.7 23.8 - - + -
10C SER 2.9 18.3 + - - +
11C ARG* 3.9 6.1 - - - +
12C ALA 3.4 0.2 - - - -
13C VAL* 1.4 76.6 - - - +
15C ALA* 1.4 53.8 + - - +
17C PHE* 3.2 27.1 + + - +
18C LEU* 2.9 42.6 + - + +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 3.9 12.3 - - + -
11C ARG 3.0 19.2 + - - +
12C ALA 3.5 5.6 - - - +
14C PHE* 1.4 73.6 - - - +
16C GLU* 1.4 54.4 + - - +
18C LEU* 3.4 3.5 + - - -
19C ALA* 2.8 38.0 + - - +
59C LEU* 3.8 12.1 - - + +
62C ILE* 3.5 27.4 - - + -
63C SER* 3.8 11.0 - - - +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 3.0 16.7 + - - +
13C VAL* 3.3 9.4 + - - +
15C ALA* 1.4 74.6 - - - +
17C PHE* 1.4 58.4 + - - +
19C ALA* 3.9 3.9 - - - +
20C THR* 2.6 32.9 + - - -
63C SER* 2.9 19.3 + - - +
65C ALA* 3.3 4.7 + - - -
66C HIS* 2.9 28.7 + - - +
67C ILE* 3.0 18.1 + - - -
89C TYR* 3.7 33.0 - - + +
92C ALA* 4.2 12.8 - - + -
93C GLN* 3.0 24.8 - - + +
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Residues in contact with PHE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 3.0 14.1 + - + +
14C PHE* 3.4 31.9 - + - +
16C GLU* 1.4 74.5 - - - +
18C LEU* 1.4 63.6 + - + +
20C THR 3.4 1.9 + - - -
21C LEU* 3.0 50.9 + - + +
92C ALA* 3.4 19.9 - - + +
95C LEU* 3.9 16.8 - - + -
96C GLY* 3.4 39.4 - - - -
99C ALA* 4.4 5.8 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 5.9 2.7 - - + -
139B LEU* 4.6 7.6 - - + -
143B LEU* 4.0 19.3 - - + -
218B LEU* 3.8 32.1 - - + -
223B LEU* 4.1 17.7 - - + -
14C PHE* 2.9 31.0 + - + +
15C ALA 3.9 2.2 - - - +
17C PHE* 1.4 81.0 - - + +
19C ALA* 1.4 59.8 + - - +
21C LEU* 3.4 14.1 + - + +
22C LEU* 3.0 50.9 + - + +
59C LEU* 4.7 7.0 - - + -
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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
----------------------------------------------------------
15C ALA 2.8 23.1 + - - +
16C GLU* 3.9 6.3 - - - +
18C LEU* 1.4 72.5 - - - +
20C THR* 1.4 57.2 + - - +
22C LEU 3.4 0.7 + - - -
23C PHE* 2.9 30.3 + - - +
55C LEU* 3.4 13.0 - - + +
59C LEU* 3.6 21.9 - - + +
65C ALA* 5.7 1.1 - - - -
67C ILE* 3.6 30.7 - - + -
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU 2.6 23.8 + - - -
17C PHE 4.1 1.6 - - - -
19C ALA* 1.4 72.9 - - - +
21C LEU* 1.4 59.9 + - - +
23C PHE* 4.3 2.5 - - + -
24C VAL* 3.0 39.7 + - + +
67C ILE* 3.6 29.7 - - + +
93C GLN* 3.4 43.3 - - - +
96C GLY 4.0 2.9 - - - -
97C ALA* 3.9 13.3 - - + -
184C ASN* 5.1 0.2 - - - +
186C ALA* 4.1 9.2 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.1 18.4 - - + -
17C PHE* 3.0 45.1 + - + +
18C LEU* 3.4 17.0 - - + +
20C THR* 1.4 76.5 - - - +
22C LEU* 1.4 63.7 + - + +
25C PHE* 3.0 34.1 + - + +
96C GLY 3.1 17.1 + - - +
99C ALA* 3.8 14.1 - - + -
100C GLY* 3.5 13.9 - - - +
103C LEU* 4.1 24.7 - - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.8 33.7 - - + +
139B LEU* 4.0 21.8 - - + -
140B GLN* 4.5 8.7 - - + -
143B LEU* 4.1 10.8 - - + -
18C LEU* 3.0 37.8 + - + +
19C ALA* 3.9 2.9 - - - +
21C LEU* 1.4 75.7 - - + +
23C PHE* 1.3 59.3 + - - +
25C PHE* 4.3 5.2 - - + -
26C PHE* 3.0 55.2 + - + +
55C LEU* 3.9 26.9 - - + -
59C LEU* 5.5 0.2 - - + -
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Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 2.9 18.7 + - - +
20C THR* 3.9 2.9 - - + +
22C LEU* 1.3 75.0 - - - +
24C VAL* 1.3 64.1 + - + +
26C PHE* 4.0 2.7 - - - +
27C GLY* 2.8 34.6 + - - -
48C PHE* 3.6 45.3 - + + -
51C GLY* 4.6 5.6 - - - -
52C ILE* 3.5 38.1 - - + -
55C LEU* 3.7 10.9 - - + +
67C ILE* 3.7 20.2 - - + -
168C VAL* 5.0 4.0 - - + -
172C HIS* 5.5 1.1 - - - -
182C SER 6.0 0.9 - - - -
184C ASN* 3.4 27.4 - - + -
187C ARG* 4.1 17.9 - - + -
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C THR* 3.0 22.4 + - + +
21C LEU 4.2 1.1 - - - +
23C PHE* 1.3 83.6 - - + +
25C PHE* 1.4 63.7 + - - +
27C GLY* 5.1 0.2 - - - -
28C LEU* 3.0 55.8 + - + +
48C PHE* 6.0 0.9 - - - -
97C ALA* 3.3 41.3 - - + +
101C ALA 3.8 9.0 - - - +
104C LEU* 4.8 0.2 - - - +
187C ARG* 4.0 23.8 - - + -
190C ALA* 3.8 7.0 - - + -
191C PRO* 5.4 0.2 - - + -
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR 5.1 0.4 - - - -
133B VAL* 4.6 10.8 - - - -
136B PHE* 3.6 34.8 - + + -
174B LEU* 3.7 21.9 - - + +
21C LEU* 3.0 24.7 + - + +
22C LEU* 3.8 4.0 - - - +
24C VAL* 1.4 79.0 - - - +
26C PHE* 1.4 77.7 + + - +
29C GLY* 3.4 18.0 + - - -
100C GLY* 3.7 23.5 + - - +
103C LEU* 3.8 19.3 - - + -
104C LEU* 3.7 23.8 - - + +
107C ILE* 3.7 39.9 - - + -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE 3.6 18.4 - - - -
137B LEU* 3.5 32.1 - - + -
140B GLN* 3.5 28.0 - - + -
170B LEU* 3.8 38.4 - - + -
171B GLY* 3.9 14.8 - - - -
174B LEU* 3.7 16.1 - - + +
22C LEU* 3.0 38.2 + - + +
23C PHE* 4.2 2.0 - - - +
25C PHE* 1.4 91.4 - + - +
27C GLY* 1.3 63.1 + - - +
29C GLY 3.7 0.3 + - - -
30C SER* 2.7 32.8 + - - -
47C ALA* 4.8 1.7 - - - +
51C GLY* 5.8 2.0 - - - -
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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 PHE 2.8 22.9 + - - -
26C PHE* 1.3 71.7 - - - +
28C LEU* 1.3 62.2 - - - +
30C SER* 3.5 4.0 + - - -
31C ALA 3.3 12.5 + - - -
47C ALA* 5.1 2.0 + - - -
48C PHE* 3.3 49.7 - - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.0 41.2 + - + +
27C GLY* 1.3 72.0 - - - +
29C GLY* 1.3 57.0 + - - +
31C ALA* 2.9 19.0 + - - +
32C LEU* 2.9 19.3 + - - +
48C PHE* 4.3 2.5 - - + -
101C ALA* 4.2 9.2 - - + -
104C LEU* 3.7 14.8 - - + -
116C LEU* 3.6 15.9 - - + +
117C ALA* 3.6 17.7 - - + +
187C ARG* 3.5 48.5 - - + +
191C PRO* 3.8 18.8 - - + -
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.5 26.3 - - - +
177B HIS* 4.5 0.9 - - - -
25C PHE 3.4 7.9 + - - -
27C GLY 3.4 0.2 - - - -
28C LEU* 1.3 78.3 - - - +
30C SER* 1.3 57.3 + - - +
32C LEU* 3.9 4.7 - - - -
33C ASN* 3.3 32.2 + - - +
104C LEU* 3.5 19.4 - - - +
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 5.0 1.6 + - - +
173B LEU* 3.3 34.6 + - - +
174B LEU* 3.7 5.2 + - - +
177B HIS* 4.8 4.0 + - - -
26C PHE* 2.7 23.8 + - - +
27C GLY 3.9 1.3 - - - -
28C LEU 3.2 0.4 - - - -
29C GLY* 1.3 74.2 - - - +
31C ALA* 1.4 58.1 + - - +
32C LEU 3.6 1.1 - - - -
33C ASN 5.0 0.2 - - - -
39C PRO* 3.5 25.2 - - - +
43C GLN* 4.5 5.7 - - - +
44C ILE* 4.1 5.2 - - - +
47C ALA* 3.5 28.4 - - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.3 12.5 + - - +
28C LEU 2.9 9.3 + - - +
30C SER* 1.4 75.2 - - - +
32C LEU* 1.3 64.2 + - - +
34C TRP* 4.6 11.4 - - - -
39C PRO* 4.3 4.7 - - - +
44C ILE* 4.0 33.7 - - + +
48C PHE* 4.2 5.4 - - + -
117C ALA* 3.8 18.4 - - + +
187C ARG* 5.4 1.3 - - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU 2.9 22.0 + - - +
29C GLY* 3.9 7.2 - - - +
31C ALA* 1.3 82.0 - - - +
33C ASN* 1.4 95.0 + - - +
34C TRP* 3.2 37.0 - - + +
39C PRO* 3.4 7.4 - - - +
104C LEU* 3.8 11.2 - - + -
108C THR* 3.8 25.4 - - + +
112C ILE* 4.1 5.2 - - + +
113C ARG 4.1 11.7 - - - +
115C ASP* 5.5 0.2 - - - -
116C LEU* 3.8 43.3 - - + -
117C ALA* 4.5 6.0 - - - +
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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