Contacts of the helix formed by residues 7 - 32 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER* 1.4 78.2 + - - +
8B ALA* 1.4 71.2 + - + +
10B SER* 3.1 12.4 + - - +
11B ARG* 3.1 56.6 + - + +
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER 5.2 4.5 - - - +
7B ILE* 1.4 84.3 - - + +
9B PHE* 1.3 56.4 + - - +
11B ARG* 3.4 15.9 + - - +
12B ALA* 3.1 27.0 + - - +
62B ILE 5.0 1.7 - - - +
85B ARG* 5.8 0.7 - - - -
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Residues in contact with PHE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER* 3.8 20.0 + - - +
7B ILE 3.2 0.8 - - - -
8B ALA* 1.3 76.9 - - - +
10B SER* 1.4 61.7 + - - +
12B ALA* 3.3 6.3 + - - +
13B VAL* 3.0 41.1 + - + +
84B LEU* 3.8 23.3 - - + -
85B ARG* 3.8 55.9 - - + +
88B PHE* 3.5 45.3 - + + -
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER 2.9 15.6 + - - -
7B ILE* 3.1 16.0 + - - +
9B PHE* 1.4 79.6 - - - +
11B ARG* 1.4 58.1 + - - +
13B VAL* 3.4 6.4 + - - +
14B PHE* 2.9 32.0 + - - +
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.1 48.4 + - + +
8B ALA* 3.6 13.5 - - - +
9B PHE 3.3 0.2 - - - -
10B SER* 1.4 75.3 - - - +
12B ALA* 1.3 56.3 - - - +
14B PHE* 3.6 6.8 + - - +
15B ALA* 3.0 29.6 + - - +
62B ILE* 3.7 8.3 - - + +
221D TYR 5.2 2.0 + - - -
222D VAL* 3.2 28.0 + - + +
223D LEU* 3.3 25.0 - - - +
224D PHE* 6.3 0.4 - - - -
225D PRO* 3.6 28.2 + - - +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 3.1 14.4 + - - +
9B PHE 3.3 9.2 + - - +
11B ARG* 1.3 72.7 - - - +
13B VAL* 1.3 59.6 + - - +
15B ALA* 3.4 0.7 + - - -
16B GLU* 3.0 25.8 + - - +
62B ILE* 3.7 16.5 - - - +
63B SER* 3.3 18.3 - - - -
85B ARG* 3.6 13.0 - - - +
89B TYR* 3.2 25.6 - - + +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.0 52.3 + - + +
10B SER* 3.9 6.1 - - - +
12B ALA* 1.3 71.2 - - - +
14B PHE* 1.4 59.2 + - - +
16B GLU* 3.3 3.4 + - - +
17B PHE* 3.0 24.3 + - + +
88B PHE* 3.6 38.8 - - + +
89B TYR* 4.1 12.1 - - + -
92B ALA* 3.5 13.0 - - + +
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER 2.9 19.1 + - - +
11B ARG* 3.9 5.2 - - - +
13B VAL* 1.4 76.4 - - - +
15B ALA* 1.4 54.7 + - - +
17B PHE* 3.2 27.1 + + + +
18B LEU* 2.9 41.0 + - + +
218D LEU* 4.2 29.6 - - + -
222D VAL* 3.8 27.4 - - + -
223D LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG 3.0 19.2 + - - +
12B ALA 3.5 5.2 - - - +
13B VAL 3.3 0.2 - - - -
14B PHE* 1.4 74.7 - - - +
16B GLU* 1.4 53.6 + - - +
18B LEU* 3.4 3.6 + - - -
19B ALA* 2.8 37.6 + - - +
59B LEU* 3.8 15.2 - - + +
62B ILE* 3.8 20.9 - - + -
63B SER* 4.0 11.9 - - - +
223D LEU* 3.9 16.2 - - + -
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 3.0 16.5 + - - +
13B VAL* 3.3 10.3 + - - +
15B ALA* 1.4 74.5 - - - +
17B PHE* 1.3 57.6 + - - +
19B ALA* 4.0 3.3 - - - +
20B THR* 2.6 33.4 + - - -
63B SER* 2.6 23.0 + - - +
65B ALA* 3.3 3.4 + - - -
66B HIS* 2.9 26.7 + - - -
67B ILE* 3.0 18.0 + - - -
89B TYR* 3.7 26.9 - - + +
92B ALA* 4.2 11.7 - - + -
93B GLN* 2.9 31.5 + - + +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.0 13.4 + - + +
14B PHE* 3.4 31.4 - + - +
16B GLU* 1.3 73.1 - - - +
18B LEU* 1.4 65.3 + - + +
20B THR 3.4 2.4 + - - -
21B LEU* 3.0 50.7 + - + +
92B ALA* 3.4 20.4 - - + +
95B LEU* 3.9 17.3 - - + -
96B GLY* 3.4 40.0 - - - -
99B ALA* 4.4 6.3 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 2.9 29.9 + - + +
15B ALA 3.9 2.2 - - - +
17B PHE* 1.4 80.8 - - + +
19B ALA* 1.4 58.5 + - - +
21B LEU* 3.4 12.7 + - + +
22B LEU* 3.0 51.1 + - + +
59B LEU* 4.7 6.5 - - + -
136D PHE* 6.0 2.5 - - + -
139D LEU* 4.6 7.2 - - + -
143D LEU* 4.0 19.5 - - + -
218D LEU* 3.8 32.5 - - + -
223D LEU* 4.0 17.3 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 2.8 24.3 + - - +
16B GLU* 4.0 6.3 - - - +
18B LEU* 1.4 72.5 - - - +
20B THR* 1.4 56.7 + - - +
22B LEU 3.4 1.0 + - - -
23B PHE* 2.9 30.3 + - - +
55B LEU* 3.4 13.6 - - + +
59B LEU* 3.6 22.2 - - + +
65B ALA* 5.7 0.9 - - - -
67B ILE* 3.6 30.3 - - + -
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU 2.6 24.4 + - - -
17B PHE 4.1 1.6 - - - -
19B ALA* 1.4 72.5 - - - +
21B LEU* 1.4 59.6 + - - +
23B PHE* 4.3 1.8 - - + -
24B VAL* 3.0 38.5 + - + +
67B ILE* 3.6 30.0 - - + +
93B GLN* 3.4 42.0 - - + +
96B GLY 4.0 2.7 - - - -
97B ALA* 3.9 12.9 - - + -
184B ASN* 5.1 0.4 - - - +
186B ALA* 4.1 10.3 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.0 44.5 + - + +
18B LEU* 3.4 17.7 - - + +
20B THR* 1.4 75.9 - - - +
22B LEU* 1.3 63.8 + - + +
25B PHE* 3.0 34.6 + - + +
96B GLY 3.1 17.6 + - - +
99B ALA* 3.8 14.4 - - + -
100B GLY* 3.5 13.8 - - - +
103B LEU* 4.1 17.5 - - + -
136D PHE* 4.1 26.5 - - + -
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Residues in contact with LEU 22 (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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18B LEU* 3.0 35.8 + - + +
19B ALA 3.9 2.9 - - - +
21B LEU* 1.3 75.7 - - + +
23B PHE* 1.3 59.3 + - - +
25B PHE* 3.8 4.2 - - + +
26B PHE* 3.0 55.1 + - + +
55B LEU* 3.8 26.2 - - + -
59B LEU* 5.5 0.2 - - + -
136D PHE* 3.7 33.9 - - + +
139D LEU* 3.9 25.1 - - + -
140D GLN* 4.6 8.7 - - + -
143D LEU* 4.2 10.8 - - + -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 2.9 18.8 + - - +
20B THR* 3.9 2.7 - - + +
21B LEU 3.4 0.2 - - - -
22B LEU* 1.3 74.9 - - - +
24B VAL* 1.3 62.6 + - + +
26B PHE* 4.0 2.3 - - - +
27B GLY* 2.8 34.4 + - - -
48B PHE* 3.6 44.9 - + + -
51B GLY* 4.6 5.2 - - - -
52B ILE* 3.5 38.8 - - + -
55B LEU* 3.7 13.2 - - + +
67B ILE* 3.7 17.0 - - + -
168B VAL* 5.0 4.3 - - + -
172B HIS* 5.5 1.3 - - - -
182B SER 6.0 0.7 - - - -
184B ASN* 3.5 26.7 - - + -
187B ARG* 4.1 18.4 - - + -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.0 22.5 + - + +
21B LEU 4.2 1.1 - - - +
23B PHE* 1.3 82.3 - - + +
25B PHE* 1.4 65.6 + - - +
27B GLY* 5.1 0.2 - - - -
28B LEU* 3.0 56.1 + - + +
48B PHE* 6.0 0.7 - - - -
97B ALA* 3.3 41.3 - - + +
101B ALA 3.7 8.5 - - - +
187B ARG* 4.0 24.2 - - + -
190B ALA* 3.8 7.2 - - + -
191B PRO* 5.4 0.2 - - + -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.0 23.9 + - + +
22B LEU* 3.8 4.0 - - - +
24B VAL* 1.4 78.3 - - - +
26B PHE* 1.4 76.5 + + - +
29B GLY* 3.4 18.0 + - - -
100B GLY* 3.7 23.8 + - - +
103B LEU* 3.7 21.8 - - + -
104B LEU* 3.8 21.3 - - + +
107B ILE* 3.7 40.2 - - + -
132D THR 5.5 0.2 - - - -
133D VAL* 4.7 10.8 - - + -
136D PHE* 3.7 34.3 - + + -
174D LEU* 3.7 23.8 - - + +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.0 38.9 + - + +
23B PHE* 4.1 2.7 - - - +
25B PHE* 1.4 91.6 - + - +
27B GLY* 1.3 63.5 + - - +
29B GLY 4.0 0.2 - - - -
30B SER* 2.8 32.9 + - - -
47B ALA* 4.8 2.4 - - - +
51B GLY* 5.8 1.8 - - - -
136D PHE 3.5 27.4 - - - -
137D LEU* 3.5 31.4 - - + -
140D GLN* 3.5 21.3 - - + -
170D LEU* 3.9 38.6 - - + -
171D GLY* 4.0 13.2 - - - -
174D LEU* 3.8 16.3 - - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE 2.8 22.8 + - - -
26B PHE* 1.3 75.0 - - - +
28B LEU* 1.4 60.3 + - - +
30B SER* 3.5 4.0 + - - -
31B ALA 3.4 12.0 + - - -
44B ILE* 5.3 0.2 - - - +
47B ALA* 4.9 1.5 - - - +
48B PHE* 3.3 49.4 - - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.0 40.1 + - + +
27B GLY* 1.4 72.1 - - - +
29B GLY* 1.3 58.3 + - - +
31B ALA* 2.9 19.8 + - - +
32B LEU* 3.1 15.4 + - - +
48B PHE* 4.3 2.9 - - + -
101B ALA* 4.2 9.0 - - + -
104B LEU* 3.7 16.4 - - + -
116B LEU* 3.7 15.7 - - + +
117B ALA* 3.6 19.1 - - + +
187B ARG* 3.5 48.2 - - + +
191B PRO* 3.8 19.1 - - + -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE 3.4 8.1 + - - -
28B LEU* 1.3 78.7 - - - +
30B SER* 1.3 54.5 + - - +
31B ALA 3.7 0.2 + - - -
32B LEU* 3.8 6.0 - - - +
34B TRP* 3.1 31.7 + - - -
104B LEU* 3.5 20.3 - - - +
174D LEU* 3.5 26.5 - - - +
177D HIS* 4.5 1.0 + - - -
178D TYR* 4.8 0.2 - - - -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 2.8 23.1 + - - +
27B GLY 3.5 2.0 + - - -
29B GLY* 1.3 75.0 - - - +
31B ALA* 1.4 57.7 + - - +
32B LEU 3.5 0.4 - - - -
34B TRP* 4.6 3.3 + - - +
39B PRO* 3.5 25.3 - - - +
43B GLN* 4.5 6.1 + - - +
44B ILE* 4.1 5.0 - - - +
47B ALA* 3.5 28.5 - - - +
170D LEU* 5.0 1.2 + - - +
173D LEU* 3.4 35.0 + - - +
174D LEU* 3.6 6.1 + - - +
177D HIS* 4.7 1.4 - - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 3.4 12.2 + - - +
28B LEU 2.9 9.5 + - - +
30B SER* 1.4 75.9 - - - +
32B LEU* 1.4 64.9 + - - +
33B ASN* 3.8 5.9 + - - +
39B PRO* 4.3 4.5 - - - +
44B ILE* 4.0 34.0 - - + +
48B PHE* 4.2 5.4 - - + -
117B ALA* 3.8 20.7 - - + +
187B ARG* 5.4 0.9 - - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU 3.1 16.5 + - - +
29B GLY* 3.8 18.6 - - - +
30B SER 3.5 1.6 - - - -
31B ALA* 1.4 79.9 - - - +
33B ASN* 1.3 62.4 + - - +
34B TRP* 3.0 36.8 + - + +
39B PRO* 3.2 7.8 - - - +
104B LEU* 4.5 4.9 - - + -
108B THR* 3.7 35.0 - - + +
112B ILE* 4.1 10.1 - - + +
113B ARG* 3.4 22.7 - - - +
116B LEU* 3.6 31.2 - - + -
117B ALA* 4.0 3.4 - - - +
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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