Contacts of the helix formed by residues 1 - 29 (chain E) in PDB entry 1VF5
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 MET 1 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 6.4 0.2 - - - +
82B TYR* 4.9 12.6 - - - -
246C GLU* 5.7 4.5 - - - +
2E ILE* 1.3 71.1 + - + +
3E LEU* 3.5 24.7 - - + -
4E GLY* 3.2 15.1 + - - +
4F GLU* 6.2 2.0 - - - -
5F MET* 3.6 28.2 - - - +
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Residues in contact with ILE 2 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 5.6 2.2 - - - +
88A TRP* 4.3 17.3 - - + -
54B LEU* 5.5 5.2 - - + -
58B ASP* 4.2 21.3 - - + +
146C LYS* 5.6 1.1 - - - +
246C GLU* 5.9 2.2 - - - +
1E MET* 1.3 72.3 - - + +
3E LEU* 1.3 69.4 + - + +
4E GLY 2.9 5.3 + - - -
5E ALA* 3.1 10.7 + - - -
6E VAL* 3.5 14.9 + - + -
4F GLU* 4.2 9.6 - - + +
5F MET* 3.9 5.5 - - - +
7F TYR* 6.0 1.8 - - + +
8F ALA* 3.2 30.5 - - + +
15G PHE* 6.5 2.0 - - + -
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Residues in contact with LEU 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 5.5 7.4 - - - +
88A TRP* 3.9 27.8 - - + -
91A SER* 4.0 28.0 - - - +
92A MET* 6.3 1.8 - - - -
79B TRP* 4.1 18.2 - - + -
1E MET* 3.6 22.4 - - + -
2E ILE* 1.3 80.2 - - + +
4E GLY* 1.3 78.4 + - - +
5E ALA 2.9 2.9 - - - -
6E VAL* 2.7 29.7 + - + -
7E PHE* 2.9 27.5 + - + -
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Residues in contact with GLY 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.2 16.2 + - - -
2E ILE 2.9 3.2 - - - -
3E LEU* 1.3 87.9 - - - +
5E ALA* 1.3 56.9 + - - +
7E PHE* 3.4 16.1 - - - -
8E TYR* 2.9 38.3 + - - +
5F MET* 4.2 4.3 - - - -
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Residues in contact with ALA 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ILE 3.1 4.1 + - - +
3E LEU 2.9 0.2 - - - -
4E GLY* 1.3 74.0 - - - +
6E VAL* 1.3 67.6 + - - +
7E PHE 3.1 2.8 + - - -
8E TYR* 3.3 15.9 + - + -
9E ILE 3.3 3.5 + - - -
5F MET* 2.8 56.4 - - + +
8F ALA* 4.2 0.2 - - + -
9F ALA* 3.2 28.8 - - + +
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Residues in contact with VAL 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 5.6 1.1 - - + -
92A MET* 5.5 13.0 - - + -
95A LEU* 5.6 1.8 - - + -
54B LEU* 5.2 18.6 - - + -
2E ILE* 3.7 20.2 - - + +
3E LEU* 2.7 36.5 + - + +
5E ALA* 1.3 73.9 - - - +
7E PHE* 1.3 60.0 + - + +
10E VAL* 2.9 33.0 + - + +
8F ALA* 4.4 7.4 + - + +
12F SER* 3.4 17.6 + - - +
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Residues in contact with PHE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.2 38.1 - - + -
79B TRP* 3.5 44.9 - + - -
3E LEU* 2.9 42.4 - - + -
4E GLY* 3.4 15.5 - - - -
6E VAL* 1.3 77.3 - - + +
8E TYR* 1.3 97.8 + + - +
9E ILE 2.9 3.8 + - - -
10E VAL* 3.0 7.0 - - - -
11E PHE* 2.8 32.1 + + - +
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Residues in contact with TYR 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 5.3 6.2 - - - -
141B ILE* 5.3 16.8 - - + -
144B GLY* 4.8 2.2 - - - -
145B ILE* 3.7 32.7 + - + +
4E GLY* 2.9 24.6 + - - +
5E ALA* 3.3 9.6 + - + +
7E PHE* 1.3 107.8 - + - +
9E ILE* 1.3 57.5 + - + +
11E PHE* 3.1 30.4 - + - -
12E ILE* 3.9 11.4 - - - +
5F MET* 3.9 24.0 - - + -
9F ALA* 5.2 2.0 - - + -
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Residues in contact with ILE 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA 3.3 3.1 + - - +
8E TYR* 1.3 81.0 - - - +
10E VAL* 1.3 63.6 + - - +
11E PHE 2.9 2.0 - - - -
12E ILE* 3.4 30.7 - - + +
13E ALA* 2.7 30.0 + - - +
9F ALA* 2.6 48.0 - - + +
10F LEU* 5.0 6.5 - - + +
12F SER* 3.3 16.4 - - - -
13F PHE* 3.4 26.9 - - + +
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.6 22.7 - - + -
96A MET* 5.2 0.7 - - + -
99A LEU* 4.3 4.4 - - + +
6E VAL* 2.9 15.8 + - + +
7E PHE* 3.0 27.8 - - - +
9E ILE* 1.3 84.0 - - - +
11E PHE* 1.3 67.5 + - - +
13E ALA* 3.6 6.8 + - - +
14E LEU* 3.3 19.9 + - - +
101E BCR 3.9 30.3 - - + +
12F SER* 4.1 13.7 - - - -
16F ILE* 5.5 3.1 - - + -
22G PHE* 5.2 9.4 - - + -
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Residues in contact with PHE 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.7 3.4 - - + -
98A ILE* 6.0 0.7 - - + -
99A LEU* 3.2 31.1 - - + +
102A PHE* 3.9 18.2 - + + -
141B ILE* 4.2 28.5 - - + -
7E PHE* 2.8 27.0 + + - +
8E TYR* 3.1 28.9 - + - -
9E ILE 2.9 0.6 - - - -
10E VAL* 1.3 83.1 - - + +
12E ILE* 1.3 81.4 + - + +
13E ALA 3.1 0.2 - - - -
14E LEU* 2.9 4.7 - - - +
15E PHE* 2.9 47.5 + + - -
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Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR 3.9 14.8 - - - +
9E ILE* 2.9 32.0 + - + +
11E PHE* 1.3 103.2 - - + +
13E ALA* 1.3 62.6 + - - +
15E PHE* 3.6 8.3 - - + +
16E PHE* 3.2 32.3 + - + +
13F PHE* 3.6 12.8 - - + -
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Residues in contact with ALA 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE 2.7 15.9 + - - +
10E VAL* 3.7 7.6 - - - +
12E ILE* 1.3 77.3 - - - +
14E LEU* 1.3 57.0 + - - +
16E PHE* 3.7 0.9 - - - +
17E GLY 2.9 21.7 + - - -
101E BCR 3.2 20.5 - - + +
13F PHE* 3.4 38.6 - - + +
16F ILE* 4.1 18.2 - - + -
17F PHE* 4.9 2.0 - - + -
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.2 35.9 - - + -
36A LEU* 4.5 11.4 - - + -
99A LEU* 3.8 34.5 - - + +
102A PHE* 4.6 4.5 - - + -
10E VAL 3.3 10.1 + - - +
11E PHE* 2.9 17.7 + - - +
13E ALA* 1.3 77.2 - - - +
15E PHE* 1.3 52.3 + - - +
17E GLY* 2.9 3.3 + - - -
18E ILE* 2.7 52.7 + - + -
101E BCR 3.8 25.6 - - + -
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Residues in contact with PHE 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 3.2 44.9 - + + -
106A LEU* 3.8 16.6 - - + -
133B PHE* 3.4 35.2 - + - -
134B LEU* 5.2 8.5 - - + -
137B THR* 4.1 16.8 - - - -
11E PHE* 2.9 37.9 + + - +
12E ILE* 3.6 12.8 - - + +
14E LEU* 1.3 69.5 - - - +
16E PHE* 1.3 62.4 + - + +
18E ILE* 2.8 4.1 + - + -
19E ALA* 2.5 40.6 + - + +
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Residues in contact with PHE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 3.2 20.5 + - + +
13E ALA* 3.7 1.8 - - - +
15E PHE* 1.3 76.3 - - + +
17E GLY* 1.3 58.8 + - - +
19E ALA* 4.8 2.2 - - - -
20E VAL* 2.5 62.2 + - + +
101E BCR 3.1 44.6 - - + -
13F PHE* 4.4 18.2 - + + -
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Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.2 28.3 - - - -
13E ALA 2.9 8.1 + - - -
14E LEU 2.9 8.9 + - - -
16E PHE* 1.3 79.7 - - - +
18E ILE* 1.3 59.7 + - - +
21E GLY* 3.4 15.2 + - - -
22E ILE* 4.1 1.4 + - - +
101E BCR 3.3 22.3 - - - +
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.3 34.1 - - + -
102A PHE* 3.7 3.6 - - + -
103A ARG* 3.5 28.3 - - + +
106A LEU* 3.1 32.5 - - + -
14E LEU* 2.7 39.0 + - + +
15E PHE* 2.8 6.1 + - + +
17E GLY* 1.3 68.6 - - - +
19E ALA* 1.3 72.4 + - - +
20E VAL 2.7 3.2 + - - -
22E ILE* 2.8 56.7 + - + +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.4 13.6 - - + +
134B LEU* 6.3 2.9 - - + -
15E PHE* 2.5 24.7 + - + +
16E PHE* 4.8 2.0 - - - +
18E ILE* 1.3 74.3 - - - +
20E VAL* 1.3 63.4 + - + +
22E ILE* 4.9 1.1 - - - -
23E ILE* 3.3 21.7 + - - +
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PHE* 2.5 60.5 + - + +
17E GLY 4.4 0.4 - - - +
18E ILE 2.7 1.4 + - - -
19E ALA* 1.3 75.3 - - + +
21E GLY* 1.3 81.9 + - - +
22E ILE 2.8 2.8 + - - -
23E ILE* 3.2 16.5 + - - +
24E PHE* 3.3 9.9 + - + +
101E BCR 3.6 44.4 - - + -
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Residues in contact with GLY 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLY 3.4 11.2 + - - -
20E VAL* 1.3 85.8 - - - +
22E ILE* 1.3 52.2 + - - +
24E PHE* 3.4 5.8 - - - -
25E ALA* 2.6 36.2 + - - +
101E BCR 5.4 1.0 - - - +
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Residues in contact with ILE 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 5.3 3.4 - - + -
34A TYR* 4.5 25.6 - - + +
103A ARG* 5.5 0.7 - - - +
106A LEU* 5.0 11.2 - - + +
107A THR* 4.9 17.9 - - - +
211A ILE* 6.5 0.9 - - + -
124B PHE* 4.8 12.1 - - + -
17E GLY 4.5 0.9 - - - +
18E ILE* 2.8 61.2 + - + +
19E ALA* 4.9 0.2 - - - -
20E VAL 2.8 1.2 + - - -
21E GLY* 1.3 69.4 - - - -
23E ILE* 1.3 69.0 + - - +
24E PHE 3.1 0.9 - - - -
25E ALA* 2.7 23.0 + - + +
26E ILE* 3.6 9.9 + - + +
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Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 3.5 36.4 - - + +
125B ARG* 5.9 4.9 - - + -
19E ALA 3.3 16.4 + - - +
20E VAL* 3.2 12.5 + - - +
22E ILE* 1.3 79.9 - - - +
24E PHE* 1.3 88.6 + - + +
25E ALA 3.1 0.5 + - - -
27E LYS* 2.6 50.5 + - + +
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Residues in contact with PHE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 3.3 14.3 + - + +
21E GLY* 3.4 4.9 - - - +
22E ILE 3.1 0.4 - - - -
23E ILE* 1.3 107.1 - - + +
25E ALA* 1.3 64.7 + - - +
27E LYS* 3.5 20.7 - - + +
28E SER* 4.3 5.5 + - - -
101E BCR 4.0 39.3 - - + -
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Residues in contact with ALA 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.9 0.7 - - + -
21E GLY 2.6 21.9 + - - +
22E ILE* 2.7 24.5 + - + +
23E ILE 3.1 0.2 - - - -
24E PHE* 1.3 72.0 - - - +
26E ILE* 1.3 74.9 + - + +
27E LYS 2.8 9.5 + - - -
28E SER* 3.3 10.0 + - - -
29E ILE* 3.6 11.4 + - - +
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Residues in contact with ILE 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.8 26.2 - - + -
34A TYR* 5.6 1.6 - - - +
211A ILE* 3.3 44.9 - - + +
212A SER* 4.3 3.6 - - - +
124B PHE* 5.8 7.0 - - + -
22E ILE* 3.6 10.2 + - + +
25E ALA* 1.3 91.9 - - + +
27E LYS* 1.3 54.2 + - - +
28E SER 3.0 8.6 + - - -
29E ILE* 3.5 25.3 + - + -
30E LYS* 3.3 44.0 - - + +
31E LEU 4.5 0.5 + - - -
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE* 4.9 7.4 - - + -
125B ARG* 4.1 25.6 - - - +
23E ILE* 2.6 46.4 + - + +
24E PHE* 3.5 22.8 - - + +
25E ALA 2.8 1.6 - - - -
26E ILE* 1.3 76.8 - - - +
28E SER* 1.3 57.4 + - - +
31E LEU* 2.8 54.6 - - + +
----------------------------------------------------------
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Residues in contact with SER 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E PHE 4.4 5.6 - - - -
25E ALA 3.3 7.4 + - - -
26E ILE 3.0 0.8 + - - -
27E LYS* 1.3 83.6 - - - +
29E ILE* 1.3 60.3 + - - +
30E LYS* 3.0 7.3 + - - -
31E LEU* 3.6 17.1 + - - +
32E ILE 5.4 0.3 + - - -
----------------------------------------------------------
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Residues in contact with ILE 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.2 17.7 - - + -
212A SER* 5.5 4.3 - - - -
213A GLY* 5.9 4.9 - - - +
214A PRO* 4.2 18.9 - - + +
25E ALA 3.6 8.1 - - - +
26E ILE* 3.5 46.0 - - + -
28E SER* 1.3 76.9 - - - +
30E LYS* 1.3 65.4 + - + +
----------------------------------------------------------
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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