Contacts of the helix formed by residues 13 - 36 (chain B) in PDB entry 1VGO
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 GLU 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ARG* 3.1 31.6 + - + +
12B PRO* 1.3 80.4 - - - +
14B THR* 1.3 57.3 + - - +
15B LEU 2.9 6.3 - - - -
16B TRP* 2.9 31.7 + - + +
17B LEU* 3.0 16.6 + - + +
82B ASP* 4.6 1.9 - - - +
84B TYR* 2.7 29.1 + - + +
206B LEU* 3.3 34.8 - - + +
207B GLY* 4.5 6.4 + - - -
210B THR* 3.7 30.5 - - + +
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Residues in contact with THR 14 (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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5B ASP* 4.2 2.1 + - - -
6B LEU* 3.7 23.1 + - - +
7B LEU* 4.3 4.1 + - + -
9B ASP* 4.4 2.5 - - - +
11B ARG* 2.9 61.3 + - + +
13B GLU* 1.3 75.5 - - + +
15B LEU* 1.3 61.0 + - - +
16B TRP 3.3 0.2 - - - -
17B LEU* 3.6 11.9 - - + -
18B GLY* 2.9 23.0 + - - -
65B PHE* 3.3 32.8 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP 5.6 4.0 - - - +
6B LEU* 4.2 26.9 - - + +
12B PRO 3.4 17.0 + - - +
14B THR* 1.3 82.4 + - - +
16B TRP* 1.3 103.1 + - + +
18B GLY* 3.4 1.0 + - - -
19B ILE* 3.2 39.0 + - + +
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Residues in contact with TRP 16 (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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12B PRO 4.6 5.5 + - - -
13B GLU* 2.9 21.5 + - - +
15B LEU* 1.3 100.4 - - + +
17B LEU* 1.3 65.2 + - - +
18B GLY 3.0 1.8 - - - -
19B ILE* 3.4 17.0 + - + +
20B GLY* 2.9 22.5 + - - -
207B GLY* 3.6 30.7 + - - -
208B ILE* 5.2 7.3 - - + +
210B THR* 3.9 15.0 - - + +
211B LEU* 3.4 48.4 - - + +
214B MET* 3.9 13.7 - - + +
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Residues in contact with LEU 17 (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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11B ARG* 4.0 7.9 - - - +
13B GLU* 3.0 14.3 + - + +
14B THR* 3.7 19.7 - - + +
16B TRP* 1.3 76.6 - - - +
18B GLY* 1.3 50.8 + - - +
20B GLY 3.9 0.4 - - - -
21B THR* 2.6 34.4 + - - -
61B TYR* 3.4 17.2 - - + +
64B MET* 3.1 63.9 - - + +
65B PHE* 3.8 14.6 - - - +
84B TYR* 4.1 16.8 - - + +
87B ARG* 5.4 2.9 - - - +
210B THR* 4.0 18.6 - - + -
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Residues in contact with GLY 18 (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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6B LEU* 5.6 2.2 - - - -
14B THR 2.9 16.2 + - - -
15B LEU 3.9 1.1 - - - -
16B TRP 3.0 0.4 - - - -
17B LEU* 1.3 74.1 - - - +
19B ILE* 1.3 65.8 + - - +
20B GLY 3.0 1.3 - - - -
21B THR* 2.8 19.4 + - - -
22B LEU* 3.0 19.1 + - - +
65B PHE* 3.9 13.9 - - - -
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Residues in contact with ILE 19 (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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15B LEU* 3.2 40.2 + - + +
16B TRP* 3.7 18.8 - - + +
18B GLY* 1.3 73.7 - - - +
20B GLY* 1.3 58.0 + - - +
22B LEU* 3.3 12.9 + - + +
23B LEU* 2.8 52.6 + - + +
214B MET* 3.9 12.3 - - + -
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Residues in contact with GLY 20 (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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16B TRP 2.9 12.4 + - - -
19B ILE* 1.3 76.9 - - - +
21B THR* 1.3 63.8 + - - +
23B LEU* 4.2 3.7 - - - +
24B MET* 3.1 28.5 + - - +
61B TYR* 3.7 15.4 - - - -
214B MET* 3.7 27.3 - - - +
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Residues in contact with THR 21 (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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17B LEU 2.6 22.8 + - - -
18B GLY* 2.8 11.3 + - - -
20B GLY* 1.3 78.0 - - - +
22B LEU* 1.3 66.3 + - + +
24B MET* 3.7 3.5 - - - +
25B LEU* 3.1 34.8 + - + +
58B SER* 3.7 20.1 - - - +
61B TYR* 3.4 23.0 + - - +
62B LEU* 4.0 24.2 - - + +
65B PHE* 4.5 2.6 - - - +
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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 GLY 3.0 14.0 + - - +
19B ILE* 3.6 13.5 - - + +
21B THR* 1.3 79.9 - - + +
23B LEU* 1.3 57.4 + - + +
25B LEU* 2.6 40.0 + - + +
26B ILE* 2.8 23.4 + - + +
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Residues in contact with LEU 23 (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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19B ILE* 2.8 42.8 + - + +
20B GLY* 4.2 4.5 - - - +
22B LEU* 1.3 73.4 - - + +
24B MET* 1.3 57.4 + - - +
26B ILE* 3.7 19.1 + - + +
27B GLY* 3.2 21.7 + - - -
214B MET* 4.2 18.4 - - + -
218B VAL* 4.7 22.3 - - + +
222B VAL* 4.0 7.9 - - - +
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 3.1 20.4 + - - +
22B LEU 2.9 1.0 + - - -
23B LEU* 1.3 75.3 - - - +
25B LEU* 1.3 55.1 + - - +
28B THR* 2.5 37.5 + - - -
54B PRO* 3.3 29.8 - - + +
57B ALA* 3.4 16.2 - - + -
58B SER* 3.6 16.6 - - - +
61B TYR* 4.5 12.8 - - + -
214B MET 5.4 0.7 - - - +
217B ASP* 3.9 26.0 - - + -
218B VAL* 4.1 9.6 - - + +
221B LYS* 3.3 34.1 - - + -
222B VAL* 4.2 18.6 - - - -
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Residues in contact with LEU 25 (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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21B THR* 3.1 28.6 + - + +
22B LEU* 2.6 27.3 + - + +
24B MET* 1.3 69.4 - - - +
26B ILE* 1.3 57.0 - - + +
28B THR* 3.0 10.0 + - + -
29B PHE* 2.8 66.4 + - + +
58B SER* 4.1 16.8 - - - +
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Residues in contact with ILE 26 (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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22B LEU* 2.8 25.2 + - + +
23B LEU* 3.9 18.8 - - + +
25B LEU* 1.3 79.9 - - + +
27B GLY* 1.3 58.2 + - - +
29B PHE* 3.5 7.7 + - + +
30B TYR* 2.9 31.4 + - + +
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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
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23B LEU 3.2 8.0 + - - -
24B MET 3.6 0.2 + - - -
25B LEU 3.2 0.4 - - - -
26B ILE* 1.3 81.0 - - - +
28B THR* 1.3 62.7 + - - +
30B TYR* 3.3 6.6 + - - +
31B PHE* 3.0 34.4 + - - -
54B PRO* 4.4 2.2 - - - -
222B VAL* 3.9 33.7 - - - -
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Residues in contact with THR 28 (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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24B MET 2.5 22.2 + - - -
25B LEU* 3.0 15.4 + - + -
27B GLY* 1.3 75.5 - - - +
29B PHE* 1.3 65.5 + - + +
31B PHE* 3.2 5.4 + - - +
32B ILE* 3.1 43.0 + - + +
51B ILE* 3.9 13.0 - - + +
54B PRO* 3.2 27.3 + - - +
55B GLY* 3.5 19.2 - - - -
58B SER* 4.5 1.1 + - - -
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Residues in contact with PHE 29 (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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25B LEU* 2.8 49.2 + - + +
26B ILE* 3.9 7.4 - - + +
28B THR* 1.3 77.0 - - + +
30B TYR* 1.3 57.5 - - - +
32B ILE* 3.4 17.0 + - + +
33B ALA* 2.9 31.2 + - - +
311B BNG 3.8 35.2 - - + +
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Residues in contact with TYR 30 (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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26B ILE* 2.9 22.5 + - + +
27B GLY* 3.5 6.5 - - - +
29B PHE* 1.3 78.2 - - - +
31B PHE* 1.3 81.5 + + - +
33B ALA* 3.5 5.9 + - + +
34B ARG* 3.0 62.0 + - + +
222B VAL* 6.2 1.6 - - + -
226B PHE* 3.8 33.7 - + - -
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Residues in contact with PHE 31 (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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27B GLY 3.0 20.5 + - - +
28B THR 3.2 4.2 + - - +
30B TYR* 1.3 99.8 - + - +
32B ILE* 1.3 58.4 + - - +
34B ARG* 3.3 5.0 + - - -
35B GLY 2.8 23.9 + - - -
47B TYR* 3.2 13.4 - + - -
50B THR* 4.3 11.2 - - + -
51B ILE* 3.7 17.0 - - + -
54B PRO* 3.9 26.2 - - + -
221B LYS 4.1 11.4 - - - -
222B VAL* 3.4 34.3 - - + -
225B GLY* 3.6 10.1 - - - -
226B PHE* 3.6 23.8 - - + -
229B LEU* 4.1 18.4 - - + -
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Residues in contact with ILE 32 (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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28B THR* 3.1 28.7 + - + +
29B PHE* 3.7 17.3 - - + +
31B PHE* 1.3 73.8 - - - +
33B ALA* 1.3 66.9 + - - +
35B GLY 3.1 0.9 + - - -
36B TRP* 2.9 41.3 + - + +
51B ILE* 3.6 37.5 - - + -
311B BNG 4.1 19.1 - - + -
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Residues in contact with ALA 33 (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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29B PHE 2.9 19.3 + - - +
30B TYR* 3.8 7.6 - - + +
32B ILE* 1.3 76.6 - - - +
34B ARG* 1.3 60.7 + - - +
36B TRP* 3.6 13.3 - - - +
37B GLY 4.6 1.0 + - - -
311B BNG 3.8 45.3 - - + +
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Residues in contact with ARG 34 (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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30B TYR* 3.0 55.5 + - + +
31B PHE* 3.7 6.5 - - - +
33B ALA* 1.3 76.9 - - - +
35B GLY* 1.3 63.0 + - - +
36B TRP 3.3 0.2 - - - -
37B GLY* 4.2 4.0 + - - -
38B VAL* 3.6 13.3 - - - +
47B TYR* 3.0 26.9 + - + +
226B PHE* 5.7 1.8 - - - -
229B LEU* 3.3 19.8 + - - -
230B ARG* 4.2 24.9 + - - +
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Residues in contact with GLY 35 (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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31B PHE 2.8 11.9 + - - -
32B ILE* 3.1 2.0 + - - -
34B ARG* 1.3 74.6 - - - +
36B TRP* 1.3 66.2 + - - +
37B GLY 3.1 3.1 - - - -
38B VAL* 3.0 23.4 + - - +
44B ARG* 3.9 10.7 + - - -
47B TYR* 3.4 28.2 - - - -
51B ILE* 5.6 1.6 - - - -
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Residues in contact with TRP 36 (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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32B ILE* 2.9 32.9 + - + +
33B ALA 3.6 11.2 - - - +
34B ARG 3.3 0.4 - - - -
35B GLY* 1.3 77.0 - - - +
37B GLY* 1.3 56.9 + - - +
44B ARG* 4.5 2.5 + - - +
311B BNG 3.2 60.5 + - + +
402B SO4 3.4 14.4 + - - -
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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) + - + + + + + -
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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