Contacts of the helix formed by residues 15 - 44 (chain C) in PDB entry 6B3I
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 ASP 15 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 3.4 6.2 + - - +
14C PHE* 1.3 72.9 - - - +
16C VAL* 1.3 70.7 + - - +
17C ASP* 3.5 15.8 + - - +
18C ARG* 3.2 45.3 + - + +
19C ASP* 3.2 28.4 + - - +
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.5 37.5 - - + +
15C ASP* 1.3 74.9 + - - +
17C ASP* 1.3 63.4 + - - +
19C ASP* 3.4 4.1 + - - +
20C ALA* 3.0 31.8 + - + +
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Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 3.3 12.2 + - - +
16C VAL* 1.3 79.5 - - - +
18C ARG* 1.3 61.1 + - - +
20C ALA* 3.9 5.2 - - - +
21C LYS* 3.0 30.0 + - - +
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 3.2 25.5 + - - -
14C PHE* 5.2 0.2 - - - +
15C ASP* 3.2 34.9 + - + +
16C VAL 3.3 0.6 - - - -
17C ASP* 1.3 79.3 - - - +
19C ASP* 1.3 65.3 + - - +
21C LYS* 3.5 10.7 + - + +
22C LYS* 2.9 30.3 + - + +
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Residues in contact with ASP 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.4 26.2 - - + -
15C ASP 3.2 18.7 + - - +
16C VAL* 3.9 4.5 - - - +
18C ARG* 1.3 87.6 + - - +
20C ALA* 1.3 60.0 + - - +
22C LYS* 3.2 11.4 + - - +
23C LEU* 2.9 38.0 + - + +
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.0 20.7 + - + +
17C ASP* 4.1 5.8 - - - +
19C ASP* 1.3 76.5 - - - +
21C LYS* 1.3 58.0 + - - +
23C LEU* 3.6 11.0 + - - +
24C ASN* 3.1 26.2 + - - +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP 3.0 20.2 + - - +
18C ARG* 3.7 10.1 - - + +
20C ALA* 1.3 75.4 - - - +
22C LYS* 1.3 65.8 + - + +
24C ASN* 3.2 7.6 + - - +
25C LYS* 2.9 55.3 + - - +
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 2.9 21.6 + - + +
19C ASP* 3.2 10.7 + - - +
21C LYS* 1.3 86.1 - - + +
23C LEU* 1.3 60.3 + - + +
25C LYS* 3.4 9.5 + - + +
26C ALA* 3.0 27.4 + - + +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASP* 2.9 24.2 + - + +
20C ALA* 3.8 8.5 - - - +
22C LYS* 1.3 76.6 - - + +
24C ASN* 1.3 60.7 + - - +
26C ALA* 3.3 7.2 + - + +
27C CYS* 2.8 43.3 + - - -
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Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 3.1 17.6 + - - +
21C LYS* 3.2 8.2 + - + +
23C LEU* 1.3 76.1 - - - +
25C LYS* 1.3 59.6 + - - +
27C CYS* 4.2 4.8 - - - +
28C LYS* 3.0 50.0 + - - +
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Residues in contact with LYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 2.9 41.7 + - - +
22C LYS* 3.7 9.2 - - + +
24C ASN* 1.3 79.6 + - - +
26C ALA* 1.3 62.3 + - - +
28C LYS* 3.5 7.2 + - - +
29C GLY* 3.1 19.6 + - - -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 3.0 19.8 + - + +
23C LEU* 3.8 9.9 - - + +
25C LYS* 1.3 78.8 - - - +
27C CYS* 1.3 58.2 + - - +
29C GLY* 3.2 2.0 + - - -
30C MET* 3.0 38.5 + - + +
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Residues in contact with CYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 2.8 33.3 + - - +
24C ASN* 4.2 5.2 - - - +
26C ALA* 1.3 71.4 - - - +
28C LYS* 1.3 65.0 + - - +
30C MET* 3.5 9.8 + - - +
31C GLY* 3.3 18.4 + - - -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASN* 3.0 39.1 + - - +
25C LYS* 3.7 7.2 - - - +
27C CYS* 1.3 78.5 - - - +
29C GLY* 1.3 59.5 + - - +
31C GLY* 3.6 2.1 + - - -
32C THR* 3.1 26.0 + - - +
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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
----------------------------------------------------------
25C LYS 3.1 14.9 + - - -
26C ALA 3.2 3.1 + - - -
28C LYS* 1.3 75.9 - - - +
30C MET* 1.3 53.7 + - - +
32C THR* 3.1 7.4 + - - -
33C ASN* 2.6 48.8 + - - -
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Residues in contact with MET 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 3.0 22.0 + - + +
27C CYS* 4.0 9.0 - - - +
28C LYS 3.4 0.2 - - - -
29C GLY* 1.3 77.5 - - - +
31C GLY* 1.3 57.5 + - - +
33C ASN* 4.3 7.6 - - - +
34C GLU* 2.8 58.8 + - + +
71C GLU 5.4 7.9 - - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C CYS 3.3 12.2 + - - -
28C LYS 4.0 3.4 - - - -
30C MET* 1.3 76.8 - - - +
32C THR* 1.3 60.9 + - - +
34C GLU* 4.1 8.8 + - - +
35C ALA* 3.2 23.7 + - - +
309C LYS* 5.2 2.9 - - - -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS* 3.1 15.5 + - - +
29C GLY* 3.1 12.1 + - - -
31C GLY* 1.3 75.1 - - - +
33C ASN* 1.3 69.0 + - - +
35C ALA* 3.4 7.0 + - - +
36C ALA* 3.1 22.7 + - + +
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Residues in contact with ASN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY* 2.6 29.4 + - - +
30C MET* 4.0 7.4 - - - +
32C THR* 1.3 77.0 - - - +
34C GLU* 1.3 64.8 + - + +
36C ALA* 3.2 9.3 + - - +
37C ILE* 3.1 31.0 + - + +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C MET* 2.8 53.1 + - + +
31C GLY* 4.1 6.5 - - - +
33C ASN* 1.3 69.4 - - + +
35C ALA* 1.3 57.3 + - - +
37C ILE* 3.1 9.9 + - + +
38C ILE* 2.7 46.3 + - + +
72C LEU* 5.2 6.9 - - + +
76C PHE* 4.3 18.2 - - + -
306C ASP* 2.8 40.2 - - - +
309C LYS* 6.1 1.3 - - + -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLY 3.2 20.3 + - - +
32C THR* 3.6 6.5 - - - +
34C GLU* 1.3 78.4 - - - +
36C ALA* 1.3 56.2 + - - +
38C ILE* 3.8 2.8 - - - +
39C GLU* 2.9 29.6 + - - +
309C LYS* 4.0 26.8 - - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 3.1 14.7 + - + +
33C ASN* 3.4 11.4 - - - +
34C GLU 3.1 0.4 - - - -
35C ALA* 1.3 75.4 - - - +
37C ILE* 1.3 65.2 + - + +
39C GLU* 3.3 5.7 + - - +
40C ILE* 3.2 32.8 + - + +
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 3.1 21.3 + - + +
34C GLU* 3.7 10.5 - - + +
36C ALA* 1.3 74.2 - - + +
38C ILE* 1.3 65.7 + - - +
40C ILE* 3.3 5.4 + - + +
41C LEU* 3.0 46.8 + - + +
68C LEU* 4.4 26.9 - - + -
72C LEU* 4.7 17.9 - - + -
76C PHE* 5.0 10.8 - - + -
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 2.7 30.6 + - + +
35C ALA* 3.9 4.9 - - - +
37C ILE* 1.3 71.9 - - - +
39C GLU* 1.3 52.9 + - - +
41C LEU* 4.3 0.8 - - + +
42C SER* 2.5 40.2 + - - +
76C PHE* 3.6 31.0 - - + -
306C ASP* 4.5 2.5 - - - +
309C LYS* 3.6 45.5 - - + +
310C LEU* 3.9 22.2 - - + +
313C ALA* 3.7 26.9 - - + -
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ALA 2.9 18.6 + - - +
36C ALA* 3.5 7.8 - - - +
37C ILE 3.2 0.2 - - - -
38C ILE* 1.3 78.3 - - - +
40C ILE* 1.3 70.9 + - - +
42C SER* 4.0 3.5 + - - -
43C GLY* 3.0 24.3 + - - -
44C ARG* 3.4 24.1 + - - -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA* 3.2 20.2 + - + +
37C ILE* 4.0 6.7 - - + +
39C GLU* 1.3 93.9 - - - +
41C LEU* 1.3 77.1 + - + +
42C SER 3.3 0.7 + - - -
43C GLY 3.3 3.3 + - - -
44C ARG* 3.2 40.3 + - + +
49C ARG* 4.6 2.9 - - + +
52C ILE* 4.1 29.6 - - + -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.0 38.0 + - + +
38C ILE* 4.3 1.6 - - - +
40C ILE* 1.3 86.9 - - + +
42C SER* 1.3 59.1 + - - +
44C ARG 4.3 1.9 - - - +
49C ARG* 3.5 31.6 + - + +
64C LEU* 5.7 2.7 - - + -
68C LEU* 5.1 4.0 - - + -
76C PHE* 6.0 0.7 - - + -
80C ALA* 3.6 38.1 - - + +
83C LEU* 3.8 22.7 - - + +
84C LEU* 3.8 30.1 - - + -
310C LEU* 4.5 11.9 - - + -
314C LEU* 4.0 3.3 - - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE 2.5 23.3 + - - -
39C GLU* 4.0 3.8 + - - -
41C LEU* 1.3 76.8 - - - +
43C GLY* 1.3 59.1 + - - +
44C ARG 3.6 3.3 - - - +
310C LEU* 4.5 3.6 - - - -
313C ALA* 3.3 35.0 + - - +
314C LEU* 3.8 22.7 - - - +
316C HIS* 3.1 28.2 + - - -
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU* 3.0 20.7 + - - -
40C ILE 3.3 0.4 + - - -
42C SER* 1.3 79.2 - - - +
44C ARG* 1.3 82.8 + - - +
48C GLU* 4.6 0.9 - - - +
316C HIS* 5.0 3.8 - - - -
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU* 3.4 31.6 + - - -
40C ILE* 3.2 34.2 + - - +
41C LEU 4.3 2.8 - - - +
42C SER 4.8 1.7 - - - +
43C GLY* 1.3 110.4 + - - +
45C THR* 1.3 71.9 + - - +
48C GLU* 3.4 22.4 - - + +
49C ARG* 3.4 25.6 + - + +
52C ILE* 4.0 21.0 - - + +
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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