Contacts of the helix formed by residues 16 - 36 (chain A) in PDB entry 3IML
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 HIS 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.6 21.9 - - + +
13A SER* 3.2 19.0 + - - +
15A GLY* 1.3 76.8 - - - +
17A PRO* 1.4 81.0 - - + +
18A ASP* 3.2 49.8 + - - +
19A LYS* 2.9 5.8 + - - -
20A VAL* 2.9 19.8 + - - +
167A ASP* 3.3 16.8 - - - +
168A ALA 4.5 0.2 - - - +
169A LYS* 4.1 35.2 + - + +
242A ASP* 4.5 9.3 + - - -
243A CYS 6.0 0.7 - - - -
249A LYS* 3.7 14.0 - - - -
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Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 3.5 2.2 - - - +
16A HIS* 1.4 100.6 - - + +
18A ASP* 1.3 61.0 + - - +
20A VAL* 3.3 12.6 + - + +
21A ALA* 3.1 18.2 + - - +
47A CYS* 4.0 1.9 - - - -
167A ASP* 3.7 12.8 - - - +
238A GLY 3.5 13.5 - - - -
239A PRO* 4.0 10.1 - - + -
242A ASP* 3.4 42.4 - - - +
243A CYS 3.9 1.8 - - - +
244A GLY* 3.5 24.9 - - - +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 3.2 18.6 + - - +
17A PRO* 1.3 76.7 - - - +
19A LYS* 1.3 58.7 + - - +
21A ALA* 3.3 4.7 + - - +
22A ASP* 3.0 30.6 + - - +
243A CYS 4.1 4.4 - - - +
244A GLY* 3.4 6.0 - - - -
245A LEU* 3.0 34.4 + - - +
248A ARG* 3.8 21.1 + - + +
249A LYS* 2.7 40.5 + - + -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.5 25.6 - - + +
13A SER 3.5 17.7 - - - +
14A GLU 4.3 0.2 - - - +
16A HIS* 2.9 10.0 + - - +
18A ASP* 1.3 77.4 - - - +
20A VAL* 1.3 60.0 + - - +
22A ASP* 3.1 20.2 + - - +
23A GLN* 2.8 43.4 + - - +
249A LYS* 3.8 22.4 - - + -
252A VAL* 4.2 12.3 - - - -
253A ASP* 2.8 31.6 + - - -
359A ALA* 2.6 36.2 + - - +
360A ALA* 4.3 13.5 - - + +
361A TYR 5.1 2.0 - - - +
363A HIS* 4.9 0.2 + - - -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 4.0 5.6 - - - +
15A GLY* 3.9 15.7 - - - +
16A HIS 2.9 23.1 + - - +
17A PRO* 3.3 14.8 + - + +
19A LYS* 1.3 74.1 - - - +
21A ALA* 1.3 59.1 + - - +
23A GLN* 3.1 9.2 + - - +
24A ILE* 2.8 49.5 + - + +
47A CYS* 4.0 11.0 - - - -
74A ILE* 4.3 12.6 - - + -
77A ILE* 4.2 14.1 - - + -
79A TYR* 4.4 8.3 - - + -
239A PRO* 4.3 15.7 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO 3.1 9.5 + - - +
18A ASP 3.5 3.8 - - - +
20A VAL* 1.3 81.5 - - - +
22A ASP* 1.3 63.3 + - - +
24A ILE 3.4 0.3 + - - -
25A SER* 3.0 27.0 + - - -
45A THR* 3.6 25.5 + - - +
47A CYS* 4.1 7.4 - - - -
244A GLY 4.1 2.7 - - - -
245A LEU* 3.4 33.7 - - - +
246A THR* 3.5 4.6 + - - +
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Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP 3.0 18.7 + - - +
19A LYS* 3.1 38.1 + - - +
21A ALA* 1.3 75.4 - - - +
23A GLN* 1.3 59.1 + - - +
25A SER* 3.5 1.5 + - - -
26A ASP* 3.0 24.4 + - - +
246A THR* 3.5 7.7 - - - +
247A GLY* 2.8 32.3 + - - -
248A ARG 4.7 0.2 + - - -
249A LYS* 4.3 8.1 + - - +
253A ASP* 4.2 7.7 - - - +
267A SER* 3.4 31.9 + - - +
359A ALA* 3.8 4.0 - - - +
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.8 41.7 + - - +
19A LYS* 2.8 35.1 + - - +
20A VAL 3.6 3.3 - - - +
22A ASP* 1.3 70.5 - - - +
24A ILE* 1.3 56.8 + - - +
26A ASP* 3.2 0.5 + - - -
27A ALA* 2.7 36.9 + - - +
73A THR* 4.0 13.9 - - + -
76A ARG* 3.3 32.6 + - - +
77A ILE* 3.8 6.8 - - + +
356A GLU* 3.8 9.6 - - + +
359A ALA* 3.5 26.0 - - + +
360A ALA* 3.9 11.8 - - - +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 2.8 39.1 + - + +
21A ALA 3.8 3.4 - - - +
23A GLN* 1.3 75.8 - - - +
25A SER* 1.3 64.2 + - - +
27A ALA* 3.2 3.9 + - - +
28A ILE* 3.0 33.3 + - + +
45A THR* 3.8 24.5 - - + +
47A CYS* 4.6 2.7 - - - -
52A VAL* 4.6 10.1 - - + -
54A LEU* 3.8 19.7 - - + -
70A ALA* 4.0 15.9 - - + +
73A THR* 3.9 23.6 - - + -
74A ILE* 4.1 19.3 - - + -
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 3.0 12.3 + - - -
22A ASP 3.6 5.2 - - - -
23A GLN 3.3 0.2 - - - -
24A ILE* 1.3 77.9 - - - +
26A ASP* 1.3 56.8 + - - +
28A ILE* 3.7 5.7 + - - +
29A LEU* 3.1 23.9 + - - +
43A ALA* 2.6 35.3 + - - +
45A THR* 2.7 21.1 + - - -
246A THR* 2.7 19.6 + - - -
267A SER 4.1 0.2 - - - -
268A GLY* 3.8 17.5 - - - -
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP 3.0 12.4 + - - +
23A GLN 4.0 0.9 - - - +
24A ILE 3.2 0.2 - - - -
25A SER* 1.3 73.7 - - - +
27A ALA* 1.3 60.7 + - - +
28A ILE 3.3 0.4 - - - -
29A LEU* 3.5 8.5 - - - +
30A ASP* 2.8 32.4 + - - +
267A SER* 2.8 27.3 + - - -
268A GLY 2.9 18.4 + - - -
276A ARG* 2.9 35.6 + - - -
355A TYR* 3.5 24.7 - - - +
356A GLU* 3.7 6.5 - - - -
358A THR* 3.6 2.3 + - - -
359A ALA* 3.7 4.0 - - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN 2.7 18.6 + - - +
24A ILE 3.6 4.0 - - - +
26A ASP* 1.3 74.0 - - - +
28A ILE* 1.3 55.7 + - - +
30A ASP* 3.2 4.5 + - - +
31A ALA* 2.9 29.6 + - - +
69A ILE* 3.7 13.3 - - + +
73A THR* 3.2 26.7 - - - +
356A GLU* 3.5 24.8 - - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.0 32.5 + - + +
25A SER* 3.8 4.7 - - - +
27A ALA* 1.3 72.6 - - - +
29A LEU* 1.3 65.6 + - - +
31A ALA* 3.4 3.9 + - - +
32A ILE* 3.1 42.0 + - + +
43A ALA* 4.3 11.4 - - + -
54A LEU* 3.9 21.1 - - + -
58A ILE* 5.0 0.4 - - + -
64A ILE* 5.3 0.2 - - - +
66A TYR* 4.1 26.7 - - + +
69A ILE* 3.8 21.3 - - + -
70A ALA* 5.1 0.2 - - + -
97A TYR* 3.2 33.2 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 3.1 16.5 + - - +
26A ASP* 3.5 13.0 - - - +
27A ALA 3.3 0.2 - - - -
28A ILE* 1.3 76.5 - - - +
30A ASP* 1.3 62.9 + - - +
32A ILE* 3.3 3.3 + - - +
33A LEU* 3.0 42.5 + - + +
41A VAL* 3.6 41.3 - - + -
268A GLY* 4.8 1.3 - - - -
269A LYS 3.3 24.7 - - - +
270A ASP* 3.8 16.2 - - + +
276A ARG* 3.3 17.3 - - - +
355A TYR* 3.7 20.4 - - + -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP 2.8 19.1 + - - +
27A ALA* 3.2 7.2 + - - +
29A LEU* 1.3 72.7 - - - +
31A ALA* 1.3 62.7 + - - +
33A LEU* 3.3 0.9 + - - -
34A ALA* 3.0 22.2 + - - +
353A PRO* 3.1 38.0 - - + +
354A ILE 3.2 1.4 + - - -
355A TYR* 2.8 32.4 + - - +
356A GLU* 2.8 31.2 + - - +
357A LYS 4.7 0.2 + - - -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 2.9 12.8 + - - +
28A ILE 3.9 2.5 - - - +
29A LEU 3.3 0.2 - - - -
30A ASP* 1.3 76.7 - - - +
32A ILE* 1.3 62.2 + - - +
34A ALA* 3.5 17.8 - - - +
35A GLN* 3.7 7.0 + - - +
64A ILE* 3.8 17.4 - - + +
69A ILE* 3.1 36.8 - - + -
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.1 39.9 + - + +
29A LEU 3.7 3.6 - - - +
31A ALA* 1.3 77.4 - - - +
33A LEU* 1.3 58.7 + - + +
35A GLN* 3.1 6.4 + - - +
36A ASP* 3.0 23.2 + - - +
39A SER* 3.3 19.5 - - - +
41A VAL* 4.0 25.8 - - + -
58A ILE* 4.1 19.3 - - + -
60A THR* 3.3 28.7 - - + +
62A ALA* 3.8 3.5 - - + +
64A ILE* 4.1 20.9 - - + -
66A TYR* 4.3 7.6 - - + +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.0 47.6 + - + +
30A ASP 3.3 3.1 + - - +
32A ILE* 1.3 74.9 - - + +
34A ALA* 1.3 65.8 + - - +
35A GLN 3.2 0.7 + - - -
36A ASP 3.3 12.9 + - - +
37A LYS* 3.4 47.6 + - + +
39A SER* 4.5 14.1 - - - +
270A ASP* 5.0 3.4 - - + -
271A PRO* 4.8 8.7 - - + -
350A LEU 5.1 0.2 - - - +
351A LEU* 5.1 3.6 - - + -
352A ARG 3.8 22.9 - - - +
353A PRO* 4.4 13.9 - - + +
355A TYR* 3.9 14.1 - - + -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP 3.0 13.9 + - - +
31A ALA* 3.5 15.0 - - - +
33A LEU* 1.3 77.8 - - - +
35A GLN* 1.3 62.4 + - + +
353A PRO* 4.2 16.3 - - + +
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.0 7.6 + - - +
32A ILE 3.1 2.2 + - - -
34A ALA* 1.3 80.0 - - + +
36A ASP* 1.3 60.4 + - - +
37A LYS 4.2 0.4 - - - -
61A THR* 4.7 3.6 + - - +
62A ALA* 3.6 15.9 - - + -
63A ASN* 3.0 42.1 + - - +
64A ILE* 3.0 18.7 - - - +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE 3.0 9.8 + - - +
33A LEU* 3.3 5.9 + - - -
35A GLN* 1.3 82.3 - - - +
37A LYS* 1.3 58.5 + - - +
38A TYR* 3.2 24.1 + - - +
39A SER* 2.6 45.9 + - - +
60A THR* 3.6 9.5 - - - +
61A THR* 2.8 43.7 + - - +
62A ALA 4.3 3.6 - - - +
102A PRO* 5.4 1.9 - - - +
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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