Contacts of the helix formed by residues 17 - 44 (chain I) in PDB entry 1KYO
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 PHE 17 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ARG* 4.0 50.9 - - + -
456A TRP* 3.3 32.3 - - - +
11I PHE* 5.6 1.2 - - - -
14I ASN* 4.8 16.2 - - + -
15I ALA* 3.4 16.8 + - + -
16I VAL* 1.3 76.9 - - - +
18I VAL* 1.3 54.7 + - - +
20I THR* 2.9 20.6 + - - +
21I ILE* 2.8 35.3 + - - +
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Residues in contact with VAL 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A MET* 5.1 15.3 - - + -
455A ARG 4.0 18.0 + - - +
456A TRP* 3.8 15.5 + - + +
16I VAL 5.1 2.5 - - - +
17I PHE* 1.3 73.4 - - - +
19I GLY* 1.3 60.3 + - - +
21I ILE* 3.6 11.5 - - + +
22I PHE* 3.3 48.0 + - + -
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Residues in contact with GLY 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TRP* 2.9 46.0 + - - +
18I VAL* 1.3 75.7 - - - +
20I THR* 1.3 64.3 + - - +
21I ILE 3.2 0.2 - - - -
22I PHE* 3.5 4.2 + - - +
23I ALA* 3.1 25.2 + - - +
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Residues in contact with THR 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TRP 4.3 0.2 + - - -
65E LEU* 5.2 0.5 - - - +
11I PHE* 4.0 19.4 - - + -
16I VAL* 3.9 18.8 - - + -
17I PHE* 2.9 24.8 + - - +
19I GLY* 1.3 75.7 - - - +
21I ILE* 1.3 61.8 + - - +
23I ALA* 3.8 7.4 - - + +
24I GLY* 3.1 19.6 + - - -
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Residues in contact with ILE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLY* 3.2 33.4 - - - +
64E GLY* 3.7 19.5 - - - +
65E LEU* 3.5 15.4 - - + +
68E SER* 3.6 22.0 - - - +
16I VAL* 3.7 23.3 - - + +
17I PHE 2.8 22.4 + - - +
18I VAL* 3.6 14.4 - - + +
19I GLY 3.2 0.2 - - - -
20I THR* 1.3 74.8 - - - +
22I PHE* 1.3 57.9 + - + +
24I GLY 3.1 2.4 + - - -
25I ALA* 2.8 32.4 + - - +
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Residues in contact with PHE 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TRP* 4.0 30.7 - + + -
68E SER* 3.3 31.2 - - - -
18I VAL* 3.3 36.1 + - + +
19I GLY* 3.5 3.8 + - - +
21I ILE* 1.3 79.7 - - + +
23I ALA* 1.3 64.0 + - - +
25I ALA* 2.9 15.3 + - + +
26I PHE* 3.0 31.8 - + + -
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Residues in contact with ALA 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLY 3.1 16.5 + - - +
20I THR* 3.8 8.3 - - + +
22I PHE* 1.3 79.0 - - - +
24I GLY* 1.3 64.0 + - - +
26I PHE* 3.3 14.8 + - - +
27I VAL* 3.4 16.0 + - - +
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Residues in contact with GLY 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 3.4 15.1 - - - +
20I THR 3.1 11.8 + - - -
21I ILE 3.5 3.4 - - - -
23I ALA* 1.3 79.4 - - - +
25I ALA* 1.3 62.0 + - - +
26I PHE 3.2 0.3 + - - -
27I VAL* 3.2 11.6 + - - +
28I PHE* 3.1 22.3 + - - +
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Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 3.4 16.1 - - - +
68E SER* 3.8 28.3 - - - -
69E ALA* 4.2 13.4 - - - +
72E LYS* 5.7 2.9 - - + +
21I ILE 2.8 17.2 + - - +
22I PHE* 2.9 14.5 + - + +
24I GLY* 1.3 73.4 - - - +
26I PHE* 1.3 63.8 + - + +
28I PHE* 3.5 6.3 - - - +
29I GLN* 3.3 20.4 + - - +
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Residues in contact with PHE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS* 4.3 32.8 - - + +
22I PHE* 3.0 28.4 + + + -
23I ALA* 3.6 9.9 - - - +
24I GLY 3.2 0.4 - - - -
25I ALA* 1.3 77.3 - - + +
27I VAL* 1.3 70.0 + - + +
29I GLN* 3.1 24.1 + - - +
30I THR* 3.5 7.6 + - - -
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Residues in contact with VAL 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ALA 3.4 16.4 - - - +
24I GLY* 3.4 11.9 - - - +
26I PHE* 1.3 76.7 - - + +
28I PHE* 1.3 64.1 + - - +
30I THR* 3.3 5.8 + - - -
31I VAL* 3.0 40.3 + - + +
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Residues in contact with PHE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 3.8 21.5 - - + -
65E LEU* 4.1 17.5 - - + -
66E LEU* 3.4 30.5 - - + -
69E ALA* 3.9 19.3 - - + -
24I GLY 3.1 9.2 + - - +
25I ALA 3.5 9.4 - - - +
27I VAL* 1.3 78.0 - - - +
29I GLN* 1.3 64.3 + - - +
31I VAL* 3.0 6.8 + - + -
32I PHE* 2.6 73.4 + + + +
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LYS* 4.6 9.1 + - - +
69E ALA* 4.0 14.9 + - - +
72E LYS* 2.7 53.3 - - - +
73E SER* 3.4 22.2 + - - -
76E GLU* 3.7 7.5 + - - -
25I ALA 3.3 9.1 + - - +
26I PHE* 3.1 14.2 + - - +
28I PHE* 1.3 83.8 - - - +
30I THR* 1.3 60.3 + - - +
32I PHE* 4.4 2.6 - - - +
33I ASP* 3.1 27.5 + - - +
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Residues in contact with THR 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PHE 3.5 12.5 + - - -
27I VAL* 3.3 4.7 + - - -
28I PHE 3.2 0.6 - - - -
29I GLN* 1.3 74.0 - - - +
31I VAL* 1.3 72.6 + - - +
33I ASP* 3.4 3.9 + - - +
34I THR* 3.1 31.8 + - - +
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Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I VAL* 3.0 34.1 + - + +
28I PHE* 3.0 5.9 + - + +
30I THR* 1.3 80.5 - - - +
32I PHE* 1.3 67.1 + - - +
34I THR* 3.3 4.3 + - - -
35I ALA* 3.2 21.4 + - + +
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Residues in contact with PHE 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LYS* 3.6 40.4 - - + -
275D ILE* 4.2 18.6 - - + -
276D ILE* 3.8 28.9 - - + -
28I PHE* 2.6 59.7 + + + +
29I GLN* 4.4 2.5 - - - +
31I VAL* 1.3 76.5 - - - +
33I ASP* 1.3 63.3 + - - +
35I ALA* 3.3 10.3 - - + +
36I ILE* 3.1 47.7 + - + +
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Residues in contact with ASP 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ARG* 3.2 23.8 + - - -
272D LYS* 3.2 33.8 + - - +
29I GLN 3.1 21.1 + - - +
30I THR* 3.7 4.6 - - - +
31I VAL 3.2 0.4 + - - -
32I PHE* 1.3 75.5 - - - +
34I THR* 1.3 69.9 + - - +
36I ILE* 3.0 4.6 + - - +
37I THR* 2.8 31.2 + - - -
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Residues in contact with THR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I THR* 3.1 21.4 + - - +
31I VAL* 3.8 4.0 - - - -
33I ASP* 1.3 80.0 + - - +
35I ALA* 1.3 59.0 + - - +
37I THR* 3.3 7.6 + - + -
38I SER* 2.7 41.8 + - - +
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I VAL* 3.2 12.2 + - + +
32I PHE* 3.3 14.8 - - + +
33I ASP 3.2 0.2 - - - -
34I THR* 1.3 79.3 - - - +
36I ILE* 1.3 65.8 + - + +
38I SER* 3.3 5.2 + - - -
39I TRP* 3.0 24.2 + - - +
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Residues in contact with ILE 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ARG* 4.2 15.5 - - + +
271D LEU* 4.0 23.6 - - + -
272D LYS* 3.9 24.2 - - + -
275D ILE* 3.6 31.9 - - + -
32I PHE* 3.1 37.0 + - + +
33I ASP 3.0 6.4 + - - +
35I ALA* 1.3 74.5 - - + +
37I THR* 1.3 66.6 + - - +
38I SER 3.1 0.2 + - - -
39I TRP* 3.2 6.8 + - + +
40I TYR* 2.8 27.5 + - + +
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Residues in contact with THR 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ARG* 3.3 34.6 + - - +
33I ASP* 2.8 32.9 + - - -
34I THR* 3.6 8.7 - - + -
36I ILE* 1.3 72.5 - - - +
38I SER* 1.3 57.7 + - - +
40I TYR* 3.4 2.1 + - - +
41I GLU* 2.9 53.8 + - + +
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Residues in contact with SER 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I THR* 2.7 31.8 + - - +
35I ALA* 3.5 5.6 - - - -
37I THR* 1.3 74.5 - - - +
39I TRP* 1.3 67.6 + - - +
40I TYR 3.1 1.3 - - - -
41I GLU* 3.1 7.1 + - - +
42I ASN* 2.8 27.6 + - - +
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Residues in contact with TRP 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 3.5 50.3 - + + -
271D LEU* 3.8 21.3 - - + -
35I ALA 3.0 13.0 + - - +
36I ILE* 3.7 7.0 - - + +
38I SER* 1.3 78.7 - - - +
40I TYR* 1.3 93.3 + + + +
42I ASN* 3.6 5.3 + - - +
43I HIS* 2.9 48.0 + + + +
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Residues in contact with TYR 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 3.4 28.0 - + - -
83D GLU 4.3 3.5 + - - -
84D THR* 3.2 31.2 - - + +
264D ASP* 3.0 31.5 + - + -
267D LYS* 3.5 15.7 - - + +
268D ARG* 3.7 38.8 - - + -
271D LEU* 5.0 5.8 - - + -
36I ILE* 2.8 20.7 + - + +
37I THR 3.5 4.7 - - - +
39I TRP* 1.3 92.8 - + + +
41I GLU* 1.3 70.0 + - + +
43I HIS* 3.5 1.0 + - - +
44I ASN* 2.9 34.5 + - - -
48I LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I THR* 2.9 40.6 + - + +
38I SER* 3.1 6.4 + - - +
40I TYR* 1.3 78.3 - - + +
42I ASN* 1.3 66.0 + - - +
44I ASN 3.0 13.3 + - - -
45I LYS* 3.1 11.7 + - - +
48I LEU* 3.7 31.0 - - + +
50I LYS* 3.4 34.0 + - - +
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Residues in contact with ASN 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I SER 2.8 17.3 + - - +
39I TRP* 3.8 5.4 - - - +
41I GLU* 1.3 77.0 - - - +
43I HIS* 1.3 66.3 + - - +
45I LYS* 2.8 49.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 43 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 3.9 23.5 - + + +
83D GLU* 2.9 38.7 + - - +
39I TRP* 2.9 47.8 + + + +
40I TYR 3.8 4.5 - - - +
42I ASN* 1.3 78.8 - - - +
44I ASN* 1.3 60.9 + - - +
45I LYS 3.6 1.4 + - - +
47I LYS* 5.4 0.5 + - - +
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Residues in contact with ASN 44 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE 2.9 20.2 + - - +
83D GLU* 3.4 5.4 - - - +
84D THR* 2.8 50.6 + - - +
40I TYR* 2.9 28.6 + - - +
41I GLU 3.0 5.7 + - - +
43I HIS* 1.3 80.0 - - - +
45I LYS* 1.3 67.8 + - - +
46I GLY 3.4 0.2 + - - -
47I LYS* 2.9 41.9 + - - +
48I LEU* 3.5 16.8 + - + -
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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