Contacts of the helix formed by residues 17 - 44 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453L MET 6.1 0.4 - - - -
455L ARG* 3.4 54.3 - - + -
456L TRP* 3.6 29.2 - - - +
11T PHE* 5.6 0.8 - - - -
14T ASN* 4.8 13.9 - - + -
15T ALA* 3.3 17.2 + - + -
16T VAL* 1.3 73.8 - - - +
18T VAL* 1.3 66.5 + - - +
20T THR* 2.9 27.5 + - - +
21T ILE* 3.0 12.0 + - - +
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Residues in contact with VAL 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454L MET* 5.0 16.4 - - + -
455L ARG 3.7 18.3 + - - +
456L TRP* 3.8 16.2 + - + +
16T VAL 3.8 2.1 + - - +
17T PHE* 1.3 71.9 - - - +
19T GLY* 1.3 56.8 + - - +
21T ILE* 3.5 9.7 - - + +
22T PHE* 3.0 56.9 + - + -
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Residues in contact with GLY 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456L TRP* 2.7 45.1 + - - +
18T VAL* 1.3 70.4 - - - +
20T THR* 1.3 64.2 + - - +
22T PHE* 3.5 5.5 + - - +
23T ALA* 3.0 24.9 + - - +
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Residues in contact with THR 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456L TRP 4.5 0.6 + - - -
65P LEU* 5.0 0.3 - - - +
11T PHE* 4.4 14.6 - - + -
16T VAL* 3.9 20.6 - - + -
17T PHE* 2.9 21.3 + - - +
19T GLY* 1.3 75.4 - - - +
21T ILE* 1.3 63.6 + - - +
23T ALA* 3.3 7.8 + - + +
24T GLY* 3.0 19.8 + - - -
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Residues in contact with ILE 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P GLY* 3.4 27.4 - - - +
64P GLY* 3.6 10.8 - - - -
65P LEU* 3.3 37.4 - - + +
68P SER* 3.8 11.7 - - - +
16T VAL* 3.6 34.1 - - + +
17T PHE 3.0 19.1 + - - +
18T VAL* 3.5 11.9 - - + +
20T THR* 1.3 75.1 - - - +
22T PHE* 1.3 65.9 + - + +
24T GLY 3.0 11.8 + - - -
25T ALA* 3.0 10.6 + - - +
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Residues in contact with PHE 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456L TRP* 4.0 29.2 - + - -
68P SER* 3.7 28.3 - - - -
18T VAL* 3.0 37.3 + - + +
19T GLY* 3.8 4.3 - - - +
21T ILE* 1.3 79.1 - - + +
23T ALA* 1.3 63.4 + - - +
25T ALA* 3.0 21.0 + - + +
26T PHE* 3.3 16.3 + - + -
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Residues in contact with ALA 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T GLY 3.0 18.4 + - - +
20T THR* 3.4 9.6 - - + +
21T ILE 3.1 0.2 - - - -
22T PHE* 1.3 76.3 - - - +
24T GLY* 1.3 61.8 + - - +
26T PHE* 3.3 17.0 + - - +
27T VAL* 3.4 16.1 + - - +
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Residues in contact with GLY 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P LEU* 3.3 15.9 - - - +
20T THR 3.0 10.0 + - - -
21T ILE 3.0 7.3 + - - -
23T ALA* 1.3 74.3 - - - +
25T ALA* 1.3 55.2 - - - +
27T VAL* 3.2 8.2 + - - +
28T PHE* 2.7 36.7 + - - +
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Residues in contact with ALA 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P LEU* 3.3 10.2 - - - +
68P SER* 3.8 27.6 - - - -
69P ALA* 4.0 16.9 - - - +
72P LYS* 5.7 5.2 - - + -
21T ILE 3.0 11.2 + - - +
22T PHE* 3.0 15.2 + - + +
24T GLY* 1.3 77.4 - - - +
26T PHE* 1.3 57.5 + - + +
28T PHE* 3.9 3.8 - - - +
29T GLN* 3.0 31.0 + - - +
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Residues in contact with PHE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P LYS* 3.6 37.5 - - + +
22T PHE* 3.3 14.1 + - + -
23T ALA* 3.3 10.9 + - - +
24T GLY 3.2 0.4 - - - -
25T ALA* 1.3 77.8 - - + +
27T VAL* 1.3 67.2 + - + +
29T GLN* 3.4 9.5 + - - +
30T THR* 3.3 26.4 + - - -
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Residues in contact with VAL 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T ALA 3.4 11.6 + - - +
24T GLY* 3.2 10.4 + - - +
26T PHE* 1.3 75.8 - - + +
28T PHE* 1.3 71.0 + - - +
30T THR* 3.3 3.4 + - - -
31T VAL* 3.0 37.6 + - + +
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Residues in contact with PHE 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O ILE* 4.0 18.4 - - + -
65P LEU* 4.1 15.5 - - + -
66P LEU* 3.9 25.1 - - + -
69P ALA* 4.2 15.9 - - + -
24T GLY 2.7 21.0 + - - +
25T ALA 3.9 2.9 - - - +
27T VAL* 1.3 76.3 - - - +
29T GLN* 1.3 71.6 + - - +
30T THR 3.0 1.0 + - - -
31T VAL* 4.6 4.0 - - + -
32T PHE* 2.9 73.7 + + + +
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Residues in contact with GLN 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272O LYS* 4.9 5.1 + - - +
69P ALA* 3.8 8.2 - - + +
72P LYS* 2.6 55.1 + - - +
73P SER* 3.2 24.3 + - - +
76P GLU* 3.6 7.2 + - - +
25T ALA 3.0 16.0 + - - +
26T PHE* 3.5 9.1 + - - +
28T PHE* 1.3 88.9 - - + +
30T THR* 1.3 64.4 + - - +
32T PHE* 4.3 2.2 - - - +
33T ASP* 3.5 21.7 + - - +
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Residues in contact with THR 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T PHE* 3.3 11.9 + - - -
27T VAL* 3.9 7.2 - - - -
28T PHE 3.2 0.8 - - - -
29T GLN* 1.3 79.5 + - - +
31T VAL* 1.3 66.1 + - + +
33T ASP* 3.5 5.1 + - - +
34T THR* 3.0 30.5 + - - +
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Residues in contact with VAL 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T VAL* 3.0 30.7 + - + +
28T PHE* 3.0 5.0 + - + +
30T THR* 1.3 75.6 - - + +
32T PHE* 1.3 70.3 + - - +
33T ASP 3.0 0.7 + - - -
34T THR* 3.0 9.2 + - - -
35T ALA* 3.0 23.6 + - + +
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Residues in contact with PHE 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272O LYS* 3.8 39.5 - - + -
275O ILE* 4.1 24.7 - - + -
276O ILE* 3.5 31.6 - - + -
28T PHE* 2.9 58.3 + + + +
29T GLN* 4.3 2.5 - - - +
31T VAL* 1.3 76.2 - - - +
33T ASP* 1.3 63.1 + - - +
35T ALA* 3.3 8.2 + - + +
36T ILE* 3.0 49.1 + - + +
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Residues in contact with ASP 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268O ARG* 3.2 22.0 + - - -
272O LYS* 2.8 40.2 + - - +
29T GLN 3.5 15.1 + - - +
30T THR* 3.7 5.6 - - - +
31T VAL 3.1 1.0 - - - -
32T PHE* 1.3 76.4 - - - +
34T THR* 1.3 62.2 + - - +
35T ALA 3.1 0.3 + - - -
36T ILE* 3.1 1.9 + - - +
37T THR* 2.8 41.4 + - - -
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Residues in contact with THR 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T THR* 3.0 19.1 + - - +
31T VAL* 3.0 8.4 + - - -
33T ASP* 1.3 79.1 + - - +
35T ALA* 1.3 57.8 + - - +
37T THR* 3.9 6.1 - - - -
38T SER* 2.9 43.0 + - - +
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Residues in contact with ALA 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T VAL* 3.0 16.3 + - + +
32T PHE* 3.4 15.0 - - + +
34T THR* 1.3 78.3 - - - +
36T ILE* 1.3 61.0 + - + +
38T SER* 3.4 5.1 - - - -
39T TRP* 2.9 29.3 + - - +
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Residues in contact with ILE 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268O ARG* 4.3 11.4 - - + +
271O LEU* 3.4 31.2 - - + -
272O LYS* 3.9 21.5 - - + -
275O ILE* 3.6 30.7 - - + -
32T PHE* 3.0 41.2 + - + +
33T ASP 3.8 2.2 - - - +
35T ALA* 1.3 73.1 - - + +
37T THR* 1.3 56.7 + - - +
39T TRP* 3.7 7.4 - - + +
40T TYR* 2.8 37.6 + - - +
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Residues in contact with THR 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268O ARG* 3.2 36.3 + - - +
33T ASP* 2.8 34.7 + - - -
34T THR* 3.9 6.5 - - - -
36T ILE* 1.3 71.2 - - - +
38T SER* 1.3 59.3 + - - +
40T TYR* 3.2 2.1 + - - +
41T GLU* 2.8 49.1 + - + +
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Residues in contact with SER 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T THR* 2.9 32.1 + - - +
35T ALA* 3.2 6.0 + - - -
37T THR* 1.3 79.8 - - - +
39T TRP* 1.3 62.3 + - - +
41T GLU* 4.1 4.8 - - - +
42T ASN* 3.2 26.9 + - - +
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Residues in contact with TRP 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O PHE* 3.4 46.0 - + + -
271O LEU* 3.9 20.4 - - + -
35T ALA 2.9 16.2 + - - +
36T ILE* 3.8 6.7 - - + +
38T SER* 1.3 76.5 - - - +
40T TYR* 1.3 71.3 + + - +
42T ASN* 3.8 6.5 - - - +
43T HIS* 3.0 54.1 + + + +
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Residues in contact with TYR 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O PRO 4.7 0.4 - - - -
82O PHE* 3.3 28.7 - + - -
83O GLU 4.1 4.9 + - - -
84O THR* 3.2 31.5 - - + +
264O ASP* 3.1 23.8 + - + -
267O LYS* 3.3 18.0 - - + +
268O ARG* 3.8 43.7 - - + -
271O LEU* 4.7 6.7 - - + -
36T ILE* 2.8 21.1 + - + +
37T THR* 3.5 3.8 - - - +
39T TRP* 1.3 94.2 - + + +
41T GLU* 1.3 70.5 + - + +
43T HIS* 3.6 0.7 + - - +
44T ASN* 3.0 31.1 + - - +
48T LEU* 6.2 0.9 - - + -
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Residues in contact with GLU 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268O ARG* 6.3 0.2 - - - -
37T THR* 2.8 35.2 + - + +
38T SER* 4.1 5.0 - - - +
40T TYR* 1.3 78.2 - - + +
42T ASN* 1.3 68.1 + - - +
44T ASN 3.2 10.9 + - - -
45T LYS* 3.4 11.5 + - - +
48T LEU* 3.7 28.3 - - + +
50T LYS* 3.1 37.2 + - - +
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Residues in contact with ASN 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T SER 3.2 18.1 + - - +
39T TRP* 3.8 7.3 - - - +
41T GLU* 1.3 79.0 - - - +
43T HIS* 1.3 65.8 + - - +
44T ASN 2.8 2.3 + - - -
45T LYS* 2.9 46.3 + - - +
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Residues in contact with HIS 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O PHE* 3.8 17.8 - + + +
83O GLU* 2.8 37.5 + - - +
39T TRP* 3.0 49.6 + + + +
40T TYR 3.9 4.0 - - - +
41T GLU 3.4 0.2 - - - -
42T ASN* 1.3 77.7 - - - +
44T ASN* 1.3 66.4 + - - +
45T LYS 3.5 1.3 + - - -
47T LYS* 5.7 0.2 - - - +
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Residues in contact with ASN 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O PHE 2.8 22.8 + - - -
83O GLU* 3.3 4.5 - - - +
84O THR* 2.8 38.7 + - - +
40T TYR* 3.0 25.9 + - - +
41T GLU 3.2 6.2 + - - -
42T ASN 2.8 1.0 + - - -
43T HIS* 1.3 84.7 - - - +
45T LYS* 1.3 64.8 + - - +
46T GLY 3.4 0.2 + - - -
47T LYS* 3.0 38.5 + - + +
48T LEU* 3.3 28.1 - - + +
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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