Contacts of the helix formed by residues 15 - 37 (chain A) in PDB entry 3QJQ
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 TYR 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 2.7 36.5 - - - +
12A TYR* 2.9 5.1 + - - +
14A ALA* 1.3 92.1 - - + +
16A PRO* 1.4 57.7 - - - +
17A GLU* 3.0 19.3 - - + -
18A LYS* 3.0 57.4 + - + +
19A LYS 3.7 1.6 + - - -
95A ARG* 3.9 37.0 - - - -
98A ASN* 5.4 0.4 - - - -
502A ALA 5.3 0.2 - - - -
503A GLU* 4.0 28.5 - - + +
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Residues in contact with PRO 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR 2.8 19.1 - - - +
13A GLU* 4.4 6.1 - - - -
14A ALA 3.4 10.8 - - - +
15A TYR* 1.4 84.8 - - - +
17A GLU* 1.3 56.7 + - - +
18A LYS 3.0 3.8 - - - -
19A LYS* 3.6 15.1 - - + +
20A ALA* 3.1 30.3 + - - +
100A ARG* 3.5 24.0 - - - +
103A MET* 3.7 17.9 - - + +
107A TRP* 4.9 4.0 + - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.4 8.8 - - - +
15A TYR* 3.4 27.5 - - + -
16A PRO* 1.3 78.8 - - - +
18A LYS* 1.3 60.7 + - - +
21A THR* 2.8 31.5 + - - -
91A TYR* 3.7 16.4 - - + -
94A ALA* 4.5 3.4 - - + +
95A ARG* 3.3 19.9 + - - +
99A MET 3.1 24.3 - - - +
100A ARG* 3.5 25.9 + - - +
101A PRO* 4.0 20.3 - - + +
103A MET* 3.9 15.3 - - - -
106A MET* 4.0 5.2 - - - +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.7 23.2 - - + +
12A TYR* 5.5 0.4 - - + -
15A TYR* 3.0 54.9 + - + +
17A GLU* 1.3 77.3 - - - +
19A LYS* 1.3 55.2 + - - +
21A THR* 3.1 4.0 + - - -
22A LEU* 2.8 35.3 + - - +
91A TYR* 3.3 30.1 - - + +
95A ARG* 5.2 2.0 - - - +
407A ASN* 3.3 20.1 + - - +
408A LEU* 3.6 25.2 - - + +
502A ALA 2.6 31.7 + - - -
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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 TYR* 3.7 40.9 - - + -
15A TYR 3.7 1.6 + - - -
16A PRO* 3.4 16.8 + - + +
18A LYS* 1.3 77.7 - - - +
20A ALA* 1.3 57.6 + - - +
22A LEU* 2.8 25.2 + - - +
23A TYR* 3.2 35.1 + - + -
107A TRP* 3.7 29.5 - - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO 3.1 12.3 + - - +
19A LYS* 1.3 80.1 - - - +
21A THR* 1.3 61.6 + - - +
23A TYR* 3.4 8.5 + - - +
24A PHE* 3.1 24.8 + - + -
103A MET* 3.8 8.3 - - + -
106A MET* 3.8 21.5 - - + +
107A TRP* 3.6 39.0 - - + -
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Residues in contact with THR 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 GLU 2.8 24.2 + - - -
18A LYS* 3.1 4.4 + - - -
19A LYS 3.1 1.2 - - - -
20A ALA* 1.3 78.3 - - - +
22A LEU* 1.3 60.7 - - - +
23A TYR 3.3 0.7 + - - -
24A PHE* 3.5 9.9 + - - +
25A LEU* 3.4 17.1 + - + +
87A ALA* 4.3 18.4 + - + +
90A VAL* 5.5 0.2 - - - +
91A TYR* 3.3 41.7 + - + +
106A MET* 3.4 15.8 - - - +
404A LEU* 5.5 2.7 - - + -
408A LEU* 4.2 16.8 - - + -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 4.6 15.0 - - + +
18A LYS 2.8 12.7 + - - +
19A LYS* 2.8 12.3 + - - +
21A THR* 1.3 77.8 - - - +
23A TYR* 1.3 71.8 + - + +
25A LEU* 3.0 7.4 + - + +
26A VAL* 2.8 38.3 + - + +
405A LEU* 3.6 32.1 - - + -
408A LEU* 4.1 22.2 - - + +
409A THR* 4.2 20.9 - - + -
492A LEU* 4.8 8.7 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 5.9 2.0 - - - -
19A LYS* 3.2 33.9 + - + +
20A ALA 3.9 6.5 - - - +
21A THR 3.2 0.6 - - - -
22A LEU* 1.3 89.3 - - + +
24A PHE* 1.3 65.3 + - - +
25A LEU 3.1 1.3 - - - -
26A VAL* 4.2 8.2 - - + +
27A LEU* 3.0 28.6 + - - +
107A TRP* 3.9 25.4 - + + -
110A TRP* 3.5 36.5 + + + +
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.1 27.4 - - + -
21A THR* 3.5 9.8 + - - +
22A LEU 3.4 0.2 - - - -
23A TYR* 1.3 77.8 - - - +
25A LEU* 1.3 57.4 + - - +
27A LEU* 4.8 1.3 - - - -
28A GLY* 3.1 18.9 + - - -
83A LEU* 3.4 46.4 - - + +
86A GLN* 3.7 43.3 - - + -
87A ALA* 4.3 9.0 - - + -
106A MET* 4.0 19.3 - - + -
109A SER* 3.8 11.4 - - - -
110A TRP* 3.4 50.2 - + + +
113A ALA* 5.1 1.1 - - + -
159A SER* 5.3 1.3 - - - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.4 8.8 + - + +
22A LEU* 3.0 10.6 + - + +
24A PHE* 1.3 76.9 - - - +
26A VAL* 1.3 55.9 + - + +
28A GLY* 3.2 2.5 + - - -
29A PHE* 2.7 67.4 + - + -
80A PHE* 6.3 0.2 - - + -
84A PHE* 3.9 29.8 - - + -
87A ALA* 4.2 14.6 - - + -
401A LEU* 5.5 3.6 - - + -
404A LEU* 3.8 27.4 - - + -
405A LEU* 4.0 20.0 - - + -
408A LEU* 4.0 16.6 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.8 35.8 + - + +
23A TYR* 4.2 9.0 - - + +
25A LEU* 1.3 73.0 - - + +
27A LEU* 1.3 61.9 + - + +
29A PHE* 2.9 8.6 + - - +
30A LEU* 2.8 40.6 + - + +
405A LEU* 6.1 0.9 - - + -
488A LEU* 6.0 1.1 - - + -
492A LEU* 4.2 26.5 - - + -
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Residues in contact with LEU 27 (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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23A TYR 3.0 18.1 + - - +
24A PHE 4.5 0.4 - - - +
26A VAL* 1.3 76.2 - - + +
28A GLY* 1.3 70.1 + - - +
29A PHE 3.1 0.9 + - - -
30A LEU* 3.1 24.5 + - + +
31A ALA* 3.2 13.2 + - - +
83A LEU* 3.5 31.2 - - + -
110A TRP* 4.1 20.9 - - + +
113A ALA* 4.9 1.8 - - + -
114A PHE* 3.8 43.3 - - + +
117A LEU* 4.6 20.9 - - + -
152A PHE* 5.3 0.7 - - + -
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Residues in contact with GLY 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 PHE 3.1 17.4 + - - -
25A LEU* 3.2 5.8 + - - -
27A LEU* 1.3 81.1 - - - +
29A PHE* 1.3 59.2 + - - +
31A ALA* 3.5 4.7 - - - +
32A LEU 3.2 15.2 + - - -
80A PHE* 3.6 24.9 - - - +
83A LEU* 3.6 20.7 - - - +
84A PHE* 5.3 0.7 - - - -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.7 55.4 + - + +
26A VAL* 2.9 6.8 + - - +
28A GLY* 1.3 69.6 - - - -
30A LEU* 1.3 65.9 + - - +
32A LEU* 3.4 24.2 + - + +
33A ILE* 3.1 29.0 + - - +
80A PHE* 3.7 25.4 - + - -
84A PHE* 5.1 0.4 - + - -
397A ALA* 3.8 17.5 - - + -
398A MET* 4.8 3.1 - - + -
401A LEU* 3.1 35.9 - - + -
405A LEU* 6.2 1.3 - - + -
484A PHE* 4.1 14.6 - + - -
488A LEU* 4.0 28.9 - - + -
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Residues in contact with LEU 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 VAL* 2.8 29.9 + - + +
27A LEU* 3.6 17.9 - - + +
29A PHE* 1.3 69.3 - - - +
31A ALA* 1.3 68.6 + - - +
33A ILE* 3.0 21.2 + - + +
34A VAL* 3.0 23.8 + - + +
488A LEU* 5.8 2.2 - - + -
489A PHE* 4.8 20.6 - - + -
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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 LEU 3.2 6.0 + - - +
28A GLY 3.5 9.9 - - - +
30A LEU* 1.3 79.0 - - - +
32A LEU* 1.3 63.1 + - - +
34A VAL* 3.5 4.6 + - - -
35A GLY* 3.0 22.0 + - - -
75A LEU* 3.7 22.2 - - + +
76A ASN* 4.3 1.3 - - - -
79A VAL* 3.7 34.5 - - + -
80A PHE* 4.1 5.4 - - - +
117A LEU* 5.3 5.4 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.2 10.8 + - - +
29A PHE* 3.7 33.2 - - + +
30A LEU 3.1 1.0 - - - -
31A ALA* 1.3 77.6 - - - +
33A ILE* 1.3 59.6 + - - +
36A SER* 2.5 44.6 + - - +
76A ASN* 3.1 11.5 + - - +
80A PHE* 4.0 29.8 - - + +
394A THR* 4.4 13.2 - - + -
398A MET* 4.7 8.3 - - + -
428A TRP* 5.4 2.2 - - + -
481A LEU* 6.0 1.3 - - + -
484A PHE* 4.4 17.5 - - + -
800A HEM 3.6 31.6 - - + -
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Residues in contact with ILE 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 PHE 3.1 9.6 + - - +
30A LEU* 3.0 14.6 + - + +
32A LEU* 1.3 75.4 - - - +
34A VAL* 1.3 72.0 + - + +
35A GLY 2.9 1.2 + - - -
36A SER* 3.0 15.3 + - - -
37A LEU* 3.1 20.4 + - + +
481A LEU* 4.6 7.4 - - + +
484A PHE* 4.1 15.3 - - + -
485A ILE* 3.8 46.0 - - + -
488A LEU* 3.7 27.4 - - + -
489A PHE* 4.7 9.9 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.0 23.9 + - + +
31A ALA* 4.0 3.6 - - - +
33A ILE* 1.3 79.3 - - + +
35A GLY* 1.3 60.3 + - - +
37A LEU* 3.5 23.6 - - + +
38A PHE* 3.3 22.6 - - + -
61A PHE* 5.9 7.6 - - + -
71A LEU* 6.1 2.5 - - + -
75A LEU* 4.1 15.3 - - + -
125A LEU* 6.0 6.3 - - + -
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Residues in contact with GLY 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 3.0 11.3 + - - -
34A VAL* 1.3 76.7 - - - +
36A SER* 1.3 61.5 + - - +
38A PHE* 3.4 15.2 + - - -
71A LEU 4.2 5.2 - - - -
72A HIS* 2.9 20.3 + - - -
75A LEU* 3.7 16.5 - - - +
76A ASN* 3.5 20.4 - - - -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.5 36.2 + - - +
33A ILE 3.0 0.6 + - - -
35A GLY* 1.3 71.3 - - - +
37A LEU* 1.3 56.3 + - - +
38A PHE 3.0 3.1 - - - -
39A GLY* 2.7 21.7 + - - -
40A PRO* 3.1 12.8 - - - +
72A HIS* 4.2 5.4 - - - -
76A ASN* 3.3 14.3 + - - -
428A TRP* 4.3 5.3 - - - -
481A LEU* 3.6 26.8 - - - +
800A HEM 3.8 14.6 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.1 23.0 + - + +
34A VAL* 3.5 29.8 - - + +
35A GLY 3.2 0.2 - - - -
36A SER* 1.3 76.7 - - - +
38A PHE* 1.3 64.0 + - + +
39A GLY 3.5 0.2 + - - -
40A PRO* 3.6 8.8 - - - +
41A PHE* 3.2 28.4 - - + -
55A LEU* 5.7 0.4 - - + -
59A LEU* 4.3 24.9 - - + -
478A LEU* 6.5 0.7 - - + -
481A LEU* 4.1 17.9 - - + +
482A LEU* 5.6 5.8 - - + -
485A ILE* 5.4 6.1 - - + -
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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