Contacts of the helix formed by residues 28 - 60 (chain A) in PDB entry 2KS9
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 PRO 28 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN 4.7 0.4 - - - +
27A GLN* 1.3 86.4 - - - +
29A ALA* 1.3 63.9 + - - +
30A TRP* 3.2 24.7 - - + +
31A GLN* 2.8 43.9 + - + +
32A ILE* 2.9 18.4 - - - +
285A GLN* 5.1 1.1 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 5.0 22.1 + - + +
27A GLN 3.6 2.2 + - - -
28A PRO* 1.3 69.3 - - - +
30A TRP* 1.3 62.1 + - - +
32A ILE* 2.8 37.4 - - - +
33A VAL* 3.2 7.7 + - + +
96A ASN* 5.4 4.7 - - - +
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 3.2 30.1 - - + +
29A ALA* 1.3 78.9 - - - +
31A GLN* 1.3 84.5 + - + +
33A VAL* 2.7 21.9 - - + +
34A LEU* 2.7 74.6 + - + -
35A TRP* 4.8 0.7 - + - -
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 2.7 48.7 + - - +
28A PRO* 2.8 33.5 + - + +
30A TRP* 1.3 112.2 - - + +
32A ILE* 1.3 61.2 + - - +
34A LEU* 4.0 0.4 - - - -
35A TRP* 2.7 43.3 + - + -
285A GLN* 3.0 26.2 + - - +
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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
----------------------------------------------------------
23A ASN* 5.0 5.8 - - + +
24A GLN* 5.1 2.9 - - - -
27A GLN* 3.1 33.0 - - + +
28A PRO 2.9 30.7 - - - +
29A ALA* 2.8 14.5 + - - +
31A GLN* 1.3 77.4 - - - +
33A VAL* 1.3 70.1 + - + +
35A TRP* 3.2 3.5 + - - -
36A ALA* 3.0 20.3 + - - +
92A TYR* 4.9 5.8 - - - +
93A ALA* 2.7 32.8 - - - +
94A VAL* 4.0 7.0 - - - +
96A ASN* 2.7 33.2 - - + +
177A ARG* 5.3 2.2 - - - +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 3.9 9.9 - - + +
30A TRP* 2.7 35.4 + - + +
32A ILE* 1.3 87.7 - - + +
34A LEU* 1.3 54.1 + - - +
36A ALA* 3.4 8.1 - - + +
37A ALA* 2.7 36.3 + - + +
94A VAL* 4.6 8.3 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 2.7 50.6 + - + -
31A GLN 3.3 7.4 - - - +
32A ILE 3.1 0.2 - - - -
33A VAL* 1.3 79.4 - - - +
35A TRP* 1.3 87.4 + - + +
37A ALA* 3.1 12.0 + - + +
38A ALA* 3.0 22.4 + - + +
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Residues in contact with TRP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.5 5.6 - - - -
31A GLN* 2.7 57.2 + - + +
32A ILE 3.2 3.3 + - - +
34A LEU* 1.3 100.9 - - + +
36A ALA* 1.3 66.1 - - - +
38A ALA* 3.2 6.6 + - + +
39A TYR 3.1 17.5 + - - -
93A ALA* 4.7 0.9 - - + -
177A ARG* 4.1 16.6 - - - +
285A GLN* 4.7 12.8 - - - -
288A LEU* 2.8 38.6 - - + +
289A ALA* 5.0 8.3 - - + +
292A TRP* 3.2 53.9 - + + +
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Residues in contact with ALA 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 10.8 + - - +
33A VAL 3.4 7.2 - - - +
35A TRP* 1.3 77.0 - - - +
37A ALA* 1.3 61.2 + - - +
39A TYR* 3.2 1.5 + - - -
40A THR 2.9 8.7 + - - -
90A PHE* 2.8 40.9 - - + -
93A ALA* 3.8 11.1 - - + +
94A VAL* 3.0 38.6 - - + -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 2.7 17.4 + - - +
34A LEU* 3.1 17.5 + - + +
36A ALA* 1.3 73.9 - - - +
38A ALA* 1.3 60.4 + - - +
40A THR* 2.7 31.4 - - + +
41A VAL* 3.1 11.3 + - + +
90A PHE* 4.9 0.4 - - - -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.0 13.5 + - + +
35A TRP* 3.2 15.0 + - + +
37A ALA* 1.3 74.9 - - - +
39A TYR* 1.3 54.6 + - - +
41A VAL* 2.7 30.6 - - - +
42A ILE* 2.7 26.7 - - + +
292A TRP* 4.6 7.6 - - + -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP 3.1 5.3 + - - -
36A ALA 3.7 7.0 - - - +
38A ALA* 1.3 73.8 - - - +
40A THR* 1.3 67.1 + - - +
42A ILE* 3.1 27.9 + - + +
43A VAL* 2.9 27.7 + - - +
81A MET* 4.6 0.7 - - + +
85A ASN* 3.1 10.2 + - - -
86A THR* 2.8 46.0 - - - +
89A ASN* 2.9 34.7 + - + -
90A PHE* 3.7 11.9 - - + -
292A TRP* 2.9 31.0 - + + -
295A MET* 2.8 47.9 - - + +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 2.9 11.9 + - - -
37A ALA* 2.7 33.7 - - + +
39A TYR* 1.3 75.7 - - - +
41A VAL* 1.3 76.7 + - + +
43A VAL* 3.2 21.5 + - - +
44A VAL* 3.5 11.7 + - - +
90A PHE* 4.0 17.8 - - + -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 3.5 11.4 - - + +
38A ALA* 2.7 31.6 - - - +
40A THR* 1.3 89.0 - - + +
42A ILE* 1.3 67.9 + - + +
44A VAL* 3.1 18.6 + - - +
45A THR* 3.2 12.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 2.7 30.3 + - + +
39A TYR* 3.3 38.4 - - + +
41A VAL* 1.3 87.4 - - + +
43A VAL* 1.3 59.4 + - - +
45A THR* 2.9 12.8 - - + +
46A SER* 2.7 48.3 + - - +
82A ALA* 6.3 0.2 - - - -
86A THR* 4.8 4.3 - - - +
292A TRP* 4.9 4.5 - - + +
295A MET* 4.7 6.5 - - + +
296A SER* 4.8 16.4 - - - +
298A THR* 4.0 12.3 - - + -
299A MET* 5.2 2.7 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.9 24.7 + - + +
40A THR* 3.2 11.2 + - - +
42A ILE* 1.3 76.8 - - - +
44A VAL* 1.3 63.7 + - + +
46A SER* 4.8 2.7 - - - -
47A VAL* 2.8 46.7 + - + +
82A ALA* 4.1 9.4 - - - +
86A THR* 3.1 32.3 - - + +
87A VAL* 5.4 7.2 - - + -
90A PHE* 5.7 3.1 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.8 13.9 - - - +
41A VAL* 3.1 9.7 + - - +
43A VAL* 1.3 80.7 - - + +
45A THR* 1.3 64.8 + - - +
47A VAL* 3.9 1.5 - - - +
48A VAL* 3.0 42.2 + - + +
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 3.2 5.0 + - - +
42A ILE* 2.9 27.1 - - + +
44A VAL* 1.3 81.4 - - - +
46A SER* 1.3 74.7 + - - +
48A VAL* 3.9 2.8 - - - +
49A GLY* 2.9 24.1 + - - -
299A MET* 2.8 60.0 - - + +
302A PRO* 5.7 0.2 - - - +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 2.7 30.5 + - - +
45A THR* 1.3 75.3 - - - +
47A VAL* 1.3 62.4 + - - +
49A GLY* 5.4 0.2 - - - -
50A ASN* 2.6 34.1 + - - +
82A ALA* 3.6 23.0 - - - +
298A THR* 2.8 38.8 - - - +
299A MET* 3.9 6.8 + - - +
302A PRO* 6.2 0.4 - - - -
----------------------------------------------------------
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 2.8 35.5 + - + +
44A VAL* 3.9 2.7 - - - +
46A SER* 1.3 76.9 - - - +
48A VAL* 1.3 68.1 + - + +
50A ASN* 4.3 1.4 - - - +
51A VAL* 3.0 29.5 + - + +
79A ALA* 6.0 1.8 - - - +
82A ALA* 3.3 25.8 - - + +
83A ALA* 4.9 2.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.0 30.4 + - + +
45A THR* 4.0 2.7 - - - +
47A VAL* 1.3 79.3 - - + +
49A GLY* 1.3 61.6 + - - +
51A VAL* 2.7 27.5 - - + +
52A VAL* 2.7 26.0 - - + +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR 2.9 16.1 + - - -
48A VAL* 1.3 79.4 - - - +
50A ASN* 1.3 59.7 + - - +
52A VAL* 3.3 8.9 + - - +
53A VAL* 3.1 25.6 + - - +
302A PRO* 3.4 24.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 2.6 26.3 + - - +
47A VAL* 4.3 1.3 - - - +
49A GLY* 1.3 73.3 - - - +
51A VAL* 1.3 66.4 + - - +
53A VAL* 3.3 5.0 + - - +
54A MET* 3.0 24.1 + - - +
75A ALA* 3.8 22.1 - - - +
78A GLU* 3.2 28.7 - - + +
79A ALA* 4.5 11.0 - - + +
298A THR* 3.0 18.7 + - - +
301A ASN* 3.4 27.5 + - - +
302A PRO* 3.7 6.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.0 23.3 + - + +
48A VAL* 2.7 32.1 - - + +
50A ASN* 1.3 76.0 - - - +
52A VAL* 1.3 59.0 + - + +
54A MET* 2.8 25.8 - - + +
55A TRP* 2.6 48.5 + - + +
79A ALA* 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.7 37.2 + - + +
49A GLY* 3.4 9.4 - - - +
51A VAL* 1.3 87.2 - - + +
53A VAL* 1.3 58.0 - - - +
55A TRP* 3.8 5.5 - - + +
56A ILE* 2.7 32.2 + - + +
316A PHE* 3.1 33.0 - - + +
319A ALA* 6.1 2.9 - - + -
----------------------------------------------------------
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.1 15.6 + - - +
50A ASN* 3.7 6.7 - - - +
51A VAL 3.2 0.4 - - - -
52A VAL* 1.3 76.5 - - + +
54A MET* 1.3 62.8 + - - +
56A ILE* 2.8 26.3 - - - +
57A ILE* 3.1 18.1 + - + +
71A LEU* 5.1 2.9 - - + +
75A ALA* 4.3 14.8 - - + -
301A ASN* 5.0 1.1 - - - +
302A PRO* 4.1 11.9 - - + -
305A TYR* 3.7 46.9 - - + +
312A PHE* 4.5 12.3 - - + -
316A PHE* 3.9 9.2 - - + -
----------------------------------------------------------
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN 3.0 8.3 + - - +
51A VAL* 2.8 47.6 - - + +
53A VAL* 1.3 80.5 - - - +
55A TRP* 1.3 73.7 + - + +
57A ILE* 4.4 4.0 - - - -
58A LEU* 2.7 51.0 + - + +
72A VAL* 5.2 6.1 - - + +
75A ALA* 4.6 11.0 - - + +
76A PHE* 6.0 0.7 - - - +
79A ALA* 5.8 8.5 - - - -
----------------------------------------------------------
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Residues in contact with TRP 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 2.6 33.3 + - + +
52A VAL* 3.8 5.6 - - + +
54A MET* 1.3 84.6 - - + +
56A ILE* 1.3 54.4 + - - +
58A LEU* 3.7 4.1 - - + +
59A ALA* 2.7 53.5 + - + +
319A ALA* 4.6 17.6 - - + +
343A GLN* 6.0 1.6 - - - -
----------------------------------------------------------
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.7 21.6 + - + +
53A VAL* 2.8 26.2 - - - +
55A TRP* 1.3 76.6 - - - +
57A ILE* 1.3 69.3 + - + +
59A ALA* 3.0 2.5 + - - -
60A HIS* 2.6 56.0 + - + +
63A MET* 4.5 2.7 - - - -
312A PHE* 3.6 6.3 - - + +
315A GLY 3.3 4.3 - - - -
316A PHE* 2.9 79.9 - - + +
319A ALA* 5.1 3.6 - - + -
341A TYR* 3.6 9.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.3 19.5 - - + +
54A MET 3.7 4.3 - - - +
56A ILE* 1.3 82.0 - - + +
58A LEU* 1.3 65.6 + - + +
60A HIS 2.8 7.1 - - - +
63A MET* 3.5 28.5 - - + +
64A ARG* 2.7 34.0 + - - +
68A ASN* 3.3 22.4 - - + +
71A LEU* 4.9 3.1 - - + -
72A VAL* 2.9 41.3 - - + +
312A PHE* 3.3 34.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 2.7 45.8 + - + +
55A TRP* 3.9 3.4 - - - +
57A ILE* 1.3 87.6 - - + +
59A ALA* 1.3 63.7 + - - +
60A HIS 4.3 0.3 - - - -
61A LYS* 4.7 0.9 + - - -
64A ARG* 3.8 15.3 + - - +
72A VAL* 4.1 14.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TRP* 2.7 44.6 + - + +
56A ILE 3.5 2.9 - - - +
58A LEU* 1.3 77.0 - - - +
60A HIS* 1.3 62.4 + - + +
61A LYS* 3.5 0.7 + - - -
319A ALA* 5.9 0.4 - - + -
342A LEU* 4.5 8.1 - - + -
343A GLN* 2.7 48.5 + - + +
----------------------------------------------------------
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 2.6 42.4 + - + +
57A ILE 2.8 6.3 - - - +
59A ALA* 1.3 74.2 - - + +
61A LYS* 1.3 58.3 + - - +
63A MET* 3.1 6.8 + - + -
64A ARG* 2.8 24.2 + - - -
315A GLY 2.8 33.1 + - - -
318A HIS* 3.7 7.9 - - + -
319A ALA* 4.1 6.6 - - + +
341A TYR* 2.6 57.9 + + + -
342A LEU* 2.8 37.1 - - + +
----------------------------------------------------------
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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