Contacts of the helix formed by residues 39 - 62 (chain A) in PDB entry 1S30
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 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 2.9 15.9 + - - +
35A LYS* 4.5 1.0 + - - -
37A ASP* 3.7 34.8 - - + -
38A GLY* 1.3 79.0 - - - +
40A VAL* 1.3 58.3 + - - +
41A GLN 3.5 2.2 - - - -
42A ILE* 3.5 23.5 + - + -
43A SER* 2.9 27.3 + - - -
83A THR* 3.9 19.1 - - + -
142A ILE* 3.8 27.1 - - + -
147A VAL* 4.0 24.9 - - + -
148A PHE* 3.9 24.7 - + - -
182A ALA 4.3 0.7 - - - -
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Residues in contact with VAL 40 (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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35A LYS* 3.6 28.0 - - + +
38A GLY 5.3 0.2 - - - -
39A PHE* 1.3 70.0 - - - +
41A GLN* 1.3 68.7 + - - +
43A SER* 3.1 8.4 + - - -
44A ASP* 3.0 30.1 + - - +
148A PHE* 5.4 0.2 - - - -
159A ARG* 3.9 23.1 - - + +
182A ALA* 3.0 29.5 + - + +
183A HIS* 3.6 32.8 - - + +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE 3.5 0.6 - - - -
40A VAL* 1.3 79.6 - - - +
42A ILE* 1.3 64.9 + - + +
44A ASP* 3.2 3.1 + - - +
45A ILE* 3.0 32.7 + - + +
138A PHE* 3.6 33.5 - - + -
147A VAL* 6.1 3.8 - - - +
159A ARG* 3.7 22.4 - - - +
182A ALA 4.4 1.6 + - - -
184A PHE 4.8 5.8 + - - +
185A GLU* 3.5 43.7 - - + +
186A LEU 4.8 4.1 + - - +
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 4.1 2.7 - - + -
39A PHE* 3.5 26.1 + - + +
40A VAL 3.3 0.4 - - - -
41A GLN* 1.3 77.3 - - + +
43A SER* 1.3 63.0 + - - +
45A ILE* 3.2 10.6 + - + +
46A PHE* 3.0 44.9 + - + -
83A THR* 4.0 13.5 - - + -
87A LEU* 4.1 9.4 - - + -
138A PHE* 3.5 38.1 - - + +
142A ILE* 3.9 31.4 - - + -
147A VAL* 4.9 9.2 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 2.9 27.9 + - - -
34A ALA* 3.6 12.1 - - - -
35A LYS* 3.9 15.9 - - - +
39A PHE 2.9 15.6 + - - -
40A VAL* 3.1 13.7 + - - -
42A ILE* 1.3 76.8 - - - +
44A ASP* 1.3 62.7 + - - +
46A PHE* 3.2 5.9 + - - +
47A ALA* 3.1 25.9 + - - +
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.0 21.2 + - - +
41A GLN 3.8 5.6 - - - +
43A SER* 1.3 78.9 + - - +
45A ILE* 1.3 61.3 + - + +
47A ALA* 3.7 8.5 - - - +
48A GLU* 2.9 29.5 + - - +
159A ARG* 2.6 43.5 + - - +
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Residues in contact with ILE 45 (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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41A GLN* 3.0 26.4 + - + +
42A ILE* 3.2 10.1 + - + +
44A ASP* 1.3 74.7 - - + +
46A PHE* 1.3 58.9 + - + +
48A GLU* 3.4 5.9 + - + +
49A THR* 2.7 42.2 + - - +
87A LEU* 6.4 0.4 - - + -
134A ARG* 3.6 43.2 + - + +
135A PHE* 4.5 12.1 - - + -
138A PHE* 3.6 38.6 - - + -
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Residues in contact with PHE 46 (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 TYR* 3.3 34.4 - + + +
30A PHE* 3.6 37.0 - + + -
31A GLY* 3.6 6.3 - - - -
34A ALA* 4.3 3.1 - - + -
42A ILE* 3.0 29.7 + - + -
43A SER 3.2 7.6 + - - +
45A ILE* 1.3 78.1 - - + +
47A ALA* 1.3 57.4 + - - +
49A THR* 3.2 4.8 + - - -
50A ALA* 2.8 29.8 + - - +
83A THR* 4.7 4.5 - - + -
86A ASN* 4.2 2.0 - - + -
87A LEU* 3.3 42.2 - - + -
90A SER* 3.5 21.3 - - - -
135A PHE* 3.5 25.8 - + - -
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Residues in contact with ALA 47 (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 TYR 4.6 0.6 + - - -
28A ASN* 3.9 21.1 + - - +
31A GLY* 5.0 1.3 - - - -
43A SER 3.1 15.7 + - - +
44A ASP* 3.7 9.9 - - - +
45A ILE 3.3 0.2 - - - -
46A PHE* 1.3 77.0 - - - +
48A GLU* 1.3 56.7 + - - +
50A ALA* 3.2 3.8 + - - +
51A ASP* 3.0 34.8 + - - +
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Residues in contact with GLU 48 (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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44A ASP 2.9 18.4 + - - +
45A ILE* 3.9 5.6 - - + +
47A ALA* 1.3 73.4 - - - +
49A THR* 1.3 67.3 + - - +
51A ASP* 3.1 11.5 + - + +
52A GLN* 2.9 48.6 + - + +
134A ARG* 2.8 37.4 + - - -
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Residues in contact with THR 49 (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 TYR* 3.5 27.4 - - + -
45A ILE* 2.7 26.8 + - - +
46A PHE 3.6 4.0 - - - -
48A GLU* 1.3 76.4 - - - +
50A ALA* 1.3 58.1 + - - +
52A GLN* 3.0 7.6 + - - +
53A GLU* 2.8 31.6 + - - +
131A HIS* 3.6 28.2 - - + +
134A ARG* 2.9 20.5 + - - +
135A PHE* 3.7 22.1 - - + -
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Residues in contact with ALA 50 (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 ARG* 3.4 34.5 - - + +
27A TYR* 3.8 13.4 - - + -
28A ASN* 3.6 22.0 - - - +
46A PHE 2.8 14.5 + - - +
47A ALA 3.3 9.6 - - - +
49A THR* 1.3 77.4 - - - +
51A ASP* 1.3 62.9 + - - +
53A GLU* 3.1 7.4 + - - +
54A ARG* 3.0 17.7 + - - +
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Residues in contact with ASP 51 (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 ARG* 4.9 6.3 + - - +
28A ASN* 5.2 4.0 + - - +
47A ALA* 3.0 19.8 + - - +
48A GLU* 3.1 14.3 + - + +
50A ALA* 1.3 77.2 - - - +
52A GLN* 1.3 63.3 + - + +
54A ARG* 3.2 51.7 + - - +
55A GLU* 3.2 14.3 + - - +
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Residues in contact with GLN 52 (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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48A GLU* 2.9 41.7 + - + +
49A THR* 3.0 6.2 + - - +
51A ASP* 1.3 75.8 - - + +
53A GLU* 1.3 65.9 + - - +
55A GLU* 3.1 9.4 + - + +
56A HIS* 3.0 34.1 + - - +
131A HIS* 2.7 39.3 + - + +
134A ARG* 3.8 7.8 + - - -
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Residues in contact with GLU 53 (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 GLU* 2.9 30.5 - - - +
23A ALA* 4.3 7.4 - - + -
24A ARG* 4.2 5.4 - - - +
27A TYR* 3.7 24.3 - - + -
49A THR 2.8 16.1 + - - +
50A ALA* 3.3 8.3 - - - +
52A GLN* 1.3 75.8 - - - +
54A ARG* 1.3 64.3 + - - +
56A HIS* 3.2 3.3 + - - +
57A ALA* 2.9 25.1 + - - +
94A GLU* 3.3 2.6 - - - +
97A GLU* 5.3 0.7 - - - -
131A HIS* 3.0 12.5 + - - -
600A FE 2.1 29.6 - - - -
601A ZN 2.1 34.1 - - - -
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Residues in contact with ARG 54 (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 ARG* 3.7 50.7 - - - +
50A ALA 3.0 7.6 + - - +
51A ASP* 3.2 49.1 + - - +
53A GLU* 1.3 78.1 - - - +
55A GLU* 1.3 82.7 + - - +
57A ALA* 3.5 6.9 + - - +
58A LYS* 3.0 27.3 + - + +
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Residues in contact with GLU 55 (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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51A ASP 3.2 13.0 + - - +
52A GLN* 3.1 11.5 + - - +
54A ARG* 1.3 110.0 + - - +
56A HIS* 1.3 67.2 + - + +
58A LYS* 3.3 21.3 + - - +
59A ARG* 3.1 23.4 + - - +
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Residues in contact with HIS 56 (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 GLU* 3.2 16.1 + - + +
52A GLN* 3.0 20.7 + - + +
53A GLU* 3.2 5.4 + - - +
55A GLU* 1.3 79.8 - - + +
57A ALA* 1.3 63.7 + - - +
59A ARG* 3.3 5.1 + - - +
60A LEU* 3.2 27.8 + - - +
124A ILE* 3.6 27.8 - - + +
127A ALA* 3.6 26.8 - - + +
128A GLU* 3.3 18.1 + - - -
131A HIS* 3.9 13.1 - + - -
601A ZN 2.2 31.5 - - - -
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Residues in contact with ALA 57 (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 PHE* 3.3 30.3 - - + -
20A GLU* 4.0 18.3 - - + +
21A SER* 4.5 8.1 - - - +
53A GLU 2.9 17.0 + - - +
54A ARG* 3.5 8.7 - - - +
56A HIS* 1.3 77.9 - - - +
58A LYS* 1.3 51.2 + - - +
60A LEU* 3.2 5.8 + - - +
61A PHE* 2.7 35.9 + - - +
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Residues in contact with LYS 58 (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 PHE* 5.3 0.4 - - - -
54A ARG* 3.0 19.6 + - + +
55A GLU* 3.7 24.8 + - - +
56A HIS 3.3 0.4 - - - -
57A ALA* 1.3 73.7 - - - +
59A ARG* 1.3 66.1 + - - +
61A PHE* 3.2 9.1 + - + +
62A LYS* 3.0 52.2 + - + +
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Residues in contact with ARG 59 (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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55A GLU 3.1 11.6 + - - +
56A HIS* 3.7 10.1 - - - +
57A ALA 3.3 0.2 - - - -
58A LYS* 1.3 78.3 - - - +
60A LEU* 1.3 62.6 + - + +
62A LYS* 3.5 17.2 + - - +
63A PHE* 3.5 28.1 + - + -
116A GLU* 3.6 22.0 + - - +
120A VAL* 3.6 48.0 - - + +
124A ILE* 5.3 2.0 - - + -
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Residues in contact with LEU 60 (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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13A ILE* 3.3 34.8 - - + +
16A ALA* 3.6 28.7 - - + -
17A PHE* 4.1 11.7 - - + +
20A GLU* 4.4 6.7 - - + -
56A HIS 3.2 14.3 + - - +
57A ALA* 3.5 6.3 - - - +
58A LYS 3.2 0.2 - - - -
59A ARG* 1.3 77.7 - - - +
61A PHE* 1.3 65.3 + - - +
63A PHE* 3.2 26.9 + - + +
64A LEU* 3.9 0.5 + - - +
102A TYR* 3.9 14.8 - - + +
117A ILE* 5.8 0.2 - - + -
120A VAL* 5.0 1.6 - - + -
121A PHE* 3.6 32.5 - - + -
124A ILE* 4.1 13.7 - - + -
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Residues in contact with PHE 61 (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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14A LEU* 6.1 0.9 - - + -
17A PHE* 3.4 43.0 - + + -
57A ALA 2.7 19.8 + - - +
58A LYS* 3.2 11.4 + - + +
60A LEU* 1.3 73.1 - - - +
62A LYS* 1.3 68.2 + - + +
63A PHE 3.1 0.2 - - - -
64A LEU* 3.1 38.7 + - + +
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Residues in contact with LYS 62 (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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58A LYS* 3.0 41.9 + - + +
59A ARG* 3.8 13.2 - - - +
60A LEU 3.2 0.2 - - - -
61A PHE* 1.3 81.0 - - + +
63A PHE* 1.3 61.7 + - + +
64A LEU 3.3 5.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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