Contacts of the helix formed by residues 42 - 65 (chain A) in PDB entry 1YC3
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 GLU 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 3.0 21.7 + - - +
41A LYS* 1.3 77.2 - - - +
43A ILE* 1.3 58.0 + - - +
44A PHE* 3.0 15.0 + - - -
45A LEU* 3.3 18.0 + - - +
46A ARG 4.2 0.9 + - - -
197A TYR* 3.6 13.2 + - + +
202A ARG* 2.8 40.5 + - - +
206A ILE* 3.9 23.5 - - + +
209A LYS* 3.5 21.0 + - - +
210A HIS* 2.7 31.4 + - + +
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Residues in contact with ILE 43 (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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40A ASN* 3.3 37.7 - - - +
41A LYS 2.8 1.6 + - - -
42A GLU* 1.3 74.0 - - - +
44A PHE* 1.3 68.1 + - - +
45A LEU 3.2 0.4 - - - -
46A ARG* 3.3 32.9 + - - +
47A GLU* 3.0 25.9 + - + +
128A ILE* 4.1 15.9 - - + +
129A SER* 3.8 26.0 - - - +
131A ILE* 4.2 3.6 - - + -
140A SER* 4.0 19.5 - - - -
143A LEU* 4.1 10.5 - - + -
210A HIS* 3.8 17.3 - - + -
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Residues in contact with PHE 44 (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 LYS 3.1 24.8 + - - +
42A GLU 3.0 5.3 - - - -
43A ILE* 1.3 79.7 - - - +
45A LEU* 1.3 93.1 + - + +
47A GLU* 3.1 4.5 + - - +
48A LEU* 3.0 38.9 + - + +
89A LEU* 3.9 19.3 - - + -
140A SER* 3.3 41.2 + - - +
141A ALA* 4.3 3.1 - - - +
144A VAL* 3.7 23.6 - - + -
188A LEU* 3.6 25.1 - - + -
197A TYR* 3.6 45.3 - + + -
206A ILE* 4.8 0.4 - - + -
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Residues in contact with LEU 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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42A GLU 3.3 9.8 + - - +
43A ILE 3.2 0.4 - - - -
44A PHE* 1.3 104.0 - - + +
46A ARG* 1.3 66.2 + - - +
48A LEU* 3.2 3.4 + - + -
49A ILE* 3.0 40.4 + - + +
80A LEU* 4.4 7.0 - - + -
89A LEU* 4.7 7.2 - - + -
91A ILE* 4.2 24.0 - - + -
203A ILE* 4.4 10.3 - - + -
206A ILE* 3.6 31.6 - - + -
207A VAL* 3.6 24.9 - - + +
211A SER* 6.0 0.2 - - - +
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Residues in contact with ARG 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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42A GLU 4.2 0.8 + - - -
43A ILE* 3.3 36.6 + - - +
45A LEU* 1.3 80.0 - - - +
47A GLU* 1.3 88.2 + - - +
49A ILE* 3.5 1.6 + - - +
50A SER* 3.0 27.1 + - - -
129A SER* 2.8 47.4 + - - -
210A HIS* 3.7 51.3 + - + +
211A SER* 3.8 13.3 + - - +
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Residues in contact with GLU 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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43A ILE 3.0 18.6 + - - +
44A PHE 3.1 7.4 + - - +
46A ARG* 1.3 116.3 + - - +
48A LEU* 1.3 57.9 + - + +
50A SER* 3.4 8.2 + - - -
51A ASN* 3.0 37.2 + - - +
131A ILE* 4.3 7.0 - - + -
132A GLY* 3.1 33.4 - - - -
137A GLY* 3.6 27.9 - - - +
140A SER* 3.7 10.1 - - - +
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Residues in contact with LEU 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 PHE* 3.0 39.8 + - + +
45A LEU* 3.2 6.0 + - + +
47A GLU* 1.3 75.9 - - + +
49A ILE* 1.3 61.0 + - - +
51A ASN* 3.2 9.3 + - - +
52A SER* 2.9 31.6 + - - -
91A ILE* 4.0 26.2 - - + -
138A PHE* 4.6 18.2 - - + +
140A SER* 5.6 0.9 - - - +
141A ALA* 5.0 9.2 - - + -
186A VAL* 4.2 19.7 - - + -
188A LEU* 3.8 20.4 - - + -
237A 4BC 4.0 17.1 + - - +
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Residues in contact with ILE 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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45A LEU* 3.0 39.0 + - + +
46A ARG 4.0 2.7 - - - +
48A LEU* 1.3 76.1 - - - +
50A SER* 1.3 57.6 + - - +
52A SER* 3.2 8.7 + - - -
53A SER* 2.8 27.4 + - - -
78A ILE* 3.9 18.5 - - + +
80A LEU* 4.5 16.2 - - + -
91A ILE* 4.8 1.6 - - + -
207A VAL* 4.0 21.3 - - + -
211A SER* 3.9 20.4 - - - +
214A ILE* 3.4 31.4 - - + -
218A ILE* 4.1 11.7 - - + -
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Residues in contact with SER 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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46A ARG* 3.0 22.8 + - - -
47A GLU* 3.7 10.4 + - - -
49A ILE* 1.3 80.2 - - - +
51A ASN* 1.3 57.5 + - - +
53A SER* 3.3 7.2 + - - -
54A ASP* 2.9 40.0 + - - +
214A ILE* 4.8 9.2 - - - +
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Residues in contact with ASN 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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47A GLU* 3.0 25.0 + - - +
48A LEU* 3.5 7.6 - - - +
50A SER* 1.3 78.2 + - - +
52A SER* 1.3 63.0 + - - +
54A ASP* 3.3 2.3 + - - +
55A ALA* 3.1 18.0 + - - +
137A GLY* 5.7 1.2 - - - -
138A PHE* 4.1 24.1 + - - +
237A 4BC 2.8 87.3 + - + +
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Residues in contact with SER 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 LEU 2.9 15.2 + - - -
49A ILE* 3.4 8.5 - - - -
51A ASN* 1.3 73.4 - - - +
53A SER* 1.3 66.2 + - - +
55A ALA* 3.1 2.6 + - - +
56A LEU* 2.9 29.7 + - - +
78A ILE* 3.8 14.4 - - - -
91A ILE* 4.0 14.9 + - - +
93A ASP* 2.8 41.2 + - - +
186A VAL* 6.1 0.2 - - - +
237A 4BC 3.7 6.1 + - - -
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Residues in contact with SER 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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49A ILE 2.8 20.4 + - - -
50A SER* 3.3 8.9 + - - -
52A SER* 1.3 71.7 - - - +
54A ASP* 1.3 67.6 + - - +
56A LEU* 3.1 4.5 + - - +
57A ASP* 2.9 31.3 + - - -
78A ILE* 4.3 1.1 - - - +
214A ILE* 3.8 31.0 - - - +
215A GLY 4.8 2.4 + - - -
216A TYR* 3.8 19.3 - - - -
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Residues in contact with ASP 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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50A SER* 2.9 25.7 + - - +
51A ASN 3.6 7.4 - - - +
52A SER 3.3 0.2 - - - -
53A SER* 1.3 79.8 + - - +
55A ALA* 1.3 61.2 + - - +
57A ASP* 3.4 13.4 + - - +
58A LYS* 3.2 31.3 + - - +
237A 4BC 3.9 25.5 - - + +
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Residues in contact with ALA 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 ASN 3.1 8.6 + - - +
52A SER 3.1 2.6 + - - +
54A ASP* 1.3 74.4 - - - +
56A LEU* 1.3 64.6 + - - +
58A LYS* 3.3 9.5 + - - +
59A ILE 3.2 12.1 + - - -
95A GLY* 3.7 3.6 - - - -
96A ILE* 3.0 27.9 + - - +
237A 4BC 3.2 56.7 - - + +
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Residues in contact with LEU 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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52A SER 2.9 20.1 + - - +
53A SER 3.5 4.0 - - - +
55A ALA* 1.3 74.7 - - - +
57A ASP* 1.3 59.4 + - - +
59A ILE* 3.2 3.8 - - - +
60A ARG* 2.8 32.4 + - - +
76A LEU* 3.7 14.2 - - + +
77A HIS 3.7 14.6 - - - +
78A ILE* 3.6 32.1 - - + -
93A ASP* 4.2 2.5 - - + -
94A THR* 3.4 42.6 - - - +
95A GLY* 3.8 7.6 - - - +
216A TYR* 3.4 30.5 - - + -
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Residues in contact with ASP 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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53A SER* 2.9 21.7 + - - +
54A ASP* 3.5 18.7 - - - +
56A LEU* 1.3 75.9 - - - +
58A LYS* 1.3 57.7 + - + +
60A ARG* 3.2 14.0 + - - +
61A TYR* 2.9 46.1 + - + -
216A TYR* 2.5 35.8 + - - -
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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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54A ASP* 3.2 19.8 + - - +
55A ALA* 3.5 7.6 - - - +
56A LEU 3.2 1.0 - - - -
57A ASP* 1.3 80.6 - - + +
59A ILE* 1.3 62.5 + - - +
61A TYR* 4.2 2.9 - - - +
62A GLU* 3.0 26.0 + - - +
96A ILE* 4.0 17.0 - - + +
237A 4BC 3.0 39.2 + - - +
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Residues in contact with ILE 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 ALA 3.2 7.7 + - - +
56A LEU* 3.2 13.9 - - - +
58A LYS* 1.3 74.3 - - - +
60A ARG* 1.3 65.1 + - - +
62A GLU* 3.3 24.4 + - - +
63A THR* 2.5 41.9 + - + +
69A LYS* 3.9 17.0 - - + +
70A LEU* 3.6 14.4 - - + -
76A LEU* 3.7 22.9 - - + -
94A THR 3.8 11.4 - - - +
95A GLY 4.0 0.4 - - - -
96A ILE* 3.8 20.8 - - + +
155A ASN* 4.2 3.4 - - - +
182A ARG* 3.6 24.5 - - - +
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Residues in contact with ARG 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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56A LEU 2.8 18.8 + - - +
57A ASP* 3.4 18.0 + - - +
59A ILE* 1.3 77.3 - - - +
61A TYR* 1.3 112.2 + - - +
63A THR* 2.8 25.7 + - - +
64A LEU* 3.3 17.0 + - + +
76A LEU* 3.5 20.6 - - + -
216A TYR* 2.7 30.7 + - - +
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Residues in contact with TYR 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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57A ASP* 2.9 41.5 + - + +
58A LYS* 4.4 2.5 - - - +
60A ARG* 1.3 114.3 + - - +
62A GLU* 1.3 63.9 + - - +
64A LEU* 3.1 40.6 + - + +
65A THR* 3.9 6.6 + - - +
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Residues in contact with GLU 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 19.7 + - - +
59A ILE* 3.3 20.2 - - - +
61A TYR* 1.3 76.7 - - - +
63A THR* 1.3 61.3 + - - +
65A THR* 3.3 11.6 + - - +
66A ASP* 3.2 19.1 + - + +
69A LYS* 3.0 43.1 + - + +
96A ILE* 4.0 16.2 - - + +
154A HIS* 5.6 2.6 + - - -
155A ASN* 4.6 1.0 + - - -
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Residues in contact with THR 63 (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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59A ILE* 2.5 35.3 + - + +
60A ARG* 2.8 16.3 + - - +
62A GLU* 1.3 73.6 - - - +
64A LEU* 1.3 68.2 + - - +
65A THR 3.0 2.9 - - - -
66A ASP 2.9 19.4 + - - -
67A PRO* 3.1 17.6 - - - +
69A LYS* 3.9 4.7 - - + -
70A LEU* 3.2 51.2 - - + +
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Residues in contact with LEU 64 (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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60A ARG* 3.7 18.4 - - + +
61A TYR* 3.1 40.3 + - + +
63A THR* 1.3 81.8 + - - +
65A THR* 1.3 66.2 + - + +
67A PRO* 4.7 6.2 - - - +
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Residues in contact with THR 65 (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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61A TYR 3.9 4.2 + - - +
62A GLU* 3.3 13.7 + - - +
63A THR 3.0 0.2 - - - -
64A LEU* 1.3 87.5 - - + +
66A ASP* 1.3 60.1 + - - +
67A PRO* 4.0 3.1 - - - -
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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
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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