Contacts of the helix formed by residues 38 - 61 (chain A) in PDB entry 1P3V
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 SER 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO 3.9 2.8 - - - +
37A VAL* 1.3 95.0 - - - +
39A LYS* 1.3 62.7 + - - +
40A GLU* 4.0 8.7 + - - +
41A ASN* 3.7 16.5 + - - +
42A TYR* 3.3 21.1 + - - +
131A LEU* 3.9 12.0 - - - +
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Residues in contact with LYS 39 (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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38A SER* 1.3 72.2 - - - +
40A GLU* 1.3 69.9 + - + +
42A TYR* 3.0 7.8 + - + +
43A ILE* 2.9 48.3 + - + +
88A LEU* 4.3 24.0 + - + +
131A LEU* 4.8 8.3 - - + +
133A TYR* 3.8 21.5 - - - +
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Residues in contact with GLU 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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38A SER* 3.6 8.6 + - - +
39A LYS* 1.3 75.8 - - + +
41A ASN* 1.3 64.6 + - - +
43A ILE* 2.8 29.8 + - - +
44A LYS* 2.9 24.8 + - - +
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Residues in contact with ASN 41 (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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33A VAL 3.0 15.7 + - - -
34A GLN* 2.6 31.6 + - - +
35A PRO* 3.3 6.1 - - + +
37A VAL* 3.4 14.4 - - + +
38A SER* 3.7 15.7 + - - +
39A LYS 3.2 0.4 - - - -
40A GLU* 1.3 85.4 - - - +
42A TYR* 1.3 56.6 + - - +
44A LYS* 3.3 18.8 + - - +
45A PHE* 2.9 25.5 + - - +
192A PHE* 3.8 12.4 - - + -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO 3.1 13.3 + - - +
36A PHE* 3.5 39.5 - + - -
38A SER 3.3 9.0 + - - +
39A LYS* 3.0 10.5 + - - +
41A ASN* 1.3 76.3 - - - +
43A ILE* 1.3 58.1 + - - +
45A PHE* 3.3 20.3 + + - +
46A LEU* 3.0 56.2 + - + +
88A LEU* 4.1 9.4 - - + -
128A ALA* 4.3 7.9 - - + -
131A LEU* 4.4 8.1 - - + -
133A TYR* 4.1 30.3 - + + -
138A GLY 2.7 31.4 + - - -
139A ALA* 3.7 9.7 - - - +
141A HIS* 4.2 0.3 - - - -
142A LEU* 3.7 10.4 - - + +
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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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39A LYS* 2.9 43.7 + - + +
40A GLU* 2.8 15.1 + - - +
42A TYR* 1.3 76.8 - - - +
44A LYS* 1.3 64.3 + - + +
46A LEU* 3.1 9.4 + - + +
47A LYS* 3.0 36.1 + - - +
85A LEU* 4.3 2.9 - - + +
88A LEU* 3.9 20.2 - - + +
90A GLU* 3.7 45.1 - - + +
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Residues in contact with LYS 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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40A GLU* 2.9 22.1 + - - +
41A ASN* 3.6 19.3 + - - +
42A TYR 3.3 0.2 - - - -
43A ILE* 1.3 77.0 - - + +
45A PHE* 1.3 62.4 + - - +
47A LYS* 3.3 11.3 + - + -
48A LEU* 3.1 11.4 + - - +
191A THR* 3.0 49.8 + - + +
192A PHE* 3.8 32.8 + - + +
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Residues in contact with PHE 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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30A VAL* 4.3 19.1 - - + -
35A PRO* 4.3 18.6 - - + -
36A PHE* 4.4 5.4 - + - -
41A ASN 2.9 14.3 + - - +
42A TYR* 3.4 37.2 - + - +
43A ILE 3.1 0.2 - - - -
44A LYS* 1.3 78.9 - - - +
46A LEU* 1.3 60.1 + - + +
48A LEU* 3.5 11.4 - - + +
49A GLN* 3.1 56.1 + - + +
124A LEU* 4.1 22.2 - - + -
141A HIS* 4.1 9.4 - - - -
142A LEU* 4.2 9.9 - - + -
184A TYR* 3.9 18.2 - - - -
192A PHE* 3.7 12.5 - + + -
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Residues in contact with LEU 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 TYR* 3.0 50.7 + - + +
43A ILE* 3.1 7.8 + - - +
45A PHE* 1.3 78.6 - - + +
47A LYS* 1.3 67.3 + - - +
49A GLN* 3.1 4.5 + - - +
50A SER* 2.7 25.7 + - - -
81A VAL* 3.8 5.0 - - + +
84A ASP* 4.3 19.5 - - + +
85A LEU* 3.6 26.0 - - + +
88A LEU* 4.1 18.4 - - + -
138A GLY 4.3 2.0 - - - +
141A HIS* 3.2 35.4 - - + +
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Residues in contact with LYS 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 30.1 + - + +
44A LYS* 3.6 17.3 - - + +
46A LEU* 1.3 74.9 - - - +
48A LEU* 1.3 58.0 - - - +
50A SER* 2.9 10.9 - - - -
51A VAL* 2.9 32.3 + - - +
85A LEU* 4.4 6.8 - - + +
90A GLU* 3.2 22.7 + - - -
91A GLU 4.7 4.9 + - - -
93A TYR* 3.3 54.3 - - + +
191A THR* 3.9 9.6 - - + -
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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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30A VAL* 5.1 0.9 - - + -
44A LYS 3.1 10.5 + - - +
45A PHE* 3.5 22.0 - - + +
47A LYS* 1.3 79.4 - - - +
49A GLN* 1.3 63.7 + - - +
51A VAL* 3.1 4.3 + - - +
52A PHE* 3.0 20.7 + - + +
184A TYR* 3.4 49.4 - - + +
187A VAL* 3.3 31.9 - - + -
188A LEU* 3.4 35.9 - - + +
191A THR* 4.1 10.4 - - - +
192A PHE* 4.4 6.5 - - + -
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Residues in contact with GLN 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 PHE* 3.1 40.3 + - + +
46A LEU* 3.1 8.4 + - - +
48A LEU* 1.3 77.5 - - - +
50A SER* 1.3 57.1 + - - +
52A PHE* 3.9 1.5 - - - +
53A HIS* 2.7 57.2 + - - +
77A ARG* 5.5 0.9 + - - -
81A VAL* 4.1 4.7 - - + -
124A LEU* 5.0 2.8 - - - +
141A HIS* 3.3 34.5 + - + +
142A LEU* 4.0 6.4 - - - +
184A TYR* 2.9 35.4 + - - -
300A HEM 4.6 5.1 - - - +
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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 LEU 2.7 13.4 + - - -
47A LYS* 2.9 18.8 - - - -
49A GLN* 1.3 75.5 - - - +
51A VAL* 1.3 59.0 + - - +
54A LYS* 2.9 31.4 + - - +
78A TYR* 3.5 18.4 + - - -
81A VAL* 3.5 19.5 - - - +
82A THR* 5.2 1.7 - - - +
85A LEU* 4.3 13.0 - - - +
92A PRO* 5.0 1.4 - - - +
93A TYR* 4.2 16.5 + - - +
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Residues in contact with VAL 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 LYS 2.9 11.1 + - - +
48A LEU 3.1 5.8 + - - +
50A SER* 1.3 72.7 - - - +
52A PHE* 1.3 67.9 + - - +
54A LYS* 3.3 5.9 + - - +
55A ALA* 3.0 22.2 + - - +
93A TYR* 3.3 38.6 - - + +
95A PHE* 3.9 16.6 - - + +
99A LEU* 3.7 29.2 - - + +
183A PHE* 4.0 2.7 - - + -
187A VAL* 3.7 31.2 - - + -
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Residues in contact with PHE 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* 3.0 14.7 + - + +
49A GLN* 3.9 3.4 - - - +
51A VAL* 1.3 77.9 - - - +
53A HIS* 1.3 81.4 + + - +
55A ALA* 3.1 20.5 + - - +
56A VAL* 3.4 17.8 + - + +
110A TRP* 4.2 17.5 - + - -
113A CYS* 3.6 24.9 - - + -
114A ALA* 3.9 28.9 - - + -
117A SER* 5.1 0.7 - - - -
180A ALA* 3.8 20.0 - - + -
183A PHE* 4.2 19.7 - + + -
184A TYR* 3.6 32.8 - + + -
187A VAL* 5.0 1.0 - - + +
300A HEM 4.0 11.7 - - + -
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Residues in contact with HIS 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 GLN* 2.7 57.0 + - + +
50A SER 4.2 1.3 - - - +
52A PHE* 1.3 91.5 - + - +
54A LYS* 1.3 64.8 + - - +
56A VAL* 3.3 15.4 + - + +
57A ASP* 3.1 23.0 + - - +
60A TYR* 5.5 2.5 - + - -
77A ARG* 3.5 47.6 + - + -
78A TYR* 3.6 29.6 + - + +
81A VAL* 4.0 12.7 - - + +
114A ALA* 4.9 4.0 + - + -
117A SER* 4.2 5.1 + - - -
141A HIS* 4.8 0.9 - + - -
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Residues in contact with LYS 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 19.2 + - - +
51A VAL* 3.5 7.0 - - - +
53A HIS* 1.3 77.3 - - - +
55A ALA* 1.3 58.7 + - - +
56A VAL 3.1 4.9 + - - -
57A ASP* 3.2 23.2 + - + +
58A HIS* 4.4 2.8 + - - -
78A TYR* 3.6 43.4 + - + +
99A LEU* 3.4 24.0 - - + -
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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 VAL 3.0 13.4 + - - +
52A PHE 3.1 11.4 + - - +
54A LYS* 1.3 76.5 - - - +
56A VAL* 1.3 59.5 + - - +
58A HIS* 3.3 22.6 - - - -
59A ILE* 4.6 0.9 - - - +
99A LEU* 4.3 6.7 - - + +
100A PRO* 4.0 24.3 - - + +
101A TYR* 6.5 0.2 - - - -
102A GLU* 5.2 0.7 + - - +
110A TRP* 4.3 15.2 - - + -
183A PHE* 4.1 20.9 - - + -
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Residues in contact with VAL 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 PHE* 3.4 16.3 + - + +
53A HIS* 3.3 27.8 - - + +
55A ALA* 1.3 79.8 - - - +
57A ASP* 1.3 61.7 + - - +
58A HIS* 3.3 4.0 - - - -
59A ILE* 2.9 27.3 + - + +
60A TYR* 3.0 35.4 + - + -
110A TRP* 3.8 44.9 - - + +
111A LEU* 5.6 0.7 - - - -
114A ALA* 4.0 10.8 - - + -
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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 HIS 3.1 9.9 + - - +
54A LYS* 3.2 24.4 + - + +
56A VAL* 1.3 77.9 - - - +
58A HIS* 1.3 62.4 + - - +
60A TYR* 3.3 6.2 + - - +
61A LYS* 2.6 67.9 + - - +
76A ALA* 3.6 16.2 - - - +
78A TYR* 3.7 27.3 - - + +
79A ASP* 4.7 2.1 - - - +
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Residues in contact with HIS 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 LYS 4.4 1.8 + - - -
55A ALA* 3.3 28.0 + - - -
57A ASP* 1.3 78.8 - - - +
59A ILE* 1.3 73.4 + - + +
61A LYS* 3.7 6.7 - - - -
62A ASP* 3.1 25.6 + - - +
100A PRO 4.6 0.2 - - - -
101A TYR* 3.4 70.7 - + + +
102A GLU 2.6 30.6 + - - -
103A ALA* 5.8 1.1 - - + -
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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 4.6 1.1 - - - +
56A VAL* 2.9 17.0 + - + +
58A HIS* 1.3 106.3 - - + +
60A TYR* 1.3 63.4 + - - +
61A LYS 3.1 1.6 - - - -
62A ASP* 3.4 10.2 + - - -
65A LEU* 3.6 32.7 - - + +
72A LEU* 3.9 4.3 - - - +
102A GLU* 4.0 8.1 - - + +
107A ALA* 3.5 45.1 - - + +
110A TRP* 3.8 19.5 - - + -
111A LEU* 4.2 15.0 - - + -
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Residues in contact with TYR 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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53A HIS* 5.5 3.4 - + - -
56A VAL* 3.0 31.1 + - + -
57A ASP* 3.9 4.3 - - - +
59A ILE* 1.3 77.9 - - - +
61A LYS* 1.3 59.5 + - + +
62A ASP 3.4 0.2 - - - -
66A ASN* 2.8 16.5 + - - -
72A LEU* 3.4 39.6 - - + +
73A GLU* 3.1 16.7 + - - -
75A MET* 3.5 19.0 + - + -
76A ALA* 3.7 33.4 - - + -
77A ARG* 4.9 6.7 + - - -
111A LEU* 3.8 20.0 - - + -
114A ALA* 3.6 22.4 + - + -
115A GLU* 2.4 51.8 + - + -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 2.6 51.6 + - - +
58A HIS* 3.7 7.0 - - - +
59A ILE 3.1 0.6 - - - -
60A TYR* 1.3 81.3 - - + +
62A ASP* 1.3 62.1 + - - +
63A ALA* 3.3 3.6 + - - -
66A ASN* 3.2 9.1 + - - +
73A GLU* 4.1 27.4 - - + +
76A ALA* 4.7 8.1 - - - -
79A ASP* 4.2 15.1 + - - -
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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