Contacts of the helix formed by residues 72 - 94 (chain D) in PDB entry 1P7G
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 ASP 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 4.9 8.2 + - - -
72C ASP* 5.7 1.0 - - - +
75C ALA* 4.0 7.4 - - - +
76C VAL* 6.0 1.2 - - - +
79C ASP* 4.6 4.5 - - - +
71D ILE* 1.3 72.0 - - - +
73D ILE* 1.3 63.3 + - - +
74D ARG* 3.6 4.5 + - - +
75D ALA* 3.2 24.2 + - + +
76D VAL* 3.0 25.8 + - + +
404D BME 3.1 28.7 - - - +
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Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 4.3 17.0 - - + +
131A GLN* 3.7 31.0 - - + +
132A ALA* 4.0 16.4 - - + +
135A ASN* 4.0 17.3 - - + +
157A GLN* 4.2 0.7 - - - +
61D LEU* 4.1 18.6 - - + -
64D PHE* 5.7 0.4 - - + -
71D ILE* 3.4 24.5 + - + +
72D ASP* 1.3 73.8 + - - +
74D ARG* 1.3 60.0 + - - +
76D VAL 4.7 0.2 - - - +
77D LEU* 2.9 70.4 + - + +
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 3.0 47.7 + - + +
136A VAL 4.8 0.2 + - - -
137A GLU* 3.8 29.1 + - - +
157A GLN* 3.1 28.9 + - - +
159A GLU* 5.0 0.4 - - - -
79C ASP* 3.3 24.6 + - - +
83C HIS* 5.1 11.1 - - - -
72D ASP* 3.3 2.4 + - - +
73D ILE* 1.3 81.4 - - + +
75D ALA* 1.3 59.8 + - - +
77D LEU* 3.8 0.7 - - - +
78D ARG* 2.8 75.9 + - - +
404D BME 3.0 19.0 + - - +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASP* 3.9 8.7 - - - +
75C ALA* 3.7 15.0 - - + -
72D ASP* 3.2 31.9 + - + +
74D ARG* 1.3 80.8 - - - +
76D VAL* 1.3 59.0 + - + +
78D ARG* 3.4 1.9 + - - +
79D ASP* 2.9 36.1 + - - +
404D BME 3.4 22.5 - - - -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 3.6 34.5 - - + +
60D LYS* 3.7 24.2 - - + -
61D LEU* 4.0 19.5 - - + -
71D ILE* 3.6 24.5 - - + -
72D ASP* 3.0 19.5 + - + +
73D ILE* 4.3 1.6 - - + +
75D ALA* 1.3 74.9 - - + +
77D LEU* 1.3 57.0 + - - +
79D ASP* 3.2 8.7 + - + +
80D LEU* 2.7 33.1 + - - +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 5.0 1.8 - - - +
132A ALA* 3.7 20.0 - - + -
155A ILE* 3.3 30.7 - - + +
156A LEU* 4.2 6.0 - - + +
157A GLN* 3.8 28.5 - - + +
164A MSE 4.3 3.6 - - - +
61D LEU* 4.4 22.2 - - + -
73D ILE* 2.9 49.5 + - + +
74D ARG 4.0 1.6 - - - +
76D VAL* 1.3 74.6 - - - +
78D ARG* 1.3 65.1 + - - +
80D LEU* 4.0 8.0 - - + +
81D SER* 3.0 25.6 + - - -
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Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 2.7 33.7 + - - +
157A GLN* 4.8 2.2 - - - +
159A GLU* 3.0 26.3 + - - -
164A MSE 3.6 30.3 - - + -
137B GLU* 4.4 4.8 - - - +
78C ARG* 3.8 36.1 - - - +
79C ASP* 4.4 0.8 + - - -
160C LYS* 3.5 4.2 - - - +
74D ARG* 2.8 36.1 + - - +
75D ALA 3.6 4.0 - - - +
77D LEU* 1.3 81.0 - - - +
79D ASP* 1.3 62.3 + - - +
81D SER* 3.5 2.3 + - - -
82D PHE* 3.2 22.7 + - - +
162D ASN* 4.3 3.1 + - - -
404D BME 3.1 41.9 - - - +
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 4.5 3.9 - - - +
72C ASP* 4.6 10.1 - - - +
74C ARG* 2.9 34.5 + - - +
78C ARG* 4.7 3.1 + - - -
57D ALA* 4.5 9.6 - - + -
60D LYS* 4.8 11.3 + - - -
75D ALA* 2.9 26.9 + - - +
76D VAL* 3.4 11.8 - - - +
78D ARG* 1.3 76.9 - - - +
80D LEU* 1.3 63.1 + - - +
82D PHE* 3.1 7.9 + - - +
83D HIS* 3.1 36.4 + - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.0 23.3 - - + -
155A ILE 4.9 1.8 - - - +
156A LEU* 4.7 9.2 - - + -
18D TYR* 5.8 0.9 - - + -
54D ALA* 3.9 18.8 - - + +
57D ALA* 3.8 11.2 - - + +
58D LEU* 3.9 19.1 - - + -
61D LEU* 3.6 27.6 - - + -
76D VAL 2.7 20.2 + - - +
77D LEU* 4.0 13.7 - - + +
79D ASP* 1.3 72.2 - - - +
81D SER* 1.3 58.3 + - - +
83D HIS* 5.1 1.6 - - - -
84D LEU* 2.8 57.4 + - + +
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Residues in contact with SER 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.6 11.1 - - - +
164A MSE 2.9 47.0 + - - +
165A HIS 4.7 0.2 - - - -
166A ALA* 6.4 1.1 - - - +
77D LEU 3.0 20.1 + - - -
78D ARG 3.7 4.3 - - - -
79D ASP 3.3 0.2 - - - -
80D LEU* 1.3 76.4 - - - +
82D PHE* 1.3 63.1 + - - +
84D LEU* 4.2 3.3 - - - +
85D ASN* 2.7 34.2 + - - +
162D ASN* 3.4 10.5 + - - +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 3.2 52.0 - - + +
138B GLY 4.6 3.4 - - - -
50D TYR* 3.7 23.3 - + - -
78D ARG 3.2 6.7 + - - +
79D ASP 3.1 7.9 + - - +
81D SER* 1.3 81.4 - - - +
83D HIS* 1.3 81.2 + + - +
86D GLY* 3.0 23.0 + - - -
160D LYS* 4.2 8.3 - - + -
161D HIS* 3.5 31.1 + - + +
162D ASN* 3.5 21.0 - - - +
178D TRP* 3.8 26.2 - + - -
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 5.6 0.2 - - - -
74C ARG* 5.2 11.7 - - - -
49D GLY 3.9 3.1 + - - -
50D TYR* 3.4 36.0 - + - +
53D GLY* 3.1 34.3 + - - -
54D ALA* 3.1 21.3 - - - +
79D ASP* 3.1 23.0 + - + +
82D PHE* 1.3 99.7 - + - +
84D LEU* 1.3 67.2 + - - +
86D GLY* 3.0 2.0 + - - +
87D HIS* 2.9 22.0 + - - +
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 4.1 8.3 - - + -
154A LEU* 3.5 31.9 - - + -
156A LEU* 5.6 4.0 - - + -
166A ALA* 4.3 17.9 - - + -
18D TYR* 3.7 39.7 - - + +
54D ALA* 4.0 7.9 - - + +
80D LEU* 2.8 35.8 + - + +
81D SER* 4.2 3.6 - - - +
83D HIS* 1.3 72.7 - - - +
85D ASN* 1.3 58.3 + - - +
87D HIS* 3.0 7.2 + - + +
88D ILE* 2.9 50.4 + - + +
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Residues in contact with ASN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A HIS 3.0 17.1 - - - +
166A ALA* 3.7 4.8 - - - +
167A ALA* 2.8 36.5 - - - +
81D SER* 2.7 26.3 + - - +
84D LEU* 1.3 76.3 - - - +
86D GLY* 1.3 66.9 + - - +
88D ILE* 4.4 4.8 - - - +
89D LEU* 2.9 29.5 + - - +
161D HIS* 3.1 28.9 - - + +
162D ASN* 3.3 8.1 - - - +
165D HIS* 3.3 17.1 + - - -
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Residues in contact with GLY 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR* 4.0 10.9 - - - -
82D PHE 3.0 11.8 + - - -
83D HIS 3.0 4.2 + - - -
85D ASN* 1.3 75.7 - - - +
87D HIS* 1.3 60.9 + - - +
90D HIS* 2.8 32.8 + - - +
161D HIS* 3.5 34.0 - - - +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.7 18.3 - - + +
150A GLU* 5.4 1.6 + - - -
18D TYR* 3.3 42.6 - + + +
19D THR 3.2 27.6 + - - -
21D PRO* 3.6 7.9 - - + -
47D HIS* 2.9 28.1 + - - -
50D TYR* 3.8 7.5 - - + +
51D VAL* 3.4 17.6 - - + +
54D ALA* 5.4 1.3 - - + -
83D HIS 2.9 12.3 + - - +
84D LEU* 3.3 11.2 - - + +
86D GLY* 1.3 74.5 - - - +
88D ILE* 1.3 64.5 + - - +
90D HIS 3.4 0.7 + - - -
91D SER* 2.8 43.1 + - - -
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 4.0 14.4 - - - +
149A LEU* 4.3 17.9 - - + -
166A ALA* 4.9 2.9 - - + -
167A ALA* 3.5 41.7 - - + +
168A ASP* 4.4 6.5 - - + +
169A ALA* 6.3 0.2 - - + -
84D LEU* 2.9 48.9 + - + +
85D ASN* 4.0 5.4 - - - +
87D HIS* 1.3 71.6 - - - +
89D LEU* 1.3 64.5 + - - +
91D SER* 3.1 9.0 + - - -
92D ILE* 3.1 39.3 + - + +
220D LEU* 4.8 9.6 - - + -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA* 4.3 11.2 - - + -
85D ASN 2.9 21.7 + - - +
86D GLY 4.3 0.2 - - - +
88D ILE* 1.3 74.3 - - - +
90D HIS* 1.3 57.5 + - - +
92D ILE* 3.4 6.7 + - + +
93D PHE* 2.8 29.5 + - - +
141D TRP* 3.5 50.2 - - + +
143D ILE* 4.6 9.6 - - + -
158D ILE* 4.5 0.9 - - + -
161D HIS* 3.4 26.2 - - - +
165D HIS* 3.7 26.5 - - + +
171D VAL* 4.5 20.6 - - + -
174D ALA* 4.4 4.9 - - + +
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Residues in contact with HIS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D HIS* 2.6 42.2 + + - -
47D HIS* 3.4 27.6 - + + +
50D TYR* 3.6 25.9 - + - -
86D GLY 2.8 28.1 + - - +
89D LEU* 1.3 75.7 - - - +
91D SER* 1.3 61.3 + - - +
93D PHE* 3.4 6.5 - + - +
94D TRP* 2.9 50.3 + + - +
141D TRP* 3.6 23.5 - + - -
161D HIS* 3.8 8.1 - - - -
176D ASP* 3.2 6.2 + - - -
180D HIS* 4.7 2.0 - - - -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 4.8 7.0 - - - +
21D PRO* 3.6 16.5 - - - +
47D HIS* 3.7 4.2 - - - -
87D HIS* 2.8 42.3 + - - -
88D ILE* 3.1 8.4 + - - -
90D HIS* 1.3 77.3 - - - +
92D ILE* 1.3 56.6 + - - +
94D TRP* 4.2 4.0 - - - -
95D PRO* 2.9 24.8 - - - +
304D ACT 3.3 23.4 - - - +
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.8 23.1 - - - +
88D ILE* 3.1 25.6 + - + +
89D LEU* 3.8 9.6 - - + +
91D SER* 1.3 76.4 - - - +
93D PHE* 1.3 65.4 + - - +
94D TRP 3.4 0.2 - - - -
95D PRO* 3.4 6.6 - - - +
96D ASN* 3.1 45.2 + - - +
171D VAL* 3.9 36.6 - - + +
172D LEU 4.6 0.7 - - - +
174D ALA* 4.5 2.7 - - + -
209D ARG* 4.0 21.5 - - - +
220D LEU* 4.2 5.8 - - + -
304D ACT 4.1 14.8 - - + -
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 5.0 3.1 - - + -
39D MSE 5.8 0.9 - - - -
42D HIS* 4.0 15.5 - + - -
89D LEU 2.8 19.0 + - - +
90D HIS* 3.4 14.8 - + - +
92D ILE* 1.3 74.8 - - - +
94D TRP* 1.3 107.3 + + - +
96D ASN* 3.2 19.9 + - - +
97D MSE 3.5 28.6 + - + +
141D TRP* 3.7 13.7 - + + -
174D ALA* 3.2 22.2 - - - -
175D LEU* 4.1 2.7 - - - -
176D ASP* 3.4 23.3 - - + -
193D TYR* 3.8 20.2 - - - -
197D TRP* 4.1 12.3 - - - -
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Residues in contact with TRP 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PRO* 4.5 7.9 - - + -
22D PRO 5.7 0.9 - - - -
23D LEU* 3.4 21.8 - - + -
24D PRO* 4.0 11.4 - - + -
25D TYR* 2.9 20.1 + - - -
39D MSE 3.4 33.2 - - + -
42D HIS* 3.6 33.0 - + + -
43D HIS* 3.5 32.9 - + + -
47D HIS* 3.0 27.1 + + - -
90D HIS* 2.9 36.3 + + - -
91D SER* 4.2 4.9 - - - -
93D PHE* 1.3 102.0 - + - +
95D PRO* 1.3 65.8 - - + +
97D MSE 2.9 23.3 + - + +
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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