Contacts of the helix formed by residues 72 - 94 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 1.3 74.5 - - - +
73A ILE* 1.3 63.0 + - - +
74A ARG* 3.7 12.6 + - - +
75A ALA* 3.3 28.5 + - + +
76A VAL* 3.1 25.3 + - + +
60B LYS* 4.7 10.0 + - - -
75B ALA* 4.7 5.9 - - - +
79B ASP* 4.3 14.0 - - - +
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Residues in contact with ILE 73 (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 LEU* 3.9 22.9 - - + -
64A PHE* 5.3 0.2 - - + -
71A ILE* 3.2 25.1 + - + +
72A ASP* 1.3 73.4 + - - +
74A ARG* 1.3 65.7 + - - +
76A VAL 4.7 0.4 - - - +
77A LEU* 2.9 64.3 + - + +
128D GLU* 4.0 19.1 - - + +
131D GLN* 3.5 19.1 - - + +
132D ALA* 3.9 14.6 - - + +
135D ASN* 3.3 34.9 - - + +
157D GLN* 4.9 0.2 - - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 3.3 10.1 + - - +
73A ILE* 1.3 82.1 - - - +
75A ALA* 1.3 62.2 + - - +
77A LEU 3.9 0.5 - - - -
78A ARG* 3.0 59.6 + - - +
79B ASP* 2.8 35.9 + - - +
82B PHE* 6.2 0.2 - - - -
83B HIS* 4.8 12.1 + - - -
135D ASN* 3.2 39.9 + - + +
136D VAL 4.4 1.0 + - - -
137D GLU* 3.8 34.0 + - - +
157D GLN* 3.3 24.1 + - - +
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Residues in contact with ALA 75 (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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72A ASP* 3.2 23.4 + - + +
74A ARG* 1.3 80.2 - - - +
76A VAL* 1.3 60.3 + - + +
78A ARG 3.2 1.4 + - - -
79A ASP* 2.9 25.4 + - - -
72B ASP* 4.8 2.2 - - - +
75B ALA* 3.5 32.5 - - + -
402B BME 3.1 28.7 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 3.7 32.2 - - + +
60A LYS* 3.8 26.7 - - + +
61A LEU* 4.0 19.5 - - + -
71A ILE* 3.9 23.8 - - + -
72A ASP* 3.1 17.9 + - + +
73A ILE 4.4 1.1 - - - +
75A ALA* 1.3 78.1 - - + +
77A LEU* 1.3 57.4 + - - +
79A ASP* 3.3 9.1 + - - +
80A LEU* 2.8 26.5 + - - +
72B ASP* 6.1 0.2 - - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.1 16.4 - - + -
73A ILE* 2.9 52.9 + - + +
74A ARG 4.2 2.0 - - - +
76A VAL* 1.3 74.4 - - - +
78A ARG* 1.3 64.0 + - - +
80A LEU* 3.7 17.7 - - + +
81A SER* 3.1 23.9 + - - -
128D GLU* 4.9 2.0 - - - +
132D ALA* 3.7 19.7 - - + -
155D ILE* 3.3 30.7 - - + +
156D LEU* 4.0 5.7 - - - +
157D GLN* 4.0 29.2 + - + +
164D MSE 4.7 2.4 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.0 49.0 + - + +
75A ALA 3.2 4.7 + - - +
77A LEU* 1.3 74.0 - - - +
79A ASP* 1.3 68.3 + - - +
81A SER* 3.4 2.1 + - - -
82A PHE* 3.1 24.8 + - - +
162A ASN* 4.4 2.4 + - - -
78B ARG* 3.8 46.1 - - - +
79B ASP* 4.7 3.2 + - - -
160B LYS* 3.6 5.3 - - - +
402B BME 3.6 15.6 - - - -
137C GLU* 4.5 4.1 - - - +
137D GLU* 2.9 32.7 + - - +
157D GLN* 4.7 0.7 - - - +
159D GLU* 2.8 28.5 + - - -
164D MSE 3.6 28.8 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY 5.5 0.2 - - - +
57A ALA* 4.3 11.3 - - + +
60A LYS* 4.4 12.0 + - - +
75A ALA 2.9 16.2 + - - +
76A VAL* 3.4 15.0 - - - +
78A ARG* 1.3 77.8 - - - +
80A LEU* 1.3 62.5 + - - +
82A PHE* 3.4 0.7 + - - +
83A HIS* 3.0 39.7 + - + +
72B ASP* 4.1 5.5 - - - +
74B ARG* 2.8 29.0 + - - -
402B BME 3.0 26.0 - - - +
137C GLU* 4.4 5.8 - - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.3 11.7 - - + +
57A ALA* 4.0 11.6 - - + +
58A LEU* 4.1 26.9 - - + -
61A LEU* 4.1 20.9 - - + -
76A VAL 2.8 16.1 + - - +
77A LEU* 3.7 12.8 - - + +
78A ARG 3.3 0.2 - - - -
79A ASP* 1.3 76.4 - - - +
81A SER* 1.3 57.0 + - - +
83A HIS* 5.1 1.8 - - - -
84A LEU* 2.7 50.4 + - + +
154D LEU* 4.1 26.5 - - + -
155D ILE 4.2 2.9 - - - +
156D LEU* 3.8 22.7 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 3.1 15.9 + - - -
78A ARG 3.8 2.2 - - - -
80A LEU* 1.3 77.6 - - - +
82A PHE* 1.3 64.7 + - - +
84A LEU* 4.6 4.0 - - - -
85A ASN* 2.9 32.0 + - - +
162A ASN* 2.9 27.3 + - - +
156D LEU* 4.4 12.1 - - - +
157D GLN 5.6 0.2 - - - -
164D MSE 2.9 35.7 + - - -
166D ALA* 6.2 0.7 - - - +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.9 22.4 - + - -
78A ARG 3.1 12.2 + - - +
79A ASP 3.7 2.2 - - - +
81A SER* 1.3 80.4 + - - +
83A HIS* 1.3 81.2 + + - +
86A GLY 3.0 22.5 + - - -
160A LYS* 4.0 10.1 - - + -
161A HIS* 3.7 20.4 + - - +
162A ASN* 3.5 21.9 - - - +
178A TRP* 3.5 39.5 - + - -
137C GLU* 3.3 52.5 - - + +
138C GLY 4.5 3.1 - - - -
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Residues in contact with HIS 83 (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 GLY 3.9 4.3 + - - -
50A TYR* 3.5 33.3 - + - +
53A GLY* 3.5 31.3 + - - -
54A ALA* 3.4 20.6 - - - +
79A ASP* 3.0 29.3 + - + +
82A PHE* 1.3 97.8 - + - +
84A LEU* 1.3 67.3 + - - +
86A GLY 3.2 0.9 + - - +
87A HIS* 3.0 23.7 + - - +
74B ARG* 4.8 16.4 - - - -
137C GLU* 5.1 0.7 - - - -
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Residues in contact with LEU 84 (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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18A TYR* 3.5 45.8 - - + +
54A ALA* 4.3 7.5 - - + +
80A LEU* 2.7 35.5 + - + +
81A SER* 4.2 2.5 - - - +
83A HIS* 1.3 72.1 - - - +
85A ASN* 1.3 56.1 + - - +
87A HIS* 3.4 4.1 + - + +
88A ILE* 2.9 43.5 + - + +
147D GLU* 3.9 17.5 - - + -
154D LEU* 3.9 15.7 - - + -
156D LEU* 5.4 3.8 - - + -
166D ALA* 3.7 30.1 - - + -
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Residues in contact with ASN 85 (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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81A SER* 2.9 26.9 + - - +
84A LEU* 1.3 72.4 - - - +
86A GLY* 1.3 68.3 + - - +
87A HIS 3.1 2.0 - - - -
88A ILE* 4.3 3.9 - - - +
89A LEU* 2.8 29.1 + - - +
161A HIS* 3.1 28.7 - - + +
162A ASN* 3.2 8.1 - - - +
165A HIS* 3.4 14.3 + - - -
165D HIS 2.8 19.1 - - - +
166D ALA* 3.7 5.9 - - - +
167D ALA* 2.9 36.8 - - - +
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Residues in contact with GLY 86 (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 TYR* 4.0 8.1 - - - -
82A PHE 3.0 11.3 + - - -
83A HIS 3.2 3.3 + - - -
85A ASN* 1.3 76.2 - - - +
87A HIS* 1.3 56.4 + - - +
89A LEU* 4.0 0.6 - - - +
90A HIS* 2.7 39.5 + - - -
161A HIS* 3.2 36.0 - - - +
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Residues in contact with HIS 87 (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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18A TYR* 3.5 38.3 - + + +
19A THR 3.3 26.7 + - - -
21A PRO* 3.6 6.7 - - + -
47A HIS* 2.7 31.9 + - - -
50A TYR* 3.9 8.8 - - + +
51A VAL* 3.5 15.8 - - + +
54A ALA* 5.5 1.3 - - + -
83A HIS 3.0 12.6 + - - +
84A LEU* 3.6 9.6 - - + +
86A GLY* 1.3 74.7 - - - +
88A ILE* 1.3 65.9 + - - +
90A HIS 3.3 0.3 + - - -
91A SER* 2.9 43.5 + - - -
149D LEU* 3.5 23.5 - - + +
150D GLU* 5.9 0.4 + - - -
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Residues in contact with ILE 88 (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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84A LEU* 2.9 50.3 + - + +
85A ASN* 3.3 6.5 + - - +
87A HIS* 1.3 73.6 - - - +
89A LEU* 1.3 64.0 + - - +
91A SER* 3.3 3.3 + - - -
92A ILE* 3.2 35.3 + - + +
220A LEU* 4.4 13.8 - - + +
147D GLU* 3.9 19.5 - - - +
149D LEU* 4.3 19.3 - - + -
166D ALA* 4.6 2.2 - - + -
167D ALA* 3.6 48.2 - - + +
168D ASP* 5.0 0.7 - - + -
169D ALA* 6.1 0.2 - - + -
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Residues in contact with LEU 89 (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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85A ASN 2.8 22.0 + - - +
88A ILE* 1.3 72.6 - - - +
90A HIS* 1.3 59.3 + - - +
92A ILE* 3.3 7.7 + - + +
93A PHE* 2.9 27.4 + - - +
141A TRP* 3.5 49.0 - - + +
143A ILE* 4.6 2.9 - - + -
158A ILE* 4.4 1.8 - - + -
161A HIS* 3.5 24.7 - - - +
165A HIS* 3.7 25.1 - - + +
171A VAL* 4.3 28.5 - - + -
174A ALA* 4.5 9.6 - - + +
167D ALA* 4.3 7.0 - - + -
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Residues in contact with HIS 90 (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 HIS* 2.6 43.4 + + - -
47A HIS* 3.3 31.4 - + + +
50A TYR* 3.4 27.7 - + - -
86A GLY 2.7 29.8 + - - +
89A LEU* 1.3 74.4 - - - +
91A SER* 1.3 64.1 + - - +
93A PHE* 3.5 6.0 - + - +
94A TRP* 3.0 45.7 + + - -
141A TRP* 3.4 23.0 - + - -
161A HIS* 3.7 7.0 - - - -
176A ASP* 3.2 5.8 + - - -
180A HIS* 4.7 2.0 - - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.9 11.3 - - - +
47A HIS* 3.8 6.8 - - - -
87A HIS* 2.9 45.6 + - - -
88A ILE* 3.5 7.2 - - - -
89A LEU 3.2 0.2 - - - -
90A HIS* 1.3 77.5 - - - +
92A ILE* 1.3 54.2 + - - +
94A TRP* 4.4 2.7 - - - -
95A PRO* 2.8 33.3 - - - +
209A ARG* 4.8 0.2 + - - -
220A LEU* 5.1 7.6 - - - -
149D LEU* 4.2 11.5 - - - +
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Residues in contact with ILE 92 (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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88A ILE* 3.2 31.3 + - + +
89A LEU* 3.7 10.3 - - + +
90A HIS 3.2 0.2 - - - -
91A SER* 1.3 77.2 - - - +
93A PHE* 1.3 53.7 + - - +
95A PRO* 3.5 6.0 - - - +
96A ASN* 2.8 54.6 + - - +
171A VAL* 3.6 48.7 - - + +
172A LEU 4.7 0.9 - - - +
174A ALA* 4.6 3.4 - - + -
209A ARG* 4.3 24.6 + - - +
219A ALA 6.0 0.2 - - - +
220A LEU* 4.8 9.2 - - + -
168D ASP* 4.3 10.3 - - - +
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Residues in contact with PHE 93 (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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34A ILE* 5.0 4.0 - - + -
39A MSE 6.0 0.4 - - - -
42A HIS* 3.7 21.1 - + - -
89A LEU 2.9 17.4 + - - +
90A HIS* 3.3 7.8 + + - +
92A ILE* 1.3 74.4 - - - +
94A TRP* 1.3 98.4 + + - +
96A ASN* 2.9 20.1 - - - +
97A MSE 3.5 35.2 + - + +
141A TRP* 3.8 9.9 - + + -
174A ALA* 3.2 22.7 - - - -
175A LEU* 4.1 0.9 - - + -
176A ASP* 3.5 26.2 - - + -
193A TYR* 3.6 21.5 - - - -
197A TRP* 3.9 18.2 - + - -
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Residues in contact with TRP 94 (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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21A PRO* 4.5 7.6 - - + -
22A PRO 5.6 1.1 - - - +
23A LEU* 3.5 15.9 - - + -
24A PRO* 3.8 19.5 - - + -
25A TYR* 2.9 18.7 + - - -
39A MSE 3.4 29.8 - - + -
42A HIS* 3.3 36.3 - + + -
43A HIS* 3.6 28.4 - + + -
47A HIS* 2.9 29.0 + + - -
90A HIS* 3.0 35.4 + + - -
91A SER* 4.4 4.0 - - - -
93A PHE* 1.3 93.8 - + - +
95A PRO* 1.4 64.9 - - + +
97A MSE 2.9 31.1 + - + +
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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