Contacts of the helix formed by residues 95 - 119 (chain A) in PDB entry 5DIR
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.3 31.1 - - + +
92A LYS* 3.2 43.4 + - + +
93A LYS 3.2 0.4 + - - -
94A GLY* 1.3 76.8 - - - +
96A THR* 1.3 62.0 + - - +
97A TRP* 3.3 3.6 - - - -
98A LEU* 3.4 27.1 + - + +
99A ALA* 3.3 20.7 + - - +
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Residues in contact with THR 96 (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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12A TRP* 4.3 26.7 - - + -
94A GLY* 3.2 23.4 + - - +
95A GLU* 1.3 74.2 - - - +
97A TRP* 1.3 67.5 + - - +
99A ALA* 3.5 1.8 + - - +
100A ILE* 3.2 35.2 + - - +
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Residues in contact with TRP 97 (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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95A GLU* 5.1 0.7 - - - -
96A THR* 1.3 83.1 + - - +
98A LEU* 1.3 71.3 + - + +
100A ILE* 3.9 4.3 - - - +
101A ALA* 3.1 21.0 + - + +
152A MET* 2.7 71.3 + - + +
153A LEU* 5.5 0.7 - - + -
155A LEU* 4.8 17.0 - - + -
156A ASP* 3.7 25.1 + - + +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 4.6 18.6 - - + +
91A LEU* 3.6 31.2 - - + -
95A GLU* 3.4 26.8 + - + +
96A THR 3.4 0.2 - - - -
97A TRP* 1.3 86.6 - - + +
99A ALA* 1.3 60.9 + - - +
101A ALA* 3.3 4.9 + - - +
102A LEU* 2.9 37.1 + - + +
153A LEU* 4.8 10.1 - - + -
156A ASP* 3.2 39.7 - - - +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 5.9 0.9 - - + -
12A TRP* 3.5 45.4 - - + +
88A LEU* 3.7 18.1 - - + +
91A LEU* 3.6 7.5 - - + +
95A GLU 3.3 10.8 + - - +
96A THR* 3.8 5.2 - - - +
97A TRP 3.3 0.2 - - - -
98A LEU* 1.3 79.5 - - - +
100A ILE* 1.3 57.7 + - - +
102A LEU* 3.8 1.6 - - - +
103A ALA* 3.0 30.3 + - - +
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Residues in contact with ILE 100 (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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12A TRP* 3.5 28.9 - - + -
15A ILE* 4.3 9.4 - - + -
96A THR* 3.2 23.4 + - - +
97A TRP* 3.9 5.4 - - - +
99A ALA* 1.3 74.9 - - - +
101A ALA* 1.3 60.5 + - - +
103A ALA* 3.2 6.3 + - - +
104A LEU* 2.9 36.9 + - + +
152A MET* 4.0 16.8 - - + -
201A OLC 3.6 40.8 - - + -
204A OLC 6.2 0.4 - - + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.1 16.9 + - + +
98A LEU* 3.7 4.5 - - - +
100A ILE* 1.3 79.4 - - - +
102A LEU* 1.3 62.9 + - - +
104A LEU 3.5 0.3 + - - -
105A VAL* 3.2 29.2 + - - +
149A GLY* 3.6 26.3 - - - +
152A MET* 3.6 22.4 - - + +
153A LEU* 4.1 17.3 - - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.6 23.4 - - + +
87A TRP* 3.5 53.4 - - + +
88A LEU* 3.8 42.0 - - + +
91A LEU* 4.3 8.5 - - + -
98A LEU* 2.9 21.3 + - + +
99A ALA 3.8 3.6 - - - +
101A ALA* 1.3 76.2 - - - +
103A ALA* 1.3 60.1 - - - +
105A VAL* 3.3 6.4 + - + +
106A LEU* 2.9 30.5 + - - +
153A LEU* 4.4 12.6 - - + -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.5 29.4 - - + +
15A ILE* 3.9 16.1 - - + -
16A THR* 2.8 30.3 + - - +
88A LEU* 5.0 6.0 - - + +
99A ALA 3.0 18.4 + - - +
100A ILE* 3.6 5.4 - - - +
102A LEU* 1.3 77.8 - - - +
104A LEU* 1.3 55.4 + - - +
106A LEU* 4.4 1.3 - - - -
107A GLY* 3.0 17.5 + - - -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.3 11.0 - - + -
19A VAL* 3.9 23.1 - - + -
100A ILE* 2.9 28.1 + - + +
101A ALA 3.7 4.5 - - - +
102A LEU 3.2 0.2 - - - -
103A ALA* 1.3 77.3 - - - +
105A VAL* 1.3 61.3 + - - +
107A GLY* 3.3 1.6 + - - -
108A GLY 3.1 18.2 + - - -
145A ALA* 3.4 32.8 - - + +
148A VAL* 3.8 28.9 - - + -
149A GLY* 3.9 4.3 - - - +
152A MET* 3.9 18.2 - - - -
201A OLC 4.2 25.6 - - + -
204A OLC 4.7 3.4 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 5.6 0.2 - - + -
84A LEU* 3.6 21.3 - - + -
101A ALA 3.2 18.0 + - - +
102A LEU* 3.8 4.0 - - + +
104A LEU* 1.3 75.8 - - - +
106A LEU* 1.3 57.2 + - - +
108A GLY 3.4 0.5 + - - -
109A ALA* 2.9 27.9 + - + +
146A ILE* 3.7 19.5 - - + +
149A GLY* 3.5 26.5 - - - +
150A ALA* 3.6 8.3 - - + +
153A LEU* 4.9 9.0 - - + -
201E MLE 4.2 22.7 - - + -
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Residues in contact with LEU 106 (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 LEU* 3.7 30.5 - - + -
16A THR* 3.6 20.2 - - + +
81A SER* 3.6 47.1 - - - +
84A LEU* 4.2 11.4 - - + +
85A VAL* 3.7 19.1 - - + +
88A LEU* 5.9 0.7 - - + -
102A LEU 2.9 17.7 + - - +
103A ALA* 4.4 0.4 - - - -
104A LEU 3.2 0.2 - - - -
105A VAL* 1.3 78.0 - - - +
107A GLY* 1.3 56.8 + - - +
109A ALA* 3.2 4.1 + - + +
110A LEU* 2.9 45.9 + - + +
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.5 29.1 - - - +
19A VAL* 3.6 18.7 - - - +
20A PHE* 4.2 6.3 - - - -
23A ASP* 5.6 0.2 - - - +
103A ALA 3.0 13.1 + - - -
104A LEU 3.3 1.5 + - - -
105A VAL 3.3 0.2 - - - -
106A LEU* 1.3 76.9 - - - +
108A GLY* 1.3 55.4 + - - +
110A LEU* 3.9 2.3 - - - +
111A GLY* 3.0 25.5 + - - -
142A ALA* 5.0 0.3 - - - +
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Residues in contact with GLY 108 (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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19A VAL* 3.8 1.8 - - - +
104A LEU 3.1 10.9 + - - -
107A GLY* 1.3 72.2 - - - +
109A ALA* 1.3 65.3 + - - +
112A ASN* 3.2 21.1 + - - +
142A ALA* 3.3 40.5 - - - +
145A ALA* 4.4 1.1 - - - -
146A ILE* 3.4 15.3 - - - +
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Residues in contact with ALA 109 (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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77A ALA* 4.2 6.0 - - + +
80A VAL* 5.8 0.4 - - + -
81A SER* 3.8 18.8 - - - +
84A LEU* 5.7 2.2 - - + -
105A VAL* 2.9 20.7 + - + +
106A LEU* 3.2 7.4 + - + +
108A GLY* 1.3 76.8 - - - +
110A LEU* 1.3 57.3 + - - +
112A ASN* 3.9 1.4 - - - +
113A LEU* 2.9 30.0 + - - +
146A ILE* 3.6 7.2 - - - +
201E MLE 4.2 29.7 - - + +
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Residues in contact with LEU 110 (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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16A THR* 4.1 20.0 - - + -
20A PHE* 3.5 7.8 - - + -
81A SER* 3.7 25.8 - - - +
106A LEU* 2.9 29.1 + - + +
107A GLY* 4.1 3.6 - - - +
109A ALA* 1.3 75.1 - - - +
111A GLY* 1.3 60.7 + - - +
113A LEU* 3.6 20.9 - - + +
114A TYR* 2.9 30.8 + - - +
206A OLC 3.9 40.4 - - + +
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Residues in contact with GLY 111 (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 PHE* 3.6 17.7 - - - -
23A ASP* 3.6 22.9 - - - -
24A GLN* 3.0 20.1 + - - -
27A LYS* 3.6 4.5 + - - -
107A GLY 3.0 16.4 + - - -
108A GLY 3.7 1.6 - - - -
109A ALA 3.3 0.4 - - - -
110A LEU* 1.3 77.7 - - - +
112A ASN* 1.3 60.5 + - - +
115A ASP 3.5 8.0 + - - -
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Residues in contact with ASN 112 (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 LYS* 2.9 24.8 + - - +
108A GLY 3.2 8.6 + - - +
109A ALA 4.3 0.9 - - - +
111A GLY* 1.3 73.2 - - - +
113A LEU* 1.3 65.8 + - - +
115A ASP* 3.2 6.0 + - - +
116A ARG* 3.0 37.6 + - - +
122A VAL* 3.3 11.7 - - + +
140A ASN* 3.3 9.5 + - - -
142A ALA* 3.4 12.7 - - - +
143A ASP* 3.0 27.3 + - - -
146A ILE* 4.3 1.8 - - - +
201E MLE 3.0 26.5 + - - +
202E IIL 3.8 0.2 - - - -
203E SER 3.6 5.5 - - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.5 41.3 - - + +
77A ALA* 4.0 12.5 - - + +
78A ILE* 3.9 24.9 - - + +
109A ALA 2.9 19.7 + - - +
110A LEU* 3.6 26.2 - - + +
112A ASN* 1.3 73.2 - - - +
114A TYR* 1.3 66.1 + - - +
116A ARG* 3.2 7.9 + - - +
117A MET* 3.0 32.1 + - + +
206A OLC 4.0 21.3 - - + -
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Residues in contact with TYR 114 (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 PHE* 3.8 17.5 - + + -
24A GLN* 3.5 27.8 - - - -
110A LEU 2.9 17.4 + - - +
111A GLY 3.8 4.3 - - - +
113A LEU* 1.3 76.5 - - - +
115A ASP* 1.3 65.1 + - - +
118A VAL* 2.8 66.5 + - + +
119A LEU* 5.7 2.7 - - + -
206A OLC 3.7 34.5 - - + +
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Residues in contact with ASP 115 (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 GLN* 3.7 18.2 + - - +
27A LYS* 2.6 42.9 + - - +
111A GLY 3.5 3.5 + - - -
112A ASN 3.2 9.8 + - - +
113A LEU 3.1 0.4 - - - -
114A TYR* 1.3 84.0 - - - +
116A ARG* 1.3 50.4 + - - +
119A LEU* 2.7 62.9 + - + +
121A HIS 3.2 17.7 - - - +
122A VAL* 3.9 5.6 - - - -
123A VAL* 3.5 10.3 + - - +
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Residues in contact with ARG 116 (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 ASN 5.4 2.2 + - - +
55A THR 6.4 0.2 - - - -
69A GLN* 4.1 3.0 + - - +
70A ARG* 2.9 49.6 + - + +
73A PHE* 3.5 36.0 + - - +
74A ALA* 4.1 10.5 - - + +
77A ALA* 5.6 2.0 - - - +
112A ASN* 3.0 29.5 + - - +
113A LEU* 3.2 5.4 + - - +
115A ASP* 1.3 76.8 - - - +
117A MET* 1.3 59.2 + - - +
119A LEU 2.8 12.3 - - - +
121A HIS* 4.2 11.0 - - - +
122A VAL* 3.7 15.7 - - + +
201E MLE 3.6 22.2 + - - -
202E IIL 2.6 26.9 + - - -
203E SER* 3.0 19.6 + - - +
205E 5BV 3.6 11.9 - - - -
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Residues in contact with MET 117 (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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70A ARG* 2.8 26.3 + - - +
71A TRP* 3.4 34.8 - - + -
74A ALA* 3.4 27.8 - - + -
78A ILE* 5.3 7.4 - - + -
113A LEU* 3.0 30.5 + - + +
114A TYR 3.9 0.9 - - - +
116A ARG* 1.3 81.7 - - - +
118A VAL* 1.3 61.2 + - - +
206A OLC 3.1 68.2 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 4.5 2.8 + - - -
114A TYR* 2.8 65.0 + - + +
117A MET* 1.3 74.9 - - + +
119A LEU* 1.3 74.4 + - + +
206A OLC 4.6 19.6 - - + +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 3.7 28.9 - - - +
70A ARG* 3.8 2.6 + - - -
114A TYR* 5.7 2.5 - - + -
115A ASP* 2.7 41.6 + - - +
116A ARG 2.8 14.7 - - - +
117A MET 3.5 1.9 - - - +
118A VAL* 1.3 90.6 - - + +
120A GLY* 1.3 59.7 + - - +
121A HIS* 3.1 20.9 - - + +
123A VAL* 3.7 18.4 - - + -
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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