Contacts of the helix formed by residues 76 - 106 (chain A) in PDB entry 1EMR
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 THR 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY* 1.3 74.1 - - - +
77A GLU* 1.3 70.0 + - - +
78A LYS* 2.8 9.3 + - - +
79A ALA* 2.9 30.1 + - - +
80A LYS 3.2 4.7 + - - -
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Residues in contact with GLU 77 (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 MET* 4.0 22.6 - - + +
75A GLY 3.2 3.4 + - - -
76A THR* 1.3 69.4 - - - +
78A LYS* 1.3 64.7 + - - +
80A LYS* 3.1 32.5 + - - +
81A LEU* 3.3 17.0 + - + +
133A ARG* 3.3 29.4 + - - +
138A TYR* 3.2 33.8 + - - +
181A PHE* 5.3 2.7 - - + -
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Residues in contact with LYS 78 (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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76A THR* 2.8 13.0 + - - +
77A GLU* 1.3 74.3 - - - +
79A ALA* 1.3 64.9 + - - +
81A LEU* 3.2 15.1 + - - +
82A VAL* 3.4 15.5 + - + +
134A LEU* 5.0 2.3 - - + +
138A TYR* 3.0 59.8 + - + -
139A HIS 3.8 11.9 + - - -
140A VAL* 3.1 33.2 - - + -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY* 4.8 4.9 - - - -
76A THR* 2.9 26.6 + - - +
78A LYS* 1.3 73.4 - - - +
80A LYS* 1.3 58.1 + - + +
81A LEU 2.9 4.0 - - - -
82A VAL* 2.7 29.8 + - + +
83A GLU* 3.1 21.7 + - + +
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Residues in contact with LYS 80 (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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71A PHE* 3.6 12.1 - - + -
72A HIS 4.0 16.2 - - - +
73A ALA 3.2 23.7 + - - +
75A GLY* 3.0 30.2 + - - +
76A THR 3.2 0.8 + - - +
77A GLU* 3.1 30.4 + - - +
79A ALA* 1.3 75.3 - - + +
81A LEU* 1.3 60.1 + - - +
83A GLU* 4.0 3.1 - - - +
84A LEU* 3.0 27.7 + - - +
180A ALA* 4.2 27.0 + - + +
181A PHE* 3.4 21.1 - - + -
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Residues in contact with LEU 81 (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 MET* 4.6 10.8 - - + -
27A ILE* 6.2 2.2 - - + -
77A GLU* 3.3 20.2 + - + +
78A LYS* 3.2 8.9 + - - +
79A ALA 2.8 1.2 + - - -
80A LYS* 1.3 74.4 - - - +
82A VAL* 1.3 69.8 + - - +
83A GLU 3.2 0.4 - - - -
84A LEU* 3.8 7.2 - - + -
85A TYR* 3.2 20.3 + - - +
130A VAL* 3.2 36.3 - - + +
133A ARG* 3.9 23.6 - - + -
134A LEU* 3.3 27.0 - - + +
138A TYR* 5.5 0.7 - - + -
181A PHE* 3.2 34.1 - - + -
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Residues in contact with VAL 82 (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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78A LYS* 3.4 11.5 + - + +
79A ALA* 2.7 15.9 + - + +
81A LEU* 1.3 77.8 - - - +
83A GLU* 1.3 67.0 + - + +
85A TYR* 3.0 8.0 + - - +
86A ARG* 2.8 54.1 + - - +
134A LEU* 5.2 4.5 - - + -
140A VAL* 5.1 17.7 - - + -
143A VAL* 4.6 15.3 - - + -
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Residues in contact with GLU 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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70A PRO* 3.8 21.3 - - + +
71A PHE* 3.2 26.9 - - + -
72A HIS* 3.1 52.2 + - - +
79A ALA* 3.1 21.0 + - + +
80A LYS* 4.0 3.3 - - - +
82A VAL* 1.3 81.7 - - + +
84A LEU* 1.3 66.4 + - - +
86A ARG* 3.1 12.2 - - - +
87A ILE* 2.7 29.5 + - - +
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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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27A ILE* 3.6 23.6 - - + -
31A LEU* 4.6 4.7 - - + -
71A PHE* 4.2 0.6 - - - -
80A LYS 3.0 18.3 + - - +
81A LEU* 4.2 6.1 - - + +
83A GLU* 1.3 80.7 - - - +
85A TYR* 1.3 59.1 + - - +
87A ILE* 3.6 10.0 - - + +
88A VAL* 2.9 29.6 + - + +
126A LEU* 3.8 19.3 - - + -
130A VAL* 3.4 28.9 - - + -
177A LEU* 3.3 27.4 - - + -
181A PHE* 3.7 19.5 - - + -
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 3.2 12.8 + - - +
82A VAL* 3.0 10.4 + - - +
84A LEU* 1.3 76.4 - - - +
86A ARG* 1.3 72.1 + - + +
87A ILE 2.7 2.4 + - - -
88A VAL* 2.8 17.3 + - - +
89A VAL* 2.8 24.1 + - + +
127A LEU* 3.3 50.0 - - + +
130A VAL* 4.0 10.3 - - + +
131A LEU* 3.9 32.0 - - + +
134A LEU* 4.3 8.3 - - + -
143A VAL* 4.0 29.4 - - + -
145A VAL* 5.1 9.4 - - + -
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Residues in contact with ARG 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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69A PRO* 3.3 20.2 - - + +
70A PRO* 5.6 8.3 - - + +
82A VAL* 2.8 48.3 + - - +
83A GLU* 3.1 17.1 - - - +
85A TYR* 1.3 75.6 - - + +
87A ILE* 1.3 61.5 + - - +
89A VAL* 3.1 19.1 - - - +
90A TYR* 3.4 6.2 + - - +
143A VAL* 3.6 17.3 - - - +
144A ASP* 2.8 31.1 + - - +
145A VAL* 3.8 21.6 - - + +
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Residues in contact with ILE 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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68A PHE* 3.7 27.1 - - + -
69A PRO* 3.2 29.2 - - + +
70A PRO 3.6 16.4 - - - +
71A PHE* 3.7 22.7 - - + -
83A GLU 2.7 29.0 + - - +
84A LEU* 3.8 9.4 - - + +
85A TYR 2.7 1.0 + - - -
86A ARG* 1.3 75.4 - - - +
88A VAL* 1.3 53.2 + - + +
89A VAL 2.6 1.4 + - - -
90A TYR* 2.5 28.8 + - - +
91A LEU* 2.7 25.8 + - + -
173A VAL* 6.1 0.7 - - + -
177A LEU* 4.5 20.2 - - + -
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Residues in contact with VAL 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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34A LEU* 5.9 1.1 - - + -
84A LEU* 2.9 19.2 + - + +
85A TYR* 2.8 6.6 + - - +
87A ILE* 1.3 76.6 - - + +
89A VAL* 1.3 60.0 + - - +
91A LEU* 3.4 10.6 - - + +
92A GLY* 2.9 25.3 + - - -
123A LEU* 3.7 29.4 - - + +
126A LEU* 3.4 32.3 - - + +
127A LEU* 3.5 40.6 - - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 2.8 30.2 + - + +
86A ARG* 3.1 24.7 - - - +
87A ILE 2.6 4.6 + - - -
88A VAL* 1.3 72.7 - - - +
90A TYR* 1.3 61.1 + - - +
91A LEU 2.9 4.0 + - - -
92A GLY* 3.3 0.6 + - - -
93A THR* 2.9 27.0 + - - +
127A LEU* 4.2 15.7 - - + -
145A VAL* 3.5 18.8 - - + -
147A TYR* 3.2 39.5 - - + +
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Residues in contact with TYR 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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65A VAL* 2.8 26.2 - - + +
67A ASP 3.4 20.0 + - - -
68A PHE* 3.4 26.2 - + - -
69A PRO* 3.3 36.8 - - + -
86A ARG 3.4 4.9 - - - +
87A ILE 2.5 6.7 + - - -
89A VAL* 1.3 77.4 - - + +
91A LEU* 1.3 60.7 + - - +
93A THR* 4.1 5.1 - - - +
94A SER* 2.8 47.7 + - - -
145A VAL* 5.3 4.5 - - + -
146A THR 5.2 1.8 - - - -
147A TYR* 4.6 2.5 - - - +
148A GLY* 3.2 39.9 - - - +
149A PRO* 3.6 16.6 - - + +
166A LEU* 4.2 4.4 - - + +
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Residues in contact with LEU 91 (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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68A PHE* 3.9 15.5 - - + -
87A ILE* 2.7 26.8 + - + +
88A VAL* 3.4 15.3 - - + +
89A VAL 2.9 0.8 + - - -
90A TYR* 1.3 74.9 - - - +
92A GLY* 1.3 57.8 + - - +
94A SER* 2.6 26.5 + - - -
95A LEU* 2.7 24.3 + - + +
123A LEU* 3.6 14.1 - - + -
166A LEU* 3.7 27.6 - - + -
170A TYR* 3.5 39.5 - - + -
173A VAL* 5.7 2.7 - - + -
174A ILE* 5.9 0.9 - - + -
177A LEU* 6.0 2.5 - - + -
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Residues in contact with GLY 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 VAL 2.9 17.0 + - - -
89A VAL* 3.9 0.4 - - - -
91A LEU* 1.3 72.7 - - - +
93A THR* 1.3 62.7 + - - +
95A LEU* 3.0 8.5 + - - +
96A GLY* 2.9 21.3 + - - -
120A ALA* 5.7 5.3 - - - +
123A LEU* 3.3 19.8 - - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 2.9 17.6 + - - +
90A TYR 4.1 4.0 - - - +
92A GLY* 1.3 76.9 - - - +
94A SER* 1.3 72.7 + - - +
95A LEU 2.9 1.4 + - - -
96A GLY* 3.0 9.9 + - - -
97A ASN* 3.3 18.4 + - - +
147A TYR* 3.6 37.9 - - + -
148A GLY* 4.7 8.1 - - - +
149A PRO 5.3 4.9 - - - +
150A ASP* 6.2 0.2 - - - +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.8 41.9 + - - -
91A LEU 2.6 9.5 + - - -
93A THR* 1.3 79.8 - - - +
95A LEU* 1.3 60.2 + - - -
97A ASN* 3.1 17.9 + - - +
98A ILE* 3.2 13.7 + - - +
148A GLY* 5.6 0.2 - - - -
149A PRO* 5.3 5.6 + - - +
166A LEU* 3.1 32.8 - - - +
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Residues in contact with LEU 95 (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 LEU* 6.3 1.3 - - + -
91A LEU* 2.7 33.2 + - + +
92A GLY* 3.4 7.9 - - - +
94A SER* 1.3 77.4 - - - +
96A GLY* 1.3 70.4 + - - +
98A ILE* 2.9 18.9 + - + +
99A THR* 3.0 17.6 + - - +
116A LEU* 4.7 10.7 - - + +
119A THR* 4.2 26.9 - - + -
120A ALA* 4.3 13.7 - - + +
123A LEU* 4.1 22.2 - - + -
166A LEU* 3.6 19.5 - - + -
167A LEU* 5.1 13.7 - - + -
170A TYR* 5.7 4.9 - - + -
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Residues in contact with GLY 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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92A GLY 2.9 13.9 + - - -
93A THR* 3.0 4.0 + - - -
95A LEU* 1.3 72.4 - - - +
97A ASN* 1.3 64.0 + - - +
99A THR* 2.8 18.7 + - - -
100A ARG* 2.9 31.5 + - - +
120A ALA* 6.0 1.0 - - - +
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 3.3 17.1 + - - +
94A SER* 3.1 14.3 + - - +
95A LEU 3.0 0.8 - - - -
96A GLY* 1.3 75.3 - - - +
98A ILE* 1.3 66.3 + - + +
100A ARG* 3.1 9.7 + - - +
101A ASP* 3.0 29.4 + - - +
149A PRO 3.7 20.8 + - - -
150A ASP* 4.2 21.0 + - - +
151A THR* 4.4 25.2 - - + +
152A SER* 5.7 2.1 - - - -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.5 32.8 - - + -
94A SER 3.2 15.7 - - - +
95A LEU* 2.9 11.2 + - + +
97A ASN* 1.3 75.3 - - + +
99A THR* 1.3 58.0 + - - +
101A ASP* 3.1 8.8 + - - +
102A GLN* 2.8 36.7 + - + +
116A LEU* 4.9 11.0 - - + -
159A LYS 6.2 0.2 - - - -
163A GLY* 3.1 39.3 - - - +
166A LEU* 3.5 22.7 - - + -
167A LEU* 4.2 12.3 - - + -
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.0 12.3 + - - +
96A GLY* 2.8 11.7 + - - -
98A ILE* 1.3 73.2 - - - +
100A ARG* 1.3 70.1 + - - +
101A ASP 3.0 2.3 + - - -
102A GLN* 3.9 1.0 - - - +
103A LYS* 2.9 46.1 + - + +
113A HIS* 5.1 5.2 - - + +
116A LEU* 3.5 36.1 + - + +
117A ASN* 3.7 25.1 + - - +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY* 2.9 25.9 + - - +
97A ASN* 3.8 8.7 - - - +
99A THR* 1.3 81.8 - - - +
101A ASP* 1.3 65.4 + - - +
103A LYS* 3.5 32.4 + - - +
104A ILE* 3.8 12.6 + - - +
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Residues in contact with ASP 101 (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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97A ASN* 3.0 20.4 + - - +
98A ILE* 3.4 10.1 - - - +
99A THR 3.0 0.6 - - - -
100A ARG* 1.3 79.1 - - - +
102A GLN* 1.3 71.3 + - - +
104A ILE* 3.2 7.6 + - - +
105A LEU* 3.0 33.2 + - + +
151A THR* 4.1 8.5 - - - +
159A LYS* 2.7 56.8 + - + +
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.2 34.4 + - + -
49A GLN* 3.1 12.8 + - - -
98A ILE* 2.8 35.0 + - + +
99A THR 4.1 2.2 - - - +
101A ASP* 1.3 78.6 - - - +
103A LYS* 1.3 65.0 + - - +
105A LEU* 3.7 16.7 - - - +
106A ASN* 2.7 49.3 + - - +
112A LEU* 4.0 6.5 - - + +
113A HIS* 2.9 30.7 + - + +
116A LEU* 4.1 13.2 - - + -
159A LYS 5.2 1.4 + - - -
160A LYS* 4.9 1.0 - - - +
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Residues in contact with LYS 103 (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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99A THR* 2.9 34.2 + - + +
100A ARG* 3.6 28.3 - - - +
101A ASP 3.3 0.2 - - - -
102A GLN* 1.3 79.3 - - - +
104A ILE* 1.3 67.9 + - + +
107A PRO* 3.6 20.5 - - - +
113A HIS* 3.6 16.8 + - + -
117A ASN* 6.1 0.8 - - - +
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Residues in contact with ILE 104 (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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100A ARG 3.8 13.0 + - - +
101A ASP* 3.2 6.6 + - - +
102A GLN 3.2 0.2 - - - -
103A LYS* 1.3 77.5 - - + +
105A LEU* 1.3 70.1 + - + +
107A PRO* 2.8 23.7 - - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 3.0 29.4 + - + +
102A GLN* 4.2 14.4 - - - +
104A ILE* 1.3 88.7 - - + +
106A ASN* 1.3 76.0 + - - +
107A PRO* 3.1 5.9 - - - +
156A VAL* 4.6 18.8 - - + +
159A LYS* 5.1 11.7 - - + +
160A LYS* 3.4 43.5 - - + +
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.4 29.1 + - - +
49A GLN* 3.5 16.6 + - - +
102A GLN* 2.7 42.7 + - + +
105A LEU* 1.3 86.2 - - - +
107A PRO* 1.3 52.5 - - - +
108A SER* 2.7 18.7 + - - +
109A ALA* 2.9 18.9 + - + +
112A LEU* 4.8 0.2 - - - +
113A HIS* 2.9 15.3 - - - +
160A LYS* 4.6 8.8 + - - -
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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).
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