Contacts of the helix formed by residues 87 - 116 (chain A) in PDB entry 3KWO
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.0 1.8 - - - -
29A LYS 3.7 3.4 - - - +
86A PHE* 1.3 76.4 - - - +
88A PRO* 1.3 75.2 - - + +
89A LEU* 3.7 7.1 + - - +
90A GLU* 3.0 38.0 + - - +
91A VAL* 3.1 21.5 + - - +
151A ACY 5.5 0.9 - - - +
145B GLY* 5.8 1.1 - - - -
146B ALA* 3.7 22.2 - - + +
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.9 15.2 - - + -
29A LYS 3.2 17.9 - - - +
30A GLY* 4.5 4.5 - - - -
32A GLN* 3.4 44.2 - - + +
36A ILE* 4.0 16.9 - - + +
87A THR* 1.3 87.4 - - - +
89A LEU* 1.3 62.9 + - + +
91A VAL* 3.2 4.3 + - - +
92A ILE* 3.1 32.2 + - + +
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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
----------------------------------------------------------
87A THR* 3.3 6.1 + - - +
88A PRO* 1.3 79.5 - - + +
90A GLU* 1.3 57.8 + - - +
92A ILE* 3.2 12.9 + - + +
93A GLU* 2.9 43.4 + - - +
142A THR* 4.8 8.5 - - + +
143A LEU* 3.9 26.2 - - + +
151A ACY 5.4 3.6 - - - +
159A ACY 5.3 18.2 - - + +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 3.3 33.1 + - - -
86A PHE* 3.4 11.8 - - + -
87A THR* 3.0 46.8 + - - +
89A LEU* 1.3 75.9 - - + +
91A VAL* 1.3 58.3 + - - +
93A GLU* 3.7 7.3 - - - +
94A LEU* 2.9 40.2 + - + +
151A ACY 3.3 35.1 - - + +
146B ALA* 4.4 2.2 - - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.8 28.9 - - + -
28A VAL* 4.0 18.8 - - + -
36A ILE* 3.8 24.0 - - + -
39A TYR* 6.4 0.2 - - + -
40A THR* 4.1 4.7 - - + -
86A PHE* 3.4 31.9 - - + -
87A THR 3.1 8.4 + - - +
88A PRO 3.6 6.3 - - - +
90A GLU* 1.3 74.4 - - - +
92A ILE* 1.3 59.8 + - - +
94A LEU* 3.2 6.5 + - - +
95A ILE* 2.9 39.1 + - + +
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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
----------------------------------------------------------
36A ILE* 4.0 20.9 - - + -
88A PRO* 3.1 23.3 + - + +
89A LEU* 3.7 14.4 - - + +
91A VAL* 1.3 78.1 - - + +
93A GLU* 1.3 56.2 + - - +
95A ILE* 3.8 5.3 - - - +
96A LYS* 3.0 28.2 + - - +
139A ILE* 3.8 18.0 - - + +
142A THR* 4.1 26.2 - - + -
143A LEU* 3.5 27.1 - - + -
158A ACY 5.1 10.5 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 2.9 25.3 + - - +
90A GLU* 3.7 7.8 - - - +
92A ILE* 1.3 75.9 - - - +
94A LEU* 1.3 63.2 + - + +
96A LYS* 3.3 6.5 + - - +
97A GLN* 3.2 25.5 + - - +
143A LEU* 3.8 28.5 - - + +
151A ACY 3.0 11.7 - - - +
159A ACY 3.3 6.9 - - - +
164A ZN 2.1 36.8 - - - -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 5.0 0.4 + - - +
24A TYR* 3.5 21.5 - - + +
81A VAL* 4.0 22.2 - - + -
83A LYS* 5.1 5.6 - - + -
86A PHE* 3.6 36.8 - - + -
90A GLU* 2.9 26.6 + - + +
91A VAL* 3.7 3.6 - - - +
93A GLU* 1.3 76.7 - - + +
95A ILE* 1.3 60.6 + - - +
97A GLN* 3.1 13.7 + - + +
98A ASP* 3.0 32.3 + - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.7 24.2 - - + -
24A TYR* 3.6 30.5 - - + -
39A TYR* 4.4 18.2 - - + -
40A THR* 4.6 9.0 - - + -
43A ALA* 5.0 1.8 - - + -
91A VAL* 2.9 26.1 + - + +
92A ILE* 3.8 5.4 - - - +
94A LEU* 1.3 73.1 - - - +
96A LYS* 1.3 67.7 + - - +
98A ASP* 3.6 4.6 - - - +
99A TYR* 2.8 52.6 + - + +
139A ILE* 4.0 9.6 - - + -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE 3.0 15.4 + - - +
93A GLU* 3.4 11.0 - - - +
95A ILE* 1.3 76.6 - - - +
97A GLN* 1.3 71.0 + - + +
99A TYR* 4.7 0.2 - - - -
100A GLU* 2.9 55.1 + - - +
136A LEU* 3.8 20.3 - - + +
139A ILE* 3.6 16.1 - - + +
140A GLY* 4.7 15.5 - - - +
143A LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 4.3 14.9 - - + +
93A GLU 3.2 13.9 + - - +
94A LEU* 3.1 17.0 + - + +
96A LYS* 1.3 83.6 + - - +
98A ASP* 1.3 57.0 + - - +
100A GLU* 3.4 21.3 + - - +
101A TYR* 3.0 27.7 + - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.6 18.0 - - + +
20A LYS* 2.5 32.0 + - - -
21A PHE* 3.4 15.0 - - + -
24A TYR* 2.6 33.1 + - - -
79A PRO* 3.7 11.2 - - - +
94A LEU 3.0 16.2 + - - +
95A ILE* 3.1 6.4 + - - +
97A GLN* 1.3 76.0 - - - +
99A TYR* 1.3 58.8 + - + +
101A TYR* 3.3 9.1 + - - +
102A LEU* 2.9 30.6 + - - +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.0 22.4 - + - -
39A TYR* 3.5 26.4 + - - -
43A ALA* 3.7 24.1 - - - +
46A GLU* 4.3 9.5 + - - -
47A MSE 5.5 0.8 - - + +
95A ILE* 2.8 29.7 + - + +
98A ASP* 1.3 75.3 - - + +
100A GLU* 1.3 60.5 + - - +
102A LEU* 3.7 11.4 - - + +
103A LEU* 2.9 31.2 + - - +
132A TYR* 3.6 39.5 + + + +
135A SER* 4.2 11.7 - - - -
136A LEU* 3.7 20.2 - - + +
139A ILE* 3.5 20.0 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS* 2.9 56.1 + - - +
97A GLN* 3.8 24.5 + - - +
99A TYR* 1.3 75.9 - - - +
101A TYR* 1.3 63.5 + - - +
103A LEU* 3.5 4.0 + - + +
104A ALA* 3.0 24.3 + - - +
136A LEU* 3.7 22.2 - - + +
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 4.1 1.9 + - - +
13A ASP* 2.6 37.0 + - + -
17A LEU* 4.9 0.4 - - + -
77A LYS* 3.4 31.1 - - + +
78A SER* 3.6 28.9 - - - -
79A PRO* 4.0 16.4 - - + -
97A GLN 3.0 14.2 + - - +
98A ASP 3.4 9.9 - - - +
100A GLU* 1.3 74.5 - - - +
102A LEU* 1.3 75.7 + - + +
104A ALA* 3.2 8.6 + - + +
105A GLU* 3.0 52.7 + - + +
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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
----------------------------------------------------------
10A MSE 3.5 25.7 - - + +
13A ASP* 5.1 5.2 - - + -
14A ALA 5.7 0.7 - - - +
17A LEU* 3.8 21.1 - - + -
47A MSE 3.8 26.0 - - + -
50A LEU* 4.4 8.7 - - + -
98A ASP 2.9 14.3 + - - +
99A TYR* 3.3 17.5 + - + +
101A TYR* 1.3 82.4 - - + +
103A LEU* 1.3 53.8 + - - +
105A GLU* 3.0 4.4 + - - +
106A PHE* 2.7 47.9 + - + -
132A TYR* 3.8 30.3 - - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR 2.9 18.8 + - - +
100A GLU* 3.7 4.9 - - - +
102A LEU* 1.3 77.5 - - - +
104A ALA* 1.3 63.4 + - - +
106A PHE* 3.3 5.9 + - - +
107A LYS* 3.0 45.9 + - + +
129A ILE* 3.9 44.6 - - + +
132A TYR* 4.3 9.2 - - + +
133A GLU* 4.1 14.4 - - + +
136A LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU 3.0 17.7 + - - +
101A TYR* 3.2 7.4 + - + +
103A LEU* 1.3 76.1 - - - +
105A GLU* 1.3 66.9 + - - +
107A LYS* 3.3 11.1 + - - +
108A LYS* 3.2 26.5 + - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.1 26.2 - - - +
9A GLN* 4.2 9.4 - - - +
10A MSE 4.0 21.9 - - + +
13A ASP* 4.5 2.7 - - - +
101A TYR* 3.0 56.6 + - + +
102A LEU 3.0 7.4 + - - +
104A ALA* 1.3 78.1 - - - +
106A PHE* 1.3 63.2 + - - +
108A LYS* 3.2 30.4 + - - +
109A LEU* 2.9 26.3 + - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MSE 3.7 28.9 - - + -
50A LEU* 3.7 28.9 - - + -
102A LEU* 2.7 37.7 + - + +
103A LEU* 3.8 3.8 - - - +
105A GLU* 1.3 75.0 - - - +
107A LYS* 1.3 56.1 + - - +
109A LEU* 3.5 7.8 - - + +
110A ASN* 2.9 28.1 + - - +
124A PHE* 4.3 9.4 - + - -
125A ALA* 3.7 17.2 - - - +
128A ASN* 3.5 40.6 - - + -
129A ILE* 3.7 20.0 - - + +
132A TYR* 3.6 30.1 - + - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.0 43.9 + - + +
104A ALA* 3.6 12.1 - - - +
105A GLU 3.2 0.2 - - - -
106A PHE* 1.3 73.2 - - - +
108A LYS* 1.3 66.4 + - + +
110A ASN* 3.4 3.0 + - - +
111A GLU* 3.0 23.2 + - - +
129A ILE* 3.9 23.8 - - + -
133A GLU* 4.1 16.4 + - - -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 5.2 6.7 - - - +
6A GLN* 4.0 23.4 + - - +
104A ALA* 3.2 14.4 + - - +
105A GLU* 3.2 41.1 + - - +
107A LYS* 1.3 77.7 - - + +
109A LEU* 1.3 58.2 + - - +
111A GLU* 3.3 12.2 + - - +
112A ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.2 8.3 - - + +
6A GLN* 3.9 28.7 - - + +
7A LEU* 4.0 22.9 - - + +
10A MSE 4.2 15.9 - - - -
105A GLU 2.9 13.7 + - - +
106A PHE* 3.5 12.3 - - + +
108A LYS* 1.3 76.5 - - - +
110A ASN* 1.3 58.4 + - - +
112A ALA* 3.3 4.1 + - - +
113A ALA* 2.9 27.9 + - - +
121A THR* 3.8 20.6 - - + -
124A PHE* 4.0 32.5 - - + -
125A ALA* 4.0 10.8 - - + -
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE 2.9 16.7 + - - +
107A LYS* 3.6 5.1 + - - +
109A LEU* 1.3 76.1 - - - +
111A GLU* 1.3 64.3 + - - +
113A ALA* 3.1 4.4 + - - +
114A GLU* 2.8 48.6 + - - +
122A ALA* 3.6 11.8 - - - +
125A ALA* 3.6 11.7 - - + +
126A GLN* 2.8 38.4 + - - +
129A ILE* 4.0 11.2 - - + +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS 3.0 17.0 + - - +
108A LYS* 3.3 12.3 + - - +
110A ASN* 1.3 76.9 - - - +
112A ALA* 1.3 62.7 + - - +
114A GLU* 3.3 12.3 + - - +
115A LYS* 2.6 60.9 + - + +
167A ZN 2.1 36.7 - - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A ALA* 6.3 1.1 - - + -
1A MSE 4.1 13.7 - - - +
2A SER* 4.3 0.9 - - - +
3A VAL* 3.5 33.2 - - + +
6A GLN* 5.1 4.7 - - + +
108A LYS 2.9 17.4 + - - +
109A LEU* 3.6 5.8 - - - +
111A GLU* 1.3 77.6 - - - +
113A ALA* 1.3 61.2 + - - +
115A LYS* 3.4 10.1 + - - +
116A GLU* 3.1 23.2 + - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.5 11.3 - - + +
109A LEU 2.9 20.1 + - - +
110A ASN* 3.6 4.3 - - - +
112A ALA* 1.3 73.7 - - - +
114A GLU* 1.3 62.7 + - - +
116A GLU 3.2 1.7 + - - -
117A SER 3.0 3.5 + - - -
118A ASP* 2.9 34.4 + - - +
121A THR* 3.9 14.1 - - + -
122A ALA* 3.5 33.4 - - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 2.8 47.0 + - - +
111A GLU* 3.8 10.2 - - - +
113A ALA* 1.3 76.0 - - - +
115A LYS* 1.3 63.0 + - + +
117A SER* 3.0 18.0 + - - +
122A ALA* 4.7 8.1 - - + -
126A GLN* 3.6 11.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A ALA* 5.5 9.4 - - + +
111A GLU* 2.6 53.3 + - + +
112A ALA* 3.4 7.6 + - - +
114A GLU* 1.3 76.4 - - + +
116A GLU* 1.3 61.6 + - + +
117A SER* 3.4 2.5 + - - -
167A ZN 4.0 3.6 - - - -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.4 15.6 - - - -
3A VAL* 2.9 48.2 + - + +
4A THR* 5.2 0.9 + - - +
61A LEU* 6.0 0.3 - - - +
112A ALA* 3.1 14.0 + - - +
113A ALA 3.8 3.6 - - - +
114A GLU 3.1 0.6 - - - -
115A LYS* 1.3 81.0 - - + +
117A SER* 1.3 69.1 + - - +
118A ASP* 3.1 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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il