Contacts of the helix formed by residues 109 - 138 (chain A) in PDB entry 3MZG
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 PRO 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 6.4 0.2 - - + -
43A ARG* 3.5 28.9 - - - +
44A TYR* 3.3 23.6 - - + +
102A VAL* 4.4 6.5 - - + -
105A MET* 4.4 13.2 - - - -
107A GLU 3.6 4.7 - - - +
108A ALA* 1.4 83.1 - - + +
110A GLU* 1.3 59.9 + - - +
111A ALA 3.5 2.0 - - - +
112A ILE* 3.4 35.8 + - + +
113A LEU* 2.9 27.0 + - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 4.9 1.6 - - - +
108A ALA* 3.2 9.5 + - - +
109A PRO* 1.3 68.8 - - - +
111A ALA* 1.3 67.7 + - - +
113A LEU* 4.4 18.4 - - - +
114A SER* 3.1 38.4 + - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.4 23.3 - - + +
109A PRO 3.5 0.4 - - - -
110A GLU* 1.3 78.1 - - - +
112A ILE* 1.3 63.3 + - + +
114A SER* 3.3 7.6 - - - -
115A LYS* 3.2 33.4 + - - +
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 3.8 25.5 - - + +
39A GLU* 4.2 22.2 - - + +
40A PHE* 3.9 33.2 - - + +
43A ARG* 4.7 4.9 - - - +
44A TYR* 4.2 11.0 - - + -
98A LEU* 5.9 3.1 - - + -
102A VAL* 5.0 11.2 - - + -
109A PRO* 3.4 35.1 + - + +
110A GLU 3.2 0.4 - - - -
111A ALA* 1.3 74.9 - - + +
113A LEU* 1.3 68.7 + - - +
115A LYS* 3.1 6.1 + - - +
116A ALA* 3.0 21.3 + - + +
172A LEU* 5.3 7.4 - - + -
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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
----------------------------------------------------------
99A VAL* 4.3 10.8 - - + +
102A VAL* 3.8 24.0 - - + +
103A ARG* 4.0 39.9 - - + +
108A ALA* 4.5 11.2 - - + -
109A PRO 2.9 20.8 + - - +
110A GLU* 4.2 21.1 - - - +
112A ILE* 1.3 72.8 - - - +
114A SER* 1.3 63.3 + - - +
116A ALA* 3.0 6.2 + - + +
117A VAL* 3.0 44.4 + - + +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 3.1 29.2 + - - +
111A ALA* 3.3 13.4 - - - -
113A LEU* 1.3 77.1 - - - +
115A LYS* 1.3 66.9 + - - +
117A VAL* 3.6 6.8 + - - +
118A GLU* 3.1 23.4 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 40.4 - - + +
35A GLU* 3.6 27.6 - - + -
36A MET* 3.8 23.8 - - + +
39A GLU* 3.0 32.4 + - - -
111A ALA* 3.3 18.3 + - - +
112A ILE 3.1 6.4 + - - +
114A SER* 1.3 83.3 - - - +
116A ALA* 1.3 64.8 + - - +
118A GLU* 3.2 5.7 + - - +
119A ILE* 2.9 28.4 + - + +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 3.7 12.7 - - - -
95A LEU* 5.1 2.9 - - - +
98A LEU* 3.9 28.9 - - + +
99A VAL* 3.6 19.4 - - + +
102A VAL* 6.0 1.6 - - + -
112A ILE* 3.0 13.8 + - + +
113A LEU* 3.0 11.2 + - + +
115A LYS* 1.3 78.2 - - - +
117A VAL* 1.3 52.2 + - - +
119A ILE* 3.2 4.1 + - - +
120A GLU* 2.8 35.5 + - - +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 4.0 20.9 - - + -
103A ARG* 5.7 3.6 - - - +
113A LEU* 3.0 37.0 + - + +
114A SER* 3.7 7.2 - - - +
116A ALA* 1.3 74.7 - - - +
118A GLU* 1.3 67.5 + - + +
120A GLU* 3.3 4.4 + - - +
121A GLU* 3.0 51.1 + - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.5 34.3 + - - -
32A LEU* 4.1 12.5 - - + +
114A SER 3.1 15.1 + - - +
115A LYS* 4.0 3.6 - - - +
117A VAL* 1.3 82.7 - - + +
119A ILE* 1.3 56.2 + - - +
121A GLU* 3.3 6.7 + - + +
122A GLN* 2.9 60.1 + - - +
125A ARG* 5.5 2.3 + - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 17.7 - - + +
32A LEU* 3.7 24.7 - - + +
33A SER* 3.5 32.5 - - - +
36A MET* 3.6 27.8 - - + -
95A LEU* 3.8 21.3 - - + -
115A LYS 2.9 21.6 + - - +
116A ALA* 3.7 4.0 - - - +
118A GLU* 1.3 75.7 - - - +
120A GLU* 1.3 65.0 + - - +
122A GLN* 4.1 4.4 - - - +
123A THR* 2.8 42.6 + - - +
175A LEU* 4.2 8.3 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 5.3 1.4 - - - +
95A LEU* 4.4 22.4 - - + +
96A TYR* 3.4 34.4 - - - +
99A VAL* 3.6 32.5 - - + +
116A ALA 2.8 18.0 + - - +
117A VAL* 3.5 7.5 - - - +
119A ILE* 1.3 80.4 - - - +
121A GLU* 1.3 68.8 + - + +
123A THR* 3.9 2.6 - - - -
124A LYS* 3.3 45.0 + - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.0 36.5 + - + +
118A GLU* 4.1 6.1 - - + +
120A GLU* 1.3 85.4 - - + +
122A GLN* 1.3 65.6 + - + +
124A LYS* 3.1 29.3 + - + +
125A ARG* 3.2 33.6 + - - +
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 4.8 5.8 + - - +
25A LEU* 3.5 25.1 - - + +
28A TYR* 3.5 31.4 - - + -
29A ILE* 3.6 23.2 - - + +
32A LEU* 5.3 0.4 - - + -
118A GLU* 2.9 42.3 + - + +
119A ILE* 4.6 0.2 - - - -
121A GLU* 1.3 74.2 - - + +
123A THR* 1.3 59.8 + - - +
125A ARG* 3.2 30.0 + - - +
126A LEU* 2.8 29.1 + - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.6 17.0 - - - +
88A LEU* 3.9 32.0 - - + +
91A TRP* 4.9 2.9 - - + -
92A ASN* 4.2 14.4 - - - +
95A LEU* 3.6 26.0 - - + +
119A ILE* 2.8 35.8 + - - +
120A GLU 3.9 2.7 - - - -
122A GLN* 1.3 72.2 - - - +
124A LYS* 1.4 56.2 + - - +
126A LEU* 3.2 2.9 + - - +
127A LEU* 3.0 27.9 + - + +
175A LEU* 5.8 0.5 - - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 4.6 14.8 + - - +
120A GLU* 3.3 44.1 + - - +
121A GLU* 3.1 18.1 + - + +
123A THR* 1.4 75.6 - - - +
125A ARG* 1.3 60.9 + - + +
127A LEU* 3.3 8.7 + - - +
128A GLU* 2.9 40.6 + - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 5.2 10.3 - - - +
25A LEU* 4.0 15.3 - - + -
118A GLU* 5.5 2.2 + - - -
121A GLU* 3.2 29.2 + - - +
122A GLN* 3.2 32.5 + - - +
124A LYS* 1.3 76.1 - - + +
126A LEU* 1.3 65.0 + - - +
128A GLU* 3.1 20.9 + - - +
129A ARG* 3.0 26.0 + - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.3 43.3 - - + +
25A LEU* 3.9 11.6 - - + +
26A SER* 3.8 27.1 - - - -
29A ILE* 4.1 13.7 - - + -
88A LEU* 3.8 31.9 - - + -
122A GLN 2.8 20.0 + - - +
123A THR 3.6 5.2 - - - +
125A ARG* 1.3 70.7 - - - +
127A LEU* 1.3 65.0 + - - +
129A ARG* 3.0 3.9 + - - -
130A MET* 2.9 27.4 + - + +
182A ILE* 4.2 8.1 - - + -
186A LEU* 4.2 7.2 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.8 36.8 - - + +
88A LEU* 4.2 18.8 - - + +
89A ARG* 3.9 19.3 - - + +
92A ASN* 3.6 27.8 - - - +
123A THR* 3.0 16.5 + - + +
124A LYS* 3.8 7.9 - - - +
126A LEU* 1.3 76.2 - - - +
128A GLU* 1.3 61.8 + - - +
130A MET* 3.2 5.1 + - + +
131A GLU* 2.9 42.9 + - + +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 2.9 29.1 + - - +
125A ARG* 3.1 22.2 + - - +
127A LEU* 1.3 76.0 - - - +
129A ARG* 1.3 76.9 + - - +
131A GLU* 3.3 11.4 + - - +
132A LEU* 3.2 26.1 + - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.5 29.0 - - + +
21A ARG* 3.7 29.7 - - + +
22A ALA* 4.3 19.5 - - + -
25A LEU* 4.2 15.9 - - + -
125A ARG* 3.0 18.5 + - - +
126A LEU 3.0 7.3 + - - +
128A GLU* 1.3 90.7 + - - +
130A MET* 1.3 57.0 + - - +
132A LEU* 3.2 32.2 + - - +
133A ILE* 2.8 32.4 + - + +
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Residues in contact with MET 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 5.6 0.2 - - + -
22A ALA* 4.2 8.5 - - - -
81A LEU* 3.6 28.0 - - + -
84A ILE* 4.1 13.5 - - + -
85A VAL* 4.0 18.4 - - + -
88A LEU* 3.7 23.8 - - + -
126A LEU* 2.9 21.7 + - + +
127A LEU* 3.2 8.9 + - + +
129A ARG* 1.3 76.1 - - - +
131A GLU* 1.3 59.3 + - - +
133A ILE* 3.2 18.0 + - + +
134A VAL* 2.8 36.0 + - + +
186A LEU* 3.3 36.1 - - + -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 5.0 5.4 - - + -
89A ARG* 2.9 38.9 + - - +
127A LEU* 2.9 40.6 + - + +
128A GLU* 3.9 11.2 + - - +
129A ARG 3.2 0.2 - - - -
130A MET* 1.3 79.1 - - - +
132A LEU* 1.3 57.2 + - + +
134A VAL* 3.4 6.5 + - + +
135A SER* 3.1 30.1 + - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.0 18.5 - - + +
128A GLU* 3.2 12.2 + - + +
129A ARG* 3.3 48.5 - - - +
131A GLU* 1.3 72.0 - - - +
133A ILE* 1.3 64.6 + - - +
135A SER* 3.3 9.6 + - - +
136A GLN* 3.0 24.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.3 2.2 - - + -
18A LEU* 3.7 34.3 - - + +
19A PHE* 3.8 40.4 - - + +
22A ALA* 4.0 26.9 - - + -
81A LEU* 4.1 18.6 - - + -
129A ARG 2.8 21.8 + - - +
130A MET* 3.2 18.4 + - + +
132A LEU* 1.3 71.8 - - - +
134A VAL* 1.3 66.1 + - - +
136A GLN* 3.2 2.9 + - - -
137A VAL* 2.9 32.4 + - + +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 6.3 0.7 - - + -
81A LEU* 4.2 34.5 - - + +
82A SER* 5.8 0.9 - - - -
85A VAL* 4.2 17.9 - - + -
130A MET* 2.8 25.5 + - - +
131A GLU* 3.8 6.3 - - + +
132A LEU 3.3 0.2 - - - -
133A ILE* 1.3 74.6 - - - +
135A SER* 1.3 53.9 + - - +
138A HIS* 2.7 43.4 + - + +
141A THR* 3.6 25.8 - - + +
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU 3.1 13.9 + - - -
132A LEU* 3.6 16.2 - - - -
133A ILE 3.2 0.4 - - - -
134A VAL* 1.3 75.9 - - - +
136A GLN* 1.3 61.6 + - - +
138A HIS 4.7 0.2 - - - -
139A PRO* 3.5 26.9 - - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET 4.6 15.8 + - - +
15A LEU* 3.8 37.6 - - + +
18A LEU* 4.8 5.8 - - + -
132A LEU 3.0 17.1 + - - +
133A ILE 3.7 2.7 - - - +
135A SER* 1.3 80.1 - - - +
137A VAL* 1.3 59.0 + - - +
139A PRO* 4.2 8.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.4 44.2 - - + -
77A GLN* 3.7 13.9 - - - +
81A LEU* 4.6 7.4 - - + -
133A ILE* 2.9 20.5 + - + +
134A VAL 4.6 0.2 - - - +
136A GLN* 1.3 77.5 - - + +
138A HIS* 1.3 92.5 + - + +
139A PRO* 3.7 6.6 - - - +
193A ILE* 4.6 11.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 3.5 30.2 + - + +
78A LYS* 3.7 49.9 - - + +
81A LEU* 4.0 13.5 - - + +
134A VAL* 2.7 24.8 + - + +
135A SER* 4.7 0.5 - - - -
137A VAL* 1.3 107.6 + - + +
139A PRO* 1.3 63.4 - - - +
140A GLU 3.2 3.6 - - - -
141A THR* 2.6 36.4 + - - +
----------------------------------------------------------
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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