Contacts of the helix formed by residues 102 - 135 (chain A) in PDB entry 2GM4
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 ALA 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 1.3 72.8 - - - +
103A MET* 1.3 56.6 + - + +
104A GLY 2.5 17.3 + - - -
105A ARG* 2.6 34.1 + - - +
106A MET* 3.0 13.4 + - + -
117B ALA* 5.2 14.4 - - + +
120B GLN* 4.6 14.1 - - + +
121B ARG* 6.6 0.2 - - + -
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 4.7 5.4 - - - +
102A ALA* 1.3 79.0 - - + +
104A GLY* 1.3 52.0 - - - +
106A MET* 3.9 30.9 - - + +
107A VAL* 2.7 46.7 + - + +
117B ALA* 4.9 7.4 - - - +
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.7 15.2 - - - +
98A ASP* 3.1 20.6 - - - -
101A SER* 3.0 13.7 + - - -
102A ALA 2.5 6.8 + - - -
103A MET* 1.3 71.4 - - - +
105A ARG* 1.3 49.5 + - - -
107A VAL* 2.7 9.4 + - - +
108A VAL* 2.7 36.8 + - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.8 26.0 + - + +
81A LYS* 5.6 3.2 - - - +
84A ASP* 3.0 49.5 + - - +
98A ASP 3.4 4.6 + - - -
99A THR* 3.1 22.0 - - - +
100A SER 4.6 1.6 + - - -
101A SER 2.8 18.2 + - - +
102A ALA* 2.6 27.9 + - - +
104A GLY* 1.3 66.8 - - - -
106A MET* 1.3 71.7 + - - +
108A VAL* 2.8 20.9 + - - +
109A THR* 2.8 19.9 + - + +
120B GLN* 4.5 22.6 + - - +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.0 16.0 + - + +
103A MET* 3.6 27.6 - - + +
105A ARG* 1.3 78.5 - - - +
107A VAL* 1.3 84.6 + - + +
109A THR* 2.5 24.5 + - - -
110A ILE* 2.8 22.6 + - + +
113B ALA* 4.2 5.6 - - - +
114B VAL* 3.7 41.1 - - + +
117B ALA* 3.7 32.3 - - + +
118B GLU* 5.5 1.6 - - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.5 11.9 - - + -
103A MET* 2.7 33.6 + - + +
104A GLY 2.7 3.8 + - - +
106A MET* 1.3 84.7 - - + +
108A VAL* 1.3 61.7 + - - +
110A ILE* 3.6 19.7 - - + -
111A LEU* 3.0 40.9 + - + +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 5.7 - - + +
76A MET* 3.2 33.0 - - + -
80A ILE* 3.7 12.8 - - + -
92A PHE* 3.8 18.8 - - + -
97A ILE* 3.8 30.5 - - + -
99A THR* 4.7 7.2 - - - +
104A GLY 2.7 24.9 + - - +
105A ARG* 2.8 14.3 + - - +
107A VAL* 1.3 68.7 - - - +
109A THR* 1.3 56.8 + - - +
111A LEU* 2.8 30.8 + - - +
112A SER* 3.0 12.4 + - - -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 4.5 2.8 - - - +
76A MET* 5.7 0.2 - - - -
77A ILE* 3.3 44.9 - - + -
80A ILE* 4.4 13.7 - - + -
105A ARG* 2.8 17.2 + - + +
106A MET* 2.5 27.0 + - - -
108A VAL* 1.3 71.9 - - - +
110A ILE* 1.3 63.6 + - - +
112A SER* 3.9 8.7 - - - -
113A ALA* 3.5 18.7 + - - +
73B THR* 5.6 5.1 - - + +
109B THR* 5.9 0.5 - - - -
110B ILE* 5.3 0.5 - - - +
113B ALA* 3.9 14.9 - - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 2.8 48.9 + - + +
107A VAL* 3.6 22.2 - - + +
108A VAL 2.9 0.2 + - - -
109A THR* 1.3 77.3 + - - +
111A LEU* 1.3 71.3 + - + +
112A SER 3.2 0.2 + - - -
113A ALA* 3.4 6.2 + - - +
114A VAL* 2.9 27.0 + - + +
110B ILE* 4.0 26.4 - - + +
113B ALA* 4.5 11.4 - - + -
114B VAL* 4.1 16.4 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.4 20.2 - - + -
95A ASP* 4.9 8.3 - - + +
97A ILE* 3.8 31.0 - - + -
107A VAL* 3.0 30.7 - - + +
108A VAL 2.8 6.8 + - - +
110A ILE* 1.3 83.7 - - + +
112A SER* 1.3 61.5 + - - +
114A VAL* 3.4 8.2 + - + +
115A ALA* 3.0 23.9 + - - +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.7 10.3 - - - +
73A THR* 3.4 30.1 + - - -
76A MET* 3.6 28.0 - - - +
77A ILE* 5.2 0.4 - - - +
108A VAL 3.0 16.1 + - - -
109A THR* 3.9 4.4 - - - -
110A ILE 3.2 0.4 + - - -
111A LEU* 1.3 75.5 - - - +
113A ALA* 1.3 57.9 + - - +
115A ALA* 2.8 22.5 + - - +
116A GLN* 2.8 12.3 + - - +
119A ARG* 4.7 7.7 + - - +
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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
----------------------------------------------------------
73A THR* 3.5 21.9 + - + +
109A THR 3.5 6.0 + - - +
110A ILE 3.4 8.4 + - - +
112A SER* 1.3 78.6 - - - +
114A VAL* 1.3 62.1 + - + +
116A GLN* 4.1 5.0 - - - +
117A ALA* 3.2 23.4 + - - +
106B MET* 3.9 15.9 - - + +
109B THR* 3.3 29.2 - - + +
110B ILE* 5.2 4.0 - - + +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 2.9 29.4 - - + +
111A LEU* 3.8 8.3 - - + +
112A SER 3.1 0.4 - - - -
113A ALA* 1.3 77.8 - - - +
115A ALA* 1.3 59.5 + - - +
117A ALA* 4.0 10.2 - - - +
118A GLU* 4.2 9.7 + - - +
106B MET* 4.0 22.4 - - + -
110B ILE* 4.2 22.7 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 6.1 2.0 - - + -
111A LEU 3.0 15.8 + - - +
112A SER* 2.8 6.4 + - - +
114A VAL* 1.3 79.9 - - - +
116A GLN* 1.3 61.8 + - - +
117A ALA 3.3 0.2 - - - -
118A GLU* 3.2 21.8 - - - +
119A ARG* 3.4 28.3 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 4.1 1.4 - - - +
72A ASP* 3.9 17.1 + - - +
73A THR* 3.4 36.7 + - - +
112A SER 2.8 14.0 + - - +
113A ALA* 4.1 5.5 + - - +
115A ALA* 1.3 74.3 - - - +
117A ALA* 1.3 51.7 + - - +
118A GLU 2.8 4.7 - - - -
119A ARG* 2.7 31.0 + - + +
120A GLN* 2.6 64.3 + - + +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA 3.2 16.6 + - - +
114A VAL 4.0 6.1 - - - +
116A GLN* 1.3 78.6 - - - +
118A GLU* 1.3 58.2 + - - +
120A GLN* 4.1 13.5 + - - +
121A ARG* 3.5 22.0 + - - +
102B ALA* 5.2 4.1 - - - +
103B MET* 4.0 26.6 - - + +
106B MET* 3.7 27.4 - - + -
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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
----------------------------------------------------------
114A VAL 4.2 5.8 + - - +
115A ALA* 3.2 18.3 + - - +
116A GLN 2.8 0.8 - - - -
117A ALA* 1.3 77.9 - - - +
119A ARG* 1.3 61.3 + - + +
121A ARG* 3.3 39.0 + - - +
122A ILE* 2.9 41.7 + - + +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 5.4 2.4 + - - +
67A ASP* 4.4 23.5 - - - +
70A GLY 5.0 2.8 + - - -
71A ARG* 2.5 64.2 + - - +
73A THR* 4.7 3.4 + - - -
112A SER* 4.7 8.1 + - - +
115A ALA* 3.4 27.2 + - - +
116A GLN* 2.7 38.3 + - + +
118A GLU* 1.3 73.8 - - + +
120A GLN* 1.3 57.0 + - + +
122A ILE* 3.0 14.8 + - + +
123A LEU* 2.9 42.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 2.6 47.2 + - + +
117A ALA* 4.4 11.3 + - - +
119A ARG* 1.3 73.8 - - - +
121A ARG* 1.3 60.2 + - - +
123A LEU* 3.8 6.7 + - - +
124A GLN* 3.5 16.6 + - - +
102B ALA* 4.3 25.2 - - + +
105B ARG* 3.5 36.0 + - - +
106B MET* 5.8 0.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 3.5 16.7 + - - +
118A GLU* 3.3 41.8 + - - +
119A ARG 3.2 0.4 - - - -
120A GLN* 1.3 77.2 - - - +
122A ILE* 1.3 79.3 + - - +
124A GLN* 3.0 23.1 + - - +
125A ARG* 3.0 24.8 + - + +
102B ALA* 5.5 0.8 - - - +
103B MET* 6.4 0.9 - - + -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 2.9 30.8 + - + +
119A ARG* 3.3 13.0 - - + +
121A ARG* 1.3 91.0 - - - +
123A LEU* 1.3 65.4 + - + +
125A ARG* 3.0 7.5 + - - +
126A THR* 2.6 48.9 + - - +
18X A 5.8 6.3 - - + +
19X T 5.7 15.9 - - + +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 5.6 5.8 - - - +
119A ARG* 2.9 29.3 + - + +
120A GLN* 4.1 6.3 - - - +
122A ILE* 1.3 88.0 - - + +
124A GLN* 1.3 57.3 + - - +
126A THR* 3.5 8.2 - - + +
127A ASN* 2.9 41.3 + - - +
21Z A 3.8 42.0 - - - +
22Z A 4.3 12.6 - - - +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN 3.5 10.6 + - - +
121A ARG* 3.0 16.6 + - - +
123A LEU* 1.3 77.1 - - - +
125A ARG* 1.3 57.7 + - - +
127A ASN* 3.5 3.9 + - - +
128A GLU* 2.8 61.2 + - + +
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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
----------------------------------------------------------
121A ARG* 3.0 24.1 + - + +
122A ILE* 3.6 9.0 - - - +
124A GLN* 1.3 74.4 - - - +
126A THR* 1.3 60.3 + - - +
128A GLU* 3.9 14.8 - - + +
129A GLY* 3.0 23.7 + - - -
18X A 5.1 2.8 - - - +
19X T 4.8 17.1 + - - +
----------------------------------------------------------
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 2.6 40.3 + - - +
123A LEU* 3.5 11.9 - - + +
125A ARG* 1.3 73.1 - - - +
127A ASN* 1.3 61.8 + - - +
129A GLY* 3.3 3.5 + - - -
130A ARG* 3.1 35.0 + - + +
17X T 4.1 16.5 - - - +
18X A 3.8 44.1 + - - +
20Z A 6.2 0.7 - - + -
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 2.9 31.3 + - - +
124A GLN* 3.9 4.9 - - - +
126A THR* 1.3 79.1 - - - +
128A GLU* 1.3 58.9 + - - +
129A GLY 3.1 1.3 - - - -
130A ARG* 2.9 17.8 + - - +
131A GLN* 2.9 39.4 + - + +
21Z A 5.6 0.2 - - - +
22Z A 4.0 34.1 + - - +
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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 GLN* 2.8 55.3 + - + +
125A ARG* 3.9 14.5 - - + +
127A ASN* 1.3 71.6 - - - +
129A GLY* 1.3 56.5 + - - +
131A GLN* 3.6 7.7 + - - +
132A GLU* 3.3 34.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG 3.0 16.2 + - - -
126A THR 3.6 5.6 - - - -
127A ASN 3.1 0.4 - - - -
128A GLU* 1.3 76.2 - - - +
130A ARG* 1.3 59.5 + - - +
131A GLN 3.5 0.2 - - - -
132A GLU* 3.7 20.3 - - - +
133A ALA* 3.4 17.0 - - - +
17X T 3.8 1.4 - - - +
18X A 3.3 26.9 + - - -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.1 20.0 - - - +
127A ASN* 2.9 18.1 + - - +
129A GLY* 1.3 76.2 - - - +
131A GLN* 1.3 65.6 + - - +
132A GLU 3.3 1.8 - - - -
133A ALA* 3.6 5.2 - - - -
134A MET* 2.8 57.1 + - - +
16X T 3.8 13.9 + - - -
17X T 3.3 45.8 + - - +
23Y T 4.2 8.7 + - - -
21Z A 4.7 1.4 + - - -
22Z A 3.1 65.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 2.9 24.4 + - + +
128A GLU* 4.0 7.6 - - - +
130A ARG* 1.3 81.8 + - - +
132A GLU* 1.3 54.4 + - - +
133A ALA 3.3 2.5 - - - -
134A MET* 4.2 13.9 - - - +
135A ALA* 3.4 24.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.3 21.6 + - - +
129A GLY* 3.7 17.9 - - - +
131A GLN* 1.3 75.0 - - - +
133A ALA* 1.3 56.0 + - + +
135A ALA* 4.9 2.7 - - - -
136A LYS* 3.3 27.5 + - - +
18X A 5.5 1.0 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 3.4 18.8 + - - +
130A ARG* 3.3 8.0 + - - +
132A GLU* 1.3 79.8 - - - +
134A MET* 1.3 67.1 + - - +
135A ALA 3.3 1.1 - - - -
136A LYS* 3.4 11.8 + - - +
137A GLY 3.4 3.5 + - - -
138A VAL* 3.3 35.6 + - + +
17X T 4.8 16.2 - - - +
18X A 5.4 1.1 - - - +
----------------------------------------------------------
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 2.8 50.9 + - - +
131A GLN* 4.6 14.8 - - - +
133A ALA* 1.3 80.8 - - - +
135A ALA* 1.3 60.3 + - - +
136A LYS 3.6 0.2 + - - -
137A GLY* 3.6 8.8 + - - -
138A VAL* 4.8 2.5 - - - -
140A PHE* 3.5 58.8 - - + -
17X T 6.3 2.7 - - - +
23Y T 5.5 14.4 - - - +
24Y T 5.9 0.4 - - - +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN 3.4 19.3 + - - +
132A GLU* 4.9 2.9 - - - -
133A ALA 3.3 0.4 - - - -
134A MET* 1.3 76.9 - - - +
136A LYS* 1.3 64.3 + - - +
137A GLY* 3.5 0.9 + - - -
----------------------------------------------------------
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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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