Contacts of the helix formed by residues 114 - 142 (chain A) in PDB entry 5POM
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 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 3.5 10.1 - - + +
111A ALA* 2.7 35.4 + - + +
112A ARG 3.3 0.4 - - - -
113A ASP* 1.3 91.0 - - - +
115A VAL* 1.3 63.8 + - - +
116A PHE* 3.9 13.0 - - + -
117A TYR* 3.1 16.5 + - - +
118A ARG* 3.1 27.9 + - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.6 13.2 - - + -
113A ASP 4.1 0.6 + - - -
114A THR* 1.3 71.6 - - - +
116A PHE* 1.3 83.0 + - + +
118A ARG* 3.9 6.3 - - + +
119A ALA* 3.0 29.2 + - + +
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Residues in contact with PHE 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 ILE* 3.8 29.8 - - + -
55A PHE* 4.2 0.3 - - - -
106A CYS* 3.2 13.4 - - - -
110A ASN* 3.4 37.9 - - + +
114A THR* 3.1 10.0 - - + +
115A VAL* 1.3 91.8 - - + +
117A TYR* 1.3 65.6 + - - +
119A ALA* 3.2 7.7 + - - +
120A ALA 3.1 17.0 + - - -
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A CYS* 4.3 7.6 - - - -
107A MET* 3.3 48.5 - - + +
110A ASN* 3.3 22.2 - - + +
111A ALA 3.0 20.4 - - - +
112A ARG* 3.6 39.7 + - + +
114A THR* 3.1 5.9 + - - +
116A PHE* 1.3 79.0 - - - +
118A ARG* 1.3 68.1 + - + +
120A ALA* 3.0 15.3 + - - +
121A VAL* 3.1 30.9 + - + +
70B HIS* 4.2 16.9 + - - +
108B LYS* 3.6 25.0 + - + +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.5 26.1 + - - +
113A ASP* 3.9 20.7 + - - +
114A THR 3.1 17.6 + - - +
115A VAL* 4.1 6.1 - - - +
117A TYR* 1.3 79.0 - - + +
119A ALA* 1.3 63.0 + - - +
121A VAL* 3.4 7.4 + - + +
122A ARG* 3.1 34.6 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 5.5 1.3 - - - +
54A ILE* 3.6 24.7 - - + -
55A PHE* 4.0 13.2 - - + -
115A VAL* 3.0 19.8 + - + +
116A PHE 3.5 4.9 - - - +
117A TYR 3.2 0.2 - - - -
118A ARG* 1.3 78.3 - - - +
120A ALA* 1.3 56.9 + - - +
122A ARG* 3.4 9.7 + - - +
123A LEU* 2.9 29.6 + - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.6 12.3 - - + -
103A ILE* 3.4 23.0 - - + +
106A CYS* 3.9 21.1 - - + -
107A MET* 3.7 21.8 - - + -
116A PHE 3.1 4.6 + - - -
117A TYR 3.0 9.9 + - - +
119A ALA* 1.3 78.5 - - - +
121A VAL* 1.3 57.0 + - - +
123A LEU 3.2 0.3 + - - -
124A ARG* 2.8 31.4 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 3.6 16.6 - - + -
117A TYR* 3.1 41.9 + - + +
118A ARG* 3.7 9.9 - - + +
119A ALA 3.3 0.2 - - - -
120A ALA* 1.3 75.3 - - - +
122A ARG* 1.3 62.1 + - + +
124A ARG* 3.3 27.9 + - - +
125A ASP* 2.9 38.4 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS 5.6 2.2 - - - +
118A ARG* 3.1 25.0 + - - +
119A ALA* 3.8 7.6 - - - +
121A VAL* 1.3 79.9 - - + +
123A LEU* 1.3 58.0 + - - +
125A ASP* 3.9 5.1 - - - +
126A GLN* 2.9 61.7 + - - +
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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
----------------------------------------------------------
46A LEU* 3.5 26.2 - - - +
49A LYS* 3.9 24.8 + - + +
50A ASP* 4.9 0.9 - - + -
55A PHE* 3.6 29.8 - - + -
77A PHE* 3.9 17.5 - - + -
99A PHE* 3.7 19.8 - - + -
102A ILE* 4.7 2.7 - - + -
103A ILE* 3.6 20.4 - - + -
119A ALA 2.9 18.3 + - - +
120A ALA 3.2 4.2 + - - +
122A ARG* 1.3 74.1 - - - +
124A ARG* 1.3 55.4 + - - +
126A GLN* 4.9 1.8 - - - -
127A GLY* 2.8 35.3 + - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 4.9 6.6 - - + -
100A ASP* 6.0 1.6 - - - +
103A ILE* 4.0 27.1 - - + +
104A ASP* 6.0 0.7 - - - -
107A MET* 3.7 24.2 - - - +
120A ALA 2.8 16.8 + - - +
121A VAL* 3.5 28.1 + - - +
123A LEU* 1.3 77.1 - - - +
125A ASP* 1.3 83.3 + - - +
127A GLY* 4.0 0.2 - - - -
128A GLY* 3.2 19.9 + - - -
72B LYS* 6.3 1.4 - - - +
108B LYS* 3.9 12.5 - - - +
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 2.9 32.4 + - - +
122A ARG* 3.9 5.6 - - - +
124A ARG* 1.3 103.7 + - - +
126A GLN* 1.3 63.7 + - + +
128A GLY* 3.3 10.0 + - - -
129A VAL* 4.2 8.3 + - - +
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Residues in contact with GLN 126 (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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49A LYS* 3.7 49.9 + - + +
122A ARG* 2.9 56.0 + - - +
123A LEU 4.4 0.4 - - - +
125A ASP* 1.3 77.9 - - + +
127A GLY* 1.3 63.1 + - - +
128A GLY 3.5 0.5 + - - -
129A VAL* 3.7 18.7 + - - +
130A VAL* 4.1 8.8 - - - +
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.7 22.2 - - - -
49A LYS* 5.1 2.4 - - - +
99A PHE* 4.5 4.3 - - - -
123A LEU* 2.8 21.3 + - - -
124A ARG 4.0 0.9 - - - -
126A GLN* 1.3 77.5 - - - +
128A GLY* 1.3 65.3 + - - +
130A VAL* 3.1 6.6 + - - +
131A LEU* 3.0 30.1 + - - +
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Residues in contact with GLY 128 (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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124A ARG 3.2 15.0 + - - -
125A ASP 3.3 5.1 + - - -
126A GLN 3.2 1.4 - - - -
127A GLY* 1.3 77.1 - - - +
129A VAL* 1.3 56.4 + - - +
131A LEU* 3.5 7.9 + - - +
132A ARG* 3.0 30.5 + - - +
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Residues in contact with VAL 129 (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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125A ASP 4.2 9.4 - - - +
126A GLN* 3.9 15.3 - - - +
127A GLY 3.2 0.4 - - - -
128A GLY* 1.3 77.9 - - - +
130A VAL* 1.3 65.3 + - + +
132A ARG* 3.4 7.1 + - - +
133A GLN* 3.4 20.1 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.9 28.5 - - + -
45A GLN* 4.1 41.1 - - + +
46A LEU* 3.9 15.0 - - + -
49A LYS* 4.6 13.7 - - - +
126A GLN 4.1 12.8 - - - +
127A GLY 3.1 6.7 + - - +
129A VAL* 1.3 80.2 - - + +
131A LEU* 1.3 56.5 + - - +
133A GLN* 3.4 5.7 + - - +
134A ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.0 23.6 - - + -
46A LEU* 4.5 10.3 - - + -
92A LEU* 4.5 11.0 - - + +
95A PHE* 4.6 4.3 - - + -
96A GLU* 3.8 42.3 - - + +
99A PHE* 3.7 33.0 - - + -
100A ASP* 5.5 2.5 - - - +
127A GLY 3.0 19.3 + - - +
128A GLY* 4.1 6.1 - - - +
130A VAL* 1.3 73.8 - - - +
132A ARG* 1.3 65.2 + - - +
134A ALA* 3.7 3.4 - - + +
135A ARG* 3.0 25.1 + - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY 3.0 18.5 + - - +
129A VAL* 3.5 8.7 - - - +
131A LEU* 1.3 78.3 - - - +
133A GLN* 1.3 63.0 + - - +
135A ARG* 3.6 5.4 + - - +
136A ARG* 3.4 23.9 + - - +
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Residues in contact with GLN 133 (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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129A VAL 3.4 7.7 + - - +
130A VAL* 3.4 7.9 + - - +
131A LEU 3.3 0.4 - - - -
132A ARG* 1.3 78.8 - - - +
134A ALA* 1.3 62.2 + - - +
136A ARG* 3.0 33.6 + - - +
137A GLU* 2.9 52.5 + - - +
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Residues in contact with ALA 134 (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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38A LEU* 4.4 7.9 - - + -
42A VAL* 3.8 27.6 - - + -
92A LEU* 4.0 14.8 - - + -
130A VAL 3.0 17.5 + - - +
131A LEU* 3.7 9.6 - - - +
133A GLN* 1.3 76.3 - - - +
135A ARG* 1.3 56.7 + - - +
137A GLU* 3.1 11.0 + - - +
138A VAL* 2.9 34.0 + - - +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.5 38.0 - - + +
93A HIS* 4.0 16.6 - - - +
96A GLU* 4.1 8.8 + - - +
131A LEU 3.0 17.2 + - - +
132A ARG* 3.7 6.7 - - - +
133A GLN 3.2 0.2 - - - -
134A ALA* 1.3 76.6 - - - +
136A ARG* 1.3 65.9 + - + +
138A VAL* 3.9 5.7 - - - +
139A ASP* 3.1 50.7 + - - +
144A GLU* 3.4 24.9 + - - -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG 3.4 12.9 + - - +
133A GLN* 3.0 36.2 + - - +
135A ARG* 1.3 79.6 - - + +
137A GLU* 1.3 57.3 + - - +
139A ASP* 3.7 6.2 - - - +
140A SER* 2.8 31.2 + - - -
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Residues in contact with GLU 137 (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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38A LEU* 4.1 24.6 - - + +
133A GLN* 2.9 42.8 + - + +
134A ALA* 3.7 7.9 - - - +
136A ARG* 1.3 74.2 - - + +
138A VAL* 1.3 60.1 + - - +
140A SER* 3.6 6.6 - - - -
141A ILE* 2.9 35.2 + - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.2 17.5 - - + -
38A LEU* 4.0 24.9 - - + -
39A LEU* 5.6 0.2 - - + -
92A LEU* 4.4 12.8 - - + -
134A ALA 2.9 20.5 + - - +
135A ARG* 3.9 13.9 - - - +
137A GLU* 1.3 77.2 - - - +
139A ASP* 1.3 58.4 + - - +
142A GLY* 2.9 23.9 + - - -
143A LEU* 3.0 21.1 + - + -
144A GLU* 3.3 40.1 - - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 3.1 50.6 + - - +
136A ARG* 3.7 5.3 - - - +
138A VAL* 1.3 77.1 - - - +
140A SER* 1.3 65.7 + - - +
142A GLY* 3.2 11.2 + - - -
144A GLU* 5.2 1.6 - - - +
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG 2.8 22.5 + - - -
137A GLU* 3.3 8.5 + - - -
139A ASP* 1.3 75.1 - - - +
141A ILE* 1.3 60.1 + - - +
142A GLY* 3.1 4.2 + - - -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 6.1 0.7 - - + -
137A GLU 2.9 17.8 + - - +
140A SER* 1.3 73.3 + - - +
142A GLY* 1.3 64.5 + - - +
143A LEU* 4.3 21.3 - - + +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 5.8 1.6 - - - +
138A VAL 2.9 12.3 + - - -
139A ASP* 3.6 9.0 - - - -
140A SER 3.0 5.0 - - - -
141A ILE* 1.3 80.0 - - - +
143A LEU* 1.3 57.5 + - - +
144A GLU 3.2 14.2 + - - -
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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