Contacts of the helix formed by residues 129 - 156 (chain A) in PDB entry 4NFT
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 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.3 13.5 + - - -
87A VAL* 3.9 30.8 - - + +
90A TYR* 4.2 17.7 - - + -
91A THR* 5.0 5.2 - - - +
127A GLY 3.1 0.4 - - - -
128A ALA* 1.3 84.8 - - + +
130A ALA* 1.3 66.4 + - - +
131A ALA 3.1 3.8 - - - +
132A VAL* 3.3 11.1 + - - +
133A TYR* 3.1 22.3 + - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.6 31.9 - - + +
59A THR* 3.8 17.2 - - - +
60A SER* 4.1 8.7 - - - +
63A ILE* 4.2 4.2 - - + +
116A LEU* 4.2 2.9 - - + -
126A VAL* 4.1 9.4 - - + -
127A GLY 3.4 9.3 + - - +
129A THR* 1.3 80.5 + - - +
131A ALA* 1.3 52.6 + - - +
133A TYR* 3.5 5.4 + - - +
134A SER* 2.7 36.4 + - - -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.2 3.6 - - - +
109A VAL* 3.9 14.3 - - + +
112A ILE* 3.8 5.9 - - + +
113A HIS* 3.7 49.1 - - + +
116A LEU* 4.0 10.9 - - + +
126A VAL* 4.9 0.2 - - - +
127A GLY 4.5 1.8 + - - -
128A ALA 5.8 0.2 - - - +
129A THR* 3.1 1.2 - - - +
130A ALA* 1.3 76.2 - - - +
132A VAL* 1.3 60.1 + - - +
133A TYR 3.2 1.1 - - - -
135A ALA* 2.9 32.2 + - - +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 3.8 21.3 - - + +
87A VAL* 3.9 8.1 - - + +
90A TYR* 3.8 41.1 - - + -
99A ARG* 4.3 3.1 - - - +
103A ALA* 3.7 25.6 - - + -
105A LEU* 3.7 4.0 - - - +
109A VAL* 3.9 24.0 - - + -
128A ALA 4.9 0.2 - - - +
129A THR* 3.3 13.8 + - - +
131A ALA* 1.3 77.3 - - - +
133A TYR* 1.3 62.1 + - - +
135A ALA 3.5 0.2 + - - -
136A ALA* 3.1 22.9 + - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.7 21.1 - - - -
63A ILE* 3.6 23.3 - - + -
64A GLN* 2.6 57.9 + - + +
67A VAL* 5.2 0.9 - - + -
80A VAL* 3.6 15.4 + - + +
83A GLY* 3.4 40.8 - - - -
84A THR* 3.5 7.2 - - + -
87A VAL* 3.6 14.6 - - + -
129A THR 3.1 15.8 + - - +
130A ALA* 3.6 4.9 - - - +
132A VAL* 1.3 78.0 - - - +
134A SER* 1.3 62.2 + - - +
136A ALA* 3.2 4.5 + - - +
137A ILE* 3.1 38.1 + - + +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.1 16.6 - - - -
42A ILE* 6.0 0.9 - - - -
63A ILE* 3.5 27.2 - - - +
112A ILE* 4.0 15.7 - - - -
116A LEU* 3.8 5.0 - - - +
130A ALA 2.7 23.0 + - - -
131A ALA* 3.3 4.0 + - - -
133A TYR* 1.3 76.1 - - - +
135A ALA* 1.3 58.5 + - - +
137A ILE* 3.2 10.1 + - - +
138A LEU* 2.9 34.8 + - - +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.7 19.7 - - + -
107A PHE* 3.9 10.9 - - + +
109A VAL* 4.3 13.9 - - + -
112A ILE* 3.6 28.8 - - + +
131A ALA 2.9 18.1 + - - +
132A VAL 3.8 0.2 - - - +
134A SER* 1.3 76.4 - - - +
136A ALA* 1.3 58.5 + - - +
138A LEU* 3.4 2.3 + - - +
139A GLU* 2.9 31.2 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.5 30.8 - - + +
83A GLY* 3.8 5.4 - - - -
86A ALA* 3.6 14.1 - - + -
105A LEU* 3.7 14.3 - - + +
132A VAL 3.1 14.8 + - - +
133A TYR 3.4 8.5 - - - +
134A SER 3.1 0.2 - - - -
135A ALA* 1.3 74.5 - - - +
137A ILE* 1.3 60.3 + - - +
139A GLU* 3.4 2.5 + - - +
140A TYR* 2.9 29.0 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.1 16.4 - - + -
63A ILE* 4.6 2.0 - - + -
67A VAL* 4.0 27.8 - - + -
71A LEU* 4.9 0.4 - - + -
79A ALA* 3.2 44.6 - - + +
80A VAL* 4.2 1.8 - - - +
83A GLY* 4.1 3.8 - - - -
133A TYR* 3.1 38.7 + - + +
134A SER* 3.5 8.5 - - - +
136A ALA* 1.3 74.8 - - - +
138A LEU* 1.3 64.7 + - + +
140A TYR* 2.9 16.4 + - - +
141A LEU* 3.0 25.3 + - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 5.5 2.0 - - + -
35A VAL* 4.0 15.3 - - + +
38A ILE* 3.8 28.5 - - + -
39A PHE* 3.6 45.1 - - + -
42A ILE* 5.2 5.8 - - + -
107A PHE* 3.8 21.5 - - + -
112A ILE* 3.9 24.5 - - + -
134A SER* 2.9 23.3 + - - +
135A ALA 3.9 0.9 - - - +
137A ILE* 1.3 73.6 - - + +
139A GLU* 1.3 61.8 + - - +
141A LEU* 3.5 6.3 + - + +
142A THR* 2.8 30.2 + - - -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 19.7 - - + +
16A GLN* 5.1 2.1 - - - +
104A GLY 4.5 2.3 - - - +
105A LEU* 3.2 21.5 - - + +
106A GLN* 2.4 49.2 + - - +
107A PHE* 2.8 24.1 + - + +
135A ALA 2.9 17.9 + - - +
136A ALA* 3.8 4.9 - - - +
138A LEU* 1.3 75.5 - - - +
140A TYR* 1.3 58.5 + - - +
142A THR* 3.4 1.9 + - - -
143A ALA* 2.9 32.1 + - + +
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.6 41.0 - - + +
78A HIS* 3.1 34.8 + + + +
79A ALA* 3.7 20.9 - - + -
82A GLU* 4.2 25.4 - - + -
136A ALA 2.9 13.3 + - - +
137A ILE* 2.9 11.3 + - - +
139A GLU* 1.3 76.8 - - - +
141A LEU* 1.3 69.7 + - + +
143A ALA* 3.3 8.3 + - + +
144A GLU* 3.0 52.1 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.1 15.9 - - + -
38A ILE* 3.9 34.8 - - + -
42A ILE* 5.2 0.4 - - + -
71A LEU* 4.0 29.8 - - + -
75A LEU* 3.8 28.3 - - + -
137A ILE* 3.0 27.0 + - + +
138A LEU* 4.0 5.4 - - + +
140A TYR* 1.3 84.4 - - + +
142A THR* 1.3 63.2 + - - +
144A GLU* 3.1 14.8 + - + +
145A VAL* 3.1 18.5 + - - +
176A LEU* 5.5 2.0 - - + +
179A LEU* 4.3 14.4 - - + -
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.2 18.6 - - + -
13A VAL* 4.4 5.4 - - + -
31A MET* 3.8 23.7 - - + +
34A PHE* 4.5 4.4 - - - -
35A VAL* 3.6 13.7 - - + +
107A PHE* 3.5 23.3 - - + -
138A LEU 2.8 21.3 + - - -
139A GLU 3.7 4.0 - - - -
140A TYR 3.2 0.2 - - - -
141A LEU* 1.3 78.2 - - - +
143A ALA* 1.3 58.0 + - - +
145A VAL* 3.5 2.3 + - - +
146A LEU* 3.1 41.3 + - + +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.7 21.2 - - + +
17A VAL* 4.3 13.6 - - + +
139A GLU* 2.9 19.1 + - + +
140A TYR* 3.6 7.9 - - + +
142A THR* 1.3 76.0 - - - +
144A GLU* 1.3 60.9 + - - +
146A LEU* 4.2 2.2 - - - +
147A GLU* 2.9 34.6 + - + +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 12.5 - - + +
140A TYR* 3.0 56.4 + - + +
141A LEU* 3.1 10.5 + - - +
143A ALA* 1.3 77.4 - - - +
145A VAL* 1.3 62.9 + - - +
147A GLU* 3.6 8.2 + - - +
148A LEU* 3.3 35.2 + - - +
175A GLU* 5.4 3.3 - - - +
176A LEU* 4.8 13.0 - - + +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 3.7 27.8 - - + -
34A PHE* 4.1 24.9 - - + -
141A LEU 3.1 12.7 + - - +
142A THR 3.9 6.1 - - - +
144A GLU* 1.3 79.1 - - - +
146A LEU* 1.3 57.5 + - - +
148A LEU* 3.5 2.4 + - - +
149A ALA* 3.0 27.3 + - + +
166A LEU* 4.1 13.5 - - + -
169A ALA* 4.3 3.1 - - + +
170A ILE* 4.6 23.1 - - + -
176A LEU* 4.1 26.0 - - + -
180A ILE* 5.7 0.4 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.6 35.0 - - + +
13A VAL* 4.1 4.5 - - + -
14A LEU* 3.8 23.3 - - + +
17A VAL* 4.2 12.3 - - + -
18A HIS* 3.6 4.5 - - - -
23A ILE* 4.2 24.2 - - + -
31A MET* 4.0 20.6 - - + -
142A THR* 3.1 29.3 + - + +
143A ALA 4.2 2.7 - - - +
145A VAL* 1.3 76.9 - - - +
147A GLU* 1.3 54.5 + - - +
149A ALA* 4.1 2.9 - - - +
150A GLY* 2.8 31.5 + - - -
161A ILE* 4.2 15.3 - - + +
166A LEU* 5.2 2.9 - - + -
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.9 26.4 - - + +
18A HIS* 3.1 26.1 + - - -
143A ALA* 2.9 19.3 + - + +
144A GLU* 3.8 11.0 - - - +
145A VAL 3.2 0.2 - - - -
146A LEU* 1.3 76.0 - - - +
148A LEU* 1.3 68.1 + - + +
151A ASN* 3.1 46.0 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 3.3 19.5 + - - +
145A VAL* 4.0 1.1 - - - +
147A GLU* 1.3 84.4 - - + +
149A ALA* 1.3 58.6 + - - +
151A ASN* 3.3 15.0 + - + +
152A ALA* 2.9 26.7 + - - +
169A ALA* 3.6 21.3 - - + +
173A ASP* 4.1 22.9 - - + +
176A LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL 3.0 19.5 + - - +
146A LEU* 4.1 2.7 - - - +
148A LEU* 1.3 72.7 - - - +
150A GLY* 1.3 60.7 + - - +
152A ALA* 3.3 4.5 + - - +
153A SER* 3.0 29.6 + - - -
161A ILE* 4.2 12.1 - - + -
165A HIS* 3.7 22.1 - - - +
166A LEU* 3.8 22.9 - - + -
169A ALA* 3.6 9.8 - - + +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 3.3 27.9 - - - -
21A THR* 4.8 5.4 + - - +
146A LEU 2.8 15.8 + - - -
149A ALA* 1.3 74.0 - - - +
151A ASN* 1.3 55.3 + - - +
153A SER* 3.1 5.3 + - - -
154A LYS* 2.8 28.6 + - - +
161A ILE* 3.8 16.4 - - - +
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Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 3.3 20.3 + - - -
147A GLU* 3.1 37.4 + - - +
148A LEU* 3.4 16.9 - - + +
149A ALA 3.3 0.2 - - - -
150A GLY* 1.3 72.9 - - - +
152A ALA* 1.3 64.2 + - - +
154A LYS* 3.2 10.3 + - + +
155A ASP* 2.9 32.7 + - - +
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU 2.9 13.7 + - - +
149A ALA* 3.3 11.6 + - - +
151A ASN* 1.3 75.0 - - - +
153A SER* 1.3 62.5 + - - +
155A ASP* 3.1 18.7 + - - +
156A LEU* 3.2 17.7 + - - +
165A HIS* 4.1 11.4 - - + +
168A LEU* 4.3 27.8 - - + -
169A ALA* 5.2 2.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 4.9 4.3 - - - -
149A ALA 3.0 11.9 + - - -
150A GLY* 3.1 11.9 + - - -
152A ALA* 1.3 77.2 - - - +
154A LYS* 1.3 61.7 + - - +
156A LEU 3.1 9.4 + - - -
157A LYS 3.2 4.9 + - - -
158A VAL* 3.1 26.3 - - - +
160A ARG 3.4 16.7 + - - -
161A ILE* 3.7 6.7 - - - -
165A HIS* 3.0 43.3 + - - +
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 6.1 1.8 - - + -
150A GLY 2.8 12.7 + - - +
151A ASN* 3.2 14.8 + - + +
153A SER* 1.3 75.2 - - - +
155A ASP* 1.3 81.3 + - - +
156A LEU 3.0 0.2 - - - -
157A LYS* 3.0 24.1 + - - +
158A VAL 4.2 6.0 + - - -
----------------------------------------------------------
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 2.9 19.0 + - - +
152A ALA* 3.1 13.2 + - - +
154A LYS* 1.3 99.6 + - - +
156A LEU* 1.3 63.7 + - + +
157A LYS* 3.3 14.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ALA 3.2 12.3 + - - +
153A SER 3.5 4.9 - - - +
154A LYS 3.0 0.8 - - - -
155A ASP* 1.3 82.0 - - + +
157A LYS* 1.3 71.8 + - - +
158A VAL* 3.0 20.0 + - + +
165A HIS* 3.7 26.7 - - + +
168A LEU* 4.2 18.4 - - + -
----------------------------------------------------------
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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