Contacts of the helix formed by residues 129 - 156 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER* 3.4 19.9 + - - -
87C VAL* 3.6 34.8 - - + -
90C TYR* 5.0 6.7 - - + -
91C THR* 5.0 10.8 - - + -
127C GLY 3.3 0.4 - - - -
128C ALA* 1.3 82.8 - - + +
130C ALA* 1.3 64.2 + - - +
131C ALA 3.3 1.8 - - - -
132C VAL* 3.3 10.2 + - - +
133C TYR* 3.1 25.8 + - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.5 26.0 - - + +
59C THR 4.3 10.1 - - - -
60C SER* 4.6 7.6 - - - +
63C ILE* 4.4 7.8 - - + +
116C LEU* 4.3 4.9 - - + -
126C VAL* 4.0 9.4 - - + -
127C GLY* 3.2 14.8 + - - +
129C THR* 1.3 80.2 + - - +
131C ALA* 1.3 56.3 + - - +
133C TYR* 3.6 5.8 + - - +
134C SER* 2.9 32.2 + - - -
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 4.1 3.8 - - - +
109C VAL* 3.7 31.8 - - + +
112C ILE* 3.9 5.2 - - + +
113C HIS* 3.8 33.4 - - + +
116C LEU* 4.1 9.2 - - + -
127C GLY 4.4 2.4 + - - -
128C ALA 4.4 0.4 + - - -
129C THR 3.3 0.4 - - - -
130C ALA* 1.3 75.6 - - - +
132C VAL* 1.3 57.4 + - - +
134C SER* 3.7 0.9 - - - -
135C ALA* 2.7 36.4 + - - +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 3.8 24.2 - - + -
87C VAL* 3.7 26.2 - - + +
90C TYR* 3.8 40.4 - - + -
99C ARG* 5.4 0.2 - - - +
103C ALA* 3.9 12.6 - - + -
105C LEU* 3.9 2.8 - - + +
109C VAL* 4.0 16.8 - - + -
128C ALA 5.1 4.3 - - - +
129C THR* 3.3 9.1 + - - +
131C ALA* 1.3 74.6 - - + +
133C TYR* 1.3 66.8 + - - +
135C ALA* 3.1 4.1 + - - +
136C ALA* 2.8 24.8 + - - +
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER* 3.3 36.8 - - - -
63C ILE* 4.8 9.2 - - + -
64C GLN* 6.3 2.7 - - + -
80C VAL* 3.5 18.3 - - + +
83C GLY* 3.5 15.0 - - - -
84C THR* 2.4 50.0 + - - +
87C VAL* 3.4 29.8 - - + +
129C THR* 3.1 15.8 + - - +
130C ALA 3.7 8.5 - - - +
132C VAL* 1.3 76.0 - - - +
134C SER* 1.3 58.1 + - - +
136C ALA* 3.3 2.1 + - - +
137C ILE* 2.9 46.0 + - + +
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 4.5 11.5 - - - -
42C ILE* 5.3 2.9 - - - +
63C ILE* 3.4 30.2 - - - +
112C ILE* 3.9 17.5 - - - -
116C LEU* 3.9 5.7 - - - +
130C ALA 2.9 20.0 + - - -
131C ALA* 3.7 4.0 - - - -
133C TYR* 1.3 79.0 - - - +
135C ALA* 1.3 62.8 + - - +
137C ILE* 3.3 5.8 + - - +
138C LEU* 3.0 31.4 + - - +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 3.8 17.9 - - + -
107C PHE* 3.8 11.9 - - + +
109C VAL* 4.1 15.9 - - + -
112C ILE* 3.7 26.9 - - + +
131C ALA 2.7 21.4 + - - +
132C VAL 3.8 0.2 - - - +
134C SER* 1.3 72.9 - - - +
136C ALA* 1.3 53.4 + - - +
138C LEU* 3.5 2.9 + - - +
139C GLU* 2.8 36.0 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 5.1 1.3 - - - -
82C GLU* 3.7 28.0 - - + +
83C GLY* 3.7 6.5 - - - -
86C ALA* 3.8 13.9 - - + -
105C LEU* 3.5 17.2 - - + +
132C VAL 2.8 16.9 + - - +
133C TYR 3.6 3.8 - - - +
135C ALA* 1.3 77.9 - - - +
137C ILE* 1.3 56.7 + - - +
139C GLU* 3.3 2.4 + - - +
140C TYR* 2.8 30.9 + - - +
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 4.5 10.1 - - + -
63C ILE* 4.3 11.2 - - + -
64C GLN* 5.8 0.4 - - - -
67C VAL* 3.7 35.0 - - + -
71C LEU* 5.3 0.2 - - + -
79C ALA* 3.3 37.0 - - + +
80C VAL* 4.2 17.7 - - + -
83C GLY* 4.8 1.6 - - - -
133C TYR* 2.9 30.9 + - + +
134C SER* 3.7 4.9 - - - +
136C ALA* 1.3 72.8 - - - +
138C LEU* 1.3 67.3 + - + +
140C TYR* 3.2 5.7 + - - +
141C LEU* 3.1 37.4 + - + +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 5.5 1.8 - - + +
34C PHE* 5.5 0.2 - - - -
35C VAL* 4.4 18.4 - - + +
38C ILE* 3.9 28.3 - - + -
39C PHE* 3.7 47.3 - - + +
42C ILE* 4.8 8.1 - - + -
107C PHE* 3.8 17.9 - - + -
112C ILE* 4.4 16.6 - - + -
134C SER* 3.0 20.6 + - - +
135C ALA 3.8 0.4 - - - +
137C ILE* 1.3 76.6 - - + +
139C GLU* 1.3 62.4 + - - +
141C LEU* 3.6 4.7 + - + +
142C THR* 3.0 29.6 + - - -
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Residues in contact with GLU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 4.1 13.2 - - + +
16C GLN* 5.0 4.2 - - - +
104C GLY 4.4 2.9 - - - +
105C LEU* 3.6 18.0 - - + +
106C GLN* 2.6 49.1 + - - +
107C PHE* 2.7 29.4 + - + +
135C ALA 2.8 21.8 + - - +
136C ALA* 3.7 7.9 - - - +
137C ILE 3.2 0.2 - - - -
138C LEU* 1.3 73.0 - - - +
140C TYR* 1.3 57.8 + - - +
142C THR* 3.7 1.7 - - - -
143C ALA* 3.0 28.8 + - + +
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Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.1 33.0 + - + +
117A LYS* 4.9 16.4 - - + -
75C LEU* 3.8 22.2 - - + -
78C HIS* 3.3 27.7 + - + +
79C ALA* 3.9 18.4 - - + -
82C GLU* 3.5 37.5 - - + +
136C ALA 2.8 20.2 + - - +
137C ILE* 3.2 6.5 + - - +
139C GLU* 1.3 74.0 - - - +
141C LEU* 1.3 69.7 + - + +
143C ALA* 3.3 7.2 + - + +
144C GLU* 3.0 27.7 + - + +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PHE* 3.9 17.0 - - + -
38C ILE* 4.2 30.1 - - + -
42C ILE* 5.5 0.4 - - + -
71C LEU* 4.0 22.7 - - + -
75C LEU* 3.8 35.2 - - + -
79C ALA* 5.0 0.4 - - + -
137C ILE* 3.1 32.4 + - + +
138C LEU* 4.1 6.7 - - + +
140C TYR* 1.3 80.3 - - + +
142C THR* 1.3 63.0 + - - +
144C GLU* 3.5 5.7 + - + +
145C VAL* 3.1 28.8 + - - +
176C LEU* 5.4 3.7 - - + +
179C LEU* 4.4 7.4 - - + -
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 4.2 16.2 - - + -
13C VAL* 4.2 11.9 - - + -
31C MET* 4.2 13.7 - - + -
34C PHE* 4.1 10.5 - - - -
35C VAL* 3.7 13.0 - - - +
107C PHE* 3.5 17.9 - - + -
138C LEU 3.0 18.5 + - - -
139C GLU 3.7 4.5 - - - -
141C LEU* 1.3 74.4 - - - +
143C ALA* 1.3 66.6 + - - +
145C VAL* 3.3 2.4 + - - +
146C LEU* 3.0 48.5 + - + +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 5.3 2.9 - - - +
13C VAL* 3.6 22.6 - - + +
17C VAL* 4.4 14.1 - - + +
139C GLU* 3.0 20.9 + - + +
140C TYR* 3.7 7.6 - - + +
142C THR* 1.3 75.4 - - - +
144C GLU* 1.3 53.7 + - - +
146C LEU* 3.6 1.9 - - - +
147C GLU* 2.7 40.6 + - - +
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY* 4.7 0.7 - - - +
113A HIS* 4.0 14.1 + - - -
114A ARG* 2.8 45.1 + - - +
117A LYS* 2.2 39.2 + - - +
75C LEU* 5.8 1.3 - - + -
140C TYR* 3.0 23.3 + - + +
141C LEU* 3.8 8.1 - - + +
143C ALA* 1.3 77.1 - - - +
145C VAL* 1.3 63.2 + - + +
147C GLU* 3.4 4.0 + - - +
148C LEU* 3.3 44.1 + - + +
176C LEU* 4.4 13.5 - - + -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C MET* 3.9 26.9 - - + -
34C PHE* 3.9 24.2 - - + -
141C LEU 3.1 17.5 + - - +
142C THR 3.9 3.1 - - - +
144C GLU* 1.3 75.1 - - - +
146C LEU* 1.3 58.8 + - - +
148C LEU* 3.3 7.2 + - - +
149C ALA* 2.8 27.4 + - - +
166C LEU* 3.9 15.0 - - + -
169C ALA* 4.0 5.4 - - + +
170C ILE* 4.2 28.7 - - + -
176C LEU* 4.6 15.0 - - + -
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 14.8 - - + +
13C VAL* 4.0 4.0 - - + -
14C LEU* 3.6 35.7 - - + +
17C VAL* 4.2 12.8 - - + -
18C HIS* 3.6 4.2 - - - -
23C ILE* 4.4 8.1 - - + -
31C MET* 4.2 27.8 - - + -
142C THR* 3.0 40.5 + - + +
143C ALA* 3.8 2.5 - - - +
145C VAL* 1.3 74.8 - - - +
147C GLU* 1.3 60.1 + - - +
149C ALA* 4.0 3.3 - - - +
150C GLY* 2.8 28.4 + - - -
161C ILE* 4.0 18.5 - - + +
166C LEU* 4.9 3.1 - - + -
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 3.1 31.7 + - - +
117A LYS* 3.5 25.0 + - - +
125A ARG* 6.0 0.7 - - - +
126A VAL 3.8 13.2 + - - +
17C VAL* 4.2 17.3 - - + +
18C HIS* 3.0 31.2 + - - +
143C ALA* 2.7 21.9 + - - +
144C GLU* 3.7 7.4 - - - +
145C VAL 3.2 0.2 - - - -
146C LEU* 1.3 72.9 - - - +
148C LEU* 1.3 59.7 + - + +
151C ASN* 3.0 29.5 + - - +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.1 34.5 - - - +
110A GLY* 6.5 0.7 - - - -
113A HIS* 4.9 12.1 - - + +
144C GLU* 3.3 35.3 + - - +
147C GLU* 1.3 74.8 - - + +
149C ALA* 1.3 66.5 + - - +
151C ASN* 3.2 15.1 + - - +
152C ALA* 2.9 23.6 + - - +
169C ALA* 3.5 25.2 - - + +
173C ASP* 4.8 8.5 - - + +
176C LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C VAL 2.8 20.9 + - - +
146C LEU* 4.0 1.1 - - - +
148C LEU* 1.3 70.9 - - - +
150C GLY* 1.3 59.0 + - - +
152C ALA* 3.0 5.0 + - - +
153C SER* 2.8 28.4 + - - -
161C ILE* 3.8 33.2 - - + -
165C HIS* 3.7 22.4 - - - +
166C LEU* 3.8 16.4 - - + -
169C ALA* 3.5 2.3 - - + +
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C HIS* 3.5 23.1 - - - -
21C THR* 4.9 2.9 + - - -
146C LEU 2.8 19.2 + - - -
149C ALA* 1.3 75.8 - - - +
151C ASN* 1.3 59.9 + - - +
153C SER* 3.2 7.9 + - - -
154C LYS* 3.1 25.8 + - - +
161C ILE* 3.8 13.6 - - - +
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Residues in contact with ASN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 5.8 2.8 - - - +
113A HIS* 5.3 4.4 - - - -
128A ALA* 3.9 35.2 + - + +
18C HIS* 3.4 17.8 + - - -
147C GLU* 3.0 34.5 + - - +
148C LEU* 3.2 17.0 + - - +
150C GLY* 1.3 74.7 - - - +
152C ALA* 1.3 60.9 + - - +
154C LYS* 3.6 8.6 + - - +
155C ASP* 3.0 32.9 + - - +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU 2.9 13.8 + - - +
149C ALA* 3.3 12.6 - - - +
151C ASN* 1.3 75.6 - - - +
153C SER* 1.3 62.0 + - - +
155C ASP* 3.3 8.8 + - - +
156C LEU* 3.3 27.9 + - - +
165C HIS* 4.1 8.5 - - + +
168C LEU* 4.1 32.8 - - + -
169C ALA* 5.3 0.9 - - - +
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Residues in contact with SER 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 4.4 13.0 + - - +
149C ALA 2.8 12.0 + - - -
150C GLY* 3.4 12.9 + - - -
152C ALA* 1.3 73.6 - - - +
154C LYS* 1.3 68.6 + - - +
156C LEU 3.3 7.6 + - - -
157C LYS 3.4 0.2 + - - -
158C VAL* 3.0 39.0 + - - +
160C ARG 4.2 11.0 + - - -
161C ILE* 4.5 3.6 - - - -
165C HIS* 3.9 30.4 - - - -
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 5.8 4.0 - - - +
18C HIS* 3.1 37.3 + - + +
19C PRO* 5.9 1.4 - - - +
21C THR* 4.1 13.2 - - - +
150C GLY 3.1 14.6 + - - +
151C ASN* 4.0 8.1 - - - +
152C ALA 3.4 0.4 - - - -
153C SER* 1.3 82.6 + - - +
155C ASP* 1.3 65.2 + - - +
157C LYS* 3.3 17.8 + - - +
158C VAL 4.4 5.8 - - - +
----------------------------------------------------------
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 5.5 4.3 - - - -
91A THR* 6.0 2.1 - - - -
102A ARG* 4.4 15.6 + - - -
128A ALA* 5.8 2.9 - - - +
151C ASN* 3.0 18.2 + - - +
152C ALA* 3.6 11.7 - - - +
153C SER 3.3 0.2 - - - -
154C LYS* 1.3 80.3 - - - +
156C LEU* 1.3 62.1 + - + +
157C LYS* 3.2 15.5 + - - +
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS* 6.6 0.4 - - + -
152C ALA 3.3 18.0 + - - +
153C SER 3.3 4.0 + - - +
154C LYS 3.3 0.8 - - - -
155C ASP* 1.3 79.3 - - + +
157C LYS* 1.3 73.0 + - - +
158C VAL* 3.5 12.4 + - + +
164C ARG* 3.8 29.8 - - - +
165C HIS* 3.6 27.8 - - + +
168C LEU* 4.0 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