Contacts of the helix formed by residues 118 - 149 (chain L) in PDB entry 1NF6
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 ASP 118 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L LYS* 5.7 0.9 - - - -
12L VAL* 3.4 31.3 - - + +
66L ARG* 3.0 21.3 + - - -
70L LEU* 3.8 7.8 - - - +
113L CYS* 2.9 17.0 + - - +
116L GLN 4.4 3.6 - - - +
117L GLY* 1.3 76.3 - - - +
119L ILE* 1.3 59.9 + - - +
120L VAL 3.6 1.4 + - - -
121L THR* 2.8 35.3 + - - -
122L ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L LYS* 5.5 11.0 - - + +
117L GLY* 3.7 11.7 + - - +
118L ASP* 1.3 75.1 - - - +
120L VAL* 1.3 69.5 + - + +
122L ALA* 3.7 8.4 - - + +
123L ARG* 2.9 37.3 + - + +
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Residues in contact with VAL 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L ARG* 3.6 37.9 - - - +
69L GLU* 5.1 2.0 - - - +
118L ASP* 3.4 1.2 + - - +
119L ILE* 1.3 80.1 - - + +
121L THR* 1.3 60.4 + - - +
123L ARG* 3.4 6.0 + - - +
124L LEU* 3.2 20.2 + - + +
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Residues in contact with THR 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L VAL* 3.6 13.1 - - + +
16L LEU* 3.8 26.7 - - + -
66L ARG* 2.8 25.9 + - + +
70L LEU* 4.1 0.3 - - - +
113L CYS* 3.5 20.2 - - - -
118L ASP* 2.8 32.3 + - - -
120L VAL* 1.3 74.4 - - - +
122L ALA* 1.3 66.3 + - - +
124L LEU* 3.2 7.7 + - + +
125L PHE* 3.0 24.9 + - + -
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Residues in contact with ALA 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L LEU* 3.8 20.8 - - + +
113L CYS* 3.7 19.9 - - + +
114L LYS* 4.5 11.0 - - + -
118L ASP 3.0 19.3 + - - +
119L ILE* 3.3 10.5 + - + +
121L THR* 1.3 77.2 - - - +
123L ARG* 1.3 56.4 + - + +
125L PHE* 3.4 4.0 + - - +
126L GLU* 3.1 36.5 + - - +
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Residues in contact with ARG 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L ILE* 2.9 32.5 + - + +
120L VAL* 3.7 6.7 - - - +
122L ALA* 1.3 73.6 - - + +
124L LEU* 1.3 64.5 + - - +
126L GLU* 3.0 44.9 + - - +
127L ARG* 2.8 81.2 + - - +
130L GLU* 5.8 1.6 + - - -
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU* 4.2 6.7 - - + -
62L ASN* 4.0 32.1 - - + +
63L PHE* 3.8 25.8 - - + -
66L ARG* 4.1 19.3 - - + -
120L VAL* 3.2 11.1 + - + +
121L THR* 3.2 10.5 + - + +
123L ARG* 1.3 79.1 - - - +
125L PHE* 1.3 62.5 + - - +
127L ARG* 3.3 11.9 + - + +
128L ILE* 3.1 44.7 + - + +
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Residues in contact with PHE 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L VAL* 4.1 9.9 - - + -
16L LEU* 4.0 10.3 - - + -
19L ALA* 3.7 31.2 - - + -
63L PHE* 3.7 18.2 - + - -
106L TYR* 4.0 28.0 - + + +
109L PHE* 3.5 28.3 - + + -
110L LEU* 4.1 17.7 - - + -
113L CYS* 3.7 25.1 - - - -
121L THR* 3.0 30.6 + - + -
122L ALA 3.6 7.9 - - - +
124L LEU* 1.3 75.8 - - + +
126L GLU* 1.3 56.0 + - - +
128L ILE* 3.9 3.6 - - - +
129L ILE* 2.9 36.6 + - - +
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Residues in contact with GLU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L LEU* 3.3 34.1 - - + +
114L LYS* 4.3 9.1 - - - -
122L ALA* 3.1 19.7 + - - +
123L ARG* 3.0 41.9 + - - +
124L LEU 3.2 0.2 - - - -
125L PHE* 1.3 73.0 - - - +
127L ARG* 1.3 64.9 + - - +
129L ILE* 3.5 6.4 + - - +
130L GLU* 3.2 28.9 + - - +
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Residues in contact with ARG 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L ARG* 2.8 70.3 + - - +
124L LEU* 3.8 10.3 - - + +
126L GLU* 1.3 74.4 - - - +
128L ILE* 1.3 67.3 + - + +
130L GLU* 3.4 13.9 + - - +
131L GLU* 3.4 24.7 + - - +
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Residues in contact with ILE 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L HIS* 3.4 54.7 - - + +
62L ASN* 4.5 6.7 - - + +
63L PHE* 3.7 28.9 - - + -
106L TYR* 3.8 25.6 - - + -
124L LEU* 3.1 32.3 + - + +
125L PHE* 4.2 2.7 - - - +
127L ARG* 1.3 75.7 - - + +
129L ILE* 1.3 66.7 + - - +
130L GLU 3.1 0.2 - - - -
131L GLU* 3.1 9.1 + - - +
132L GLU* 2.9 20.7 + - + +
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Residues in contact with ILE 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ILE* 4.2 24.1 - - + +
106L TYR* 3.6 40.2 - - + +
107L SER* 4.1 9.2 - - - +
110L LEU* 3.8 25.8 - - + -
125L PHE 2.9 26.5 + - - +
126L GLU* 3.9 6.5 - - + +
127L ARG 3.3 0.4 - - - -
128L ILE* 1.3 77.6 - - - +
130L GLU* 1.3 61.4 + - + +
132L GLU* 3.2 9.8 + - - +
133L GLN* 2.9 27.3 + - + +
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Residues in contact with GLU 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L ARG* 5.8 1.9 + - - -
126L GLU 3.2 17.4 - - - +
127L ARG* 3.4 14.8 + - - +
128L ILE 3.1 0.8 - - - -
129L ILE* 1.3 82.9 - - + +
131L GLU* 1.3 62.7 + - + +
133L GLN* 3.4 8.3 + - - +
134L ALA* 3.2 19.4 + - - +
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K VAL* 3.6 38.4 - - + +
55L ASP* 4.8 1.2 - - - +
58L ARG* 3.7 14.9 + - - -
59L HIS* 2.5 38.3 + - + +
127L ARG* 3.5 14.6 - - - +
128L ILE* 3.1 10.6 + - - +
130L GLU* 1.3 76.0 - - + +
132L GLU* 1.3 67.3 - - - +
134L ALA* 3.1 5.1 + - - +
135L HIS* 3.0 28.3 + - + -
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Residues in contact with GLU 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLU* 3.7 9.7 - - - +
56L GLU* 3.4 9.3 - - - +
59L HIS* 3.4 10.4 - - - -
99L GLU* 3.3 15.8 - - - +
102L THR* 3.1 26.9 + - + +
103L ILE* 3.6 20.9 - - + +
106L TYR* 4.2 9.4 - - + -
128L ILE* 2.9 26.9 + - + +
129L ILE* 3.4 9.6 - - - +
131L GLU* 1.3 77.4 - - - +
133L GLN* 1.3 56.1 + - - +
135L HIS* 3.1 4.9 + - - -
136L LEU* 2.9 27.5 + - - +
200L FE 1.9 31.4 - - - -
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Residues in contact with GLN 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ILE* 3.8 16.7 - - + +
129L ILE* 2.9 17.6 + - + +
130L GLU* 3.7 9.6 - - - +
131L GLU 3.2 0.2 - - - -
132L GLU* 1.3 76.6 - - - +
134L ALA* 1.3 57.7 + - - +
136L LEU* 3.4 24.5 + - - +
137L THR* 3.0 39.8 + - - +
140L GLU* 5.5 0.5 - - - +
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Residues in contact with ALA 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K PHE* 4.1 11.2 - - + -
172K VAL* 4.1 17.9 - - + -
130L GLU 3.2 12.3 + - - +
131L GLU 3.1 10.0 + - - +
133L GLN* 1.3 72.3 - - - +
135L HIS* 1.3 67.9 + - + +
137L THR* 3.5 5.6 + - - +
138L TYR* 3.1 21.7 + - - +
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Residues in contact with HIS 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K PHE* 3.8 18.8 - + - +
172K VAL* 3.8 5.1 - - + +
52L ILE* 3.7 22.4 - - + +
55L ASP* 2.7 38.2 + - + +
56L GLU* 3.3 17.8 + - - -
59L HIS* 4.2 5.2 - + - -
99L GLU* 3.2 18.6 - - + +
131L GLU 3.0 12.5 + - - -
132L GLU* 3.1 8.0 + - - +
133L GLN 3.3 0.2 - - - -
134L ALA* 1.3 74.1 - - - +
136L LEU* 1.3 64.5 + - - +
138L TYR* 3.0 9.2 + - - +
139L TYR* 2.9 28.9 + - + -
200L FE 2.1 28.9 - - - -
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Residues in contact with LEU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ALA* 3.3 30.1 - - - +
99L GLU* 3.9 12.2 - - + +
100L ASP* 4.3 19.3 - - + +
103L ILE* 4.0 11.7 - - + -
132L GLU 2.9 16.5 + - - +
133L GLN* 3.6 30.7 - - - +
135L HIS* 1.3 75.2 - - - +
137L THR* 1.3 62.8 + - - +
139L TYR* 3.2 3.9 + - - +
140L GLU* 2.9 61.1 + - + +
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Residues in contact with THR 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L GLN* 3.0 29.4 + - - +
134L ALA* 3.9 6.5 - - - -
136L LEU* 1.3 75.8 - - - +
138L TYR* 1.3 63.0 + - - +
140L GLU* 3.9 9.7 + - - +
141L ASN* 3.2 40.7 + - - +
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Residues in contact with TYR 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K PHE* 3.5 28.3 - + + -
44L GLU 4.2 1.2 + - - -
45L LEU* 4.0 16.5 + - - +
48L ASN* 3.2 43.6 + - + +
49L MET* 5.2 1.3 - - - -
52L ILE* 3.5 25.1 - - + -
92L TYR* 4.2 5.6 + + - -
134L ALA 3.1 13.0 + - - +
135L HIS* 3.0 9.9 + - - +
137L THR* 1.3 79.5 - - - +
139L TYR* 1.3 78.7 + + - +
141L ASN* 3.4 7.9 + - + +
142L ILE* 3.2 55.3 + - + +
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Residues in contact with TYR 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.7 12.6 - + - -
49L MET* 3.5 29.5 - - + -
52L ILE* 3.3 31.3 - - + +
92L TYR* 3.5 32.0 - + - +
95L ASP* 3.6 42.4 - - + -
96L ALA* 3.9 17.0 - - + +
99L GLU* 3.7 22.2 - - + -
135L HIS* 2.9 23.9 + - + +
136L LEU 3.2 3.1 + - - +
138L TYR* 1.3 91.7 - + - +
140L GLU* 1.3 58.2 + - - +
142L ILE 3.3 0.9 + - - -
143L GLY* 3.0 26.2 + - - -
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ALA* 4.1 12.1 - - + +
133L GLN* 5.5 0.7 - - - +
136L LEU* 2.9 52.5 + - + +
137L THR* 3.9 9.9 + - - +
139L TYR* 1.3 76.3 - - - +
141L ASN* 1.3 59.6 + - - +
143L GLY* 4.0 1.2 - - - +
144L SER* 3.0 29.6 + - - -
147L LYS* 5.5 0.7 - - - -
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Residues in contact with ASN 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L THR* 3.2 35.8 + - - +
138L TYR* 3.6 7.6 - - + +
139L TYR 3.2 0.2 - - - -
140L GLU* 1.3 77.5 - - - +
142L ILE* 1.3 68.8 + - + +
144L SER* 3.3 6.1 + - - -
145L HIS* 3.0 42.1 + - + -
----------------------------------------------------------
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Residues in contact with ILE 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU* 4.0 13.2 - - + -
92L TYR* 3.6 32.5 - - + -
138L TYR* 3.2 50.5 + - + +
139L TYR 3.3 0.9 + - - +
141L ASN* 1.3 80.5 - - + +
143L GLY* 1.3 65.1 + - - +
145L HIS* 3.1 5.7 + - - +
146L ILE* 3.0 39.7 + - + +
153L TYR* 3.3 27.1 - - + +
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Residues in contact with GLY 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L PRO* 5.8 1.3 - - - -
92L TYR* 3.7 20.5 - - - +
93L GLU* 5.4 0.7 - - - -
139L TYR 3.0 13.4 + - - -
140L GLU* 4.1 1.1 - - - -
142L ILE* 1.3 77.1 - - - +
144L SER* 1.3 57.3 + - - +
146L ILE* 3.3 9.0 + - - +
147L LYS* 2.9 41.0 + - - +
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Residues in contact with SER 144 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLU 3.0 21.0 + - - -
141L ASN* 3.5 9.4 - - - -
142L ILE 3.1 0.2 - - - -
143L GLY* 1.3 78.1 - - - +
145L HIS* 1.3 63.6 + - - +
147L LYS* 3.4 15.4 - - - +
148L ASN* 2.6 48.0 + - - +
----------------------------------------------------------
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Residues in contact with HIS 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L ASN* 3.0 30.0 + - + -
142L ILE* 3.1 6.1 + - - +
144L SER* 1.3 82.9 + - - +
146L ILE* 1.3 56.6 + - - +
148L ASN* 4.8 1.1 - - + -
149L LEU* 2.7 56.0 + - + +
150L GLY 3.4 1.0 + - - -
153L TYR* 3.7 42.6 + + + +
----------------------------------------------------------
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Residues in contact with ILE 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L VAL* 3.3 32.3 - - + +
89L PRO* 3.9 32.3 - - + -
92L TYR* 3.8 8.7 - - + -
142L ILE* 3.0 38.9 + - + +
143L GLY* 3.6 7.6 - - - +
145L HIS* 1.3 78.4 - - - +
147L LYS* 1.3 61.2 + - + +
150L GLY* 3.1 26.9 + - - +
153L TYR* 4.2 17.0 - - + -
154L LEU* 4.7 9.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L GLU* 6.0 5.1 - - - +
140L GLU 5.5 0.7 - - - -
143L GLY* 2.9 23.2 + - - +
144L SER* 3.4 21.8 - - - +
146L ILE* 1.3 81.1 - - + +
148L ASN* 1.3 73.9 + - - +
149L LEU 3.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ASN 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L SER* 2.6 43.2 + - - +
145L HIS* 4.8 1.3 - - + -
147L LYS* 1.3 91.0 - - - +
149L LEU* 1.3 75.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145L HIS* 2.7 48.1 + - + +
148L ASN* 1.3 95.8 - - + +
150L GLY* 1.3 58.6 + - - +
151L ASP 3.7 2.1 + - - -
152L THR* 4.2 14.4 + - - -
153L TYR* 4.3 20.0 - - + +
----------------------------------------------------------
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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