Contacts of the helix formed by residues 87 - 116 (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 ALA 87 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L MET* 5.2 4.3 - - - -
85L GLY 3.6 3.0 + - - -
86L GLN* 1.3 75.6 - - - +
88L VAL* 1.3 68.0 + - - +
89L PRO* 3.3 12.1 - - + -
90L VAL* 2.8 22.8 + - + +
91L ILE* 2.9 11.0 + - - +
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Residues in contact with VAL 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L LEU* 4.1 14.6 - - + -
40L MET* 3.8 28.3 - - + +
42L TYR* 4.2 15.3 - - + -
45L LEU* 4.7 2.0 - - + -
86L GLN 4.0 0.2 + - - -
87L ALA* 1.3 70.0 - - - +
89L PRO* 1.3 73.3 - - + +
91L ILE* 3.2 18.2 + - - +
92L TYR* 3.2 28.5 - - + -
146L ILE* 3.3 30.3 - - + -
154L LEU* 4.5 18.6 - - + -
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Residues in contact with PRO 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L ALA* 3.4 13.5 - - + -
88L VAL* 1.3 96.2 - - + +
90L VAL* 1.3 63.5 + - + +
92L TYR* 3.7 1.5 + - + +
93L GLU* 3.2 24.8 + - - +
143L GLY* 5.8 2.1 - - - -
146L ILE* 3.9 31.0 - - + -
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Residues in contact with VAL 90 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L VAL* 5.9 0.2 - - + -
86L GLN* 3.5 31.9 - - + +
87L ALA* 2.8 17.5 + - + +
89L PRO* 1.3 79.5 - - + +
91L ILE* 1.3 59.3 + - - +
93L GLU* 3.8 16.7 - - - +
94L SER* 2.8 35.6 + - - +
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Residues in contact with ILE 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L GLN* 3.6 38.6 - - + +
36L SER* 4.9 4.0 - - - -
37L LEU* 4.0 26.2 - - + -
40L MET* 4.9 1.8 - - + -
49L MET* 3.6 30.1 - - + -
86L GLN* 3.6 22.7 - - + +
87L ALA 2.9 15.8 + - - +
88L VAL* 3.3 11.9 - - - +
90L VAL* 1.3 78.4 - - - +
92L TYR* 1.3 68.5 + - + +
94L SER* 3.2 3.9 + - - -
95L ASP* 2.9 34.9 + - - +
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Residues in contact with TYR 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L LEU* 3.2 27.2 - - + +
45L LEU* 3.2 31.1 + - + +
49L MET* 3.9 9.7 - - + +
88L VAL* 3.2 23.6 + - + +
89L PRO 4.6 1.6 - - - +
91L ILE* 1.3 89.9 - - + +
93L GLU* 1.3 61.6 + - - +
95L ASP* 4.4 2.5 - - - -
96L ALA* 3.1 26.0 + - - +
138L TYR* 4.2 5.5 + + - -
139L TYR* 3.5 35.2 - + - +
142L ILE* 3.6 41.1 - - + -
143L GLY* 3.7 27.1 - - - +
146L ILE* 3.8 5.4 - - + -
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Residues in contact with GLU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L PRO 3.2 18.6 + - - +
90L VAL* 3.8 20.6 - - - +
91L ILE 3.2 0.4 - - - -
92L TYR* 1.3 78.3 - - - +
94L SER* 1.3 58.2 + - - +
96L ALA* 3.7 3.5 - - - +
97L ASP* 3.1 41.3 + - - +
143L GLY* 5.4 1.3 - - - -
147L LYS* 6.0 5.4 - - - +
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Residues in contact with SER 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L GLN* 5.7 1.0 + - - +
83L VAL* 6.5 0.2 - - - -
86L GLN* 3.0 24.4 + - - -
90L VAL* 2.8 25.7 + - - -
91L ILE 3.2 4.2 + - - -
93L GLU* 1.3 76.5 - - - +
95L ASP* 1.3 63.3 + - - +
97L ASP* 3.3 10.1 + - - +
98L GLN* 2.7 36.6 + - - +
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Residues in contact with ASP 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L GLN* 4.5 2.3 - - - +
30L TYR* 3.1 24.9 - - + -
33L GLN* 2.4 41.6 + - - +
49L MET* 3.2 19.8 - - - +
91L ILE 2.9 17.7 + - - +
92L TYR 4.3 0.4 - - - +
94L SER* 1.3 74.7 + - - +
96L ALA* 1.3 60.8 + - - +
98L GLN* 3.7 3.1 - - - +
99L GLU* 3.0 36.2 + - - +
139L TYR* 3.6 26.5 - - + -
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Residues in contact with ALA 96 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L TYR 3.1 21.7 + - - +
93L GLU* 3.7 4.7 - - - +
94L SER 3.3 0.2 - - - -
95L ASP* 1.3 78.3 - - - +
97L ASP* 1.3 63.7 + - - +
100L ASP* 3.2 19.6 + - - +
136L LEU* 3.3 15.5 - - + +
139L TYR* 3.9 16.7 - - + +
140L GLU* 4.1 23.6 - - + +
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Residues in contact with ASP 97 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L GLU* 3.1 31.6 + - - +
94L SER* 3.3 10.4 + - - +
96L ALA* 1.3 77.3 - - - +
98L GLN* 1.3 59.3 + - - +
100L ASP* 3.3 7.6 + - - +
101L ALA* 2.9 29.7 + - - +
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L MET 4.5 3.0 + - - -
25L HIS* 3.2 39.6 + - - -
26L ALA* 3.6 26.5 - - - +
29L GLN* 4.0 11.8 + - - +
30L TYR* 3.6 18.3 + - - +
94L SER 2.7 20.9 + - - +
95L ASP* 3.7 6.0 - - - +
96L ALA 3.2 0.2 - - - -
97L ASP* 1.3 75.2 - - - +
99L GLU* 1.3 57.9 + - - +
101L ALA* 3.4 7.3 + - + +
102L THR* 2.8 40.7 + - - +
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Residues in contact with GLU 99 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ALA* 5.1 0.9 - - - +
30L TYR* 2.5 24.9 + - - +
56L GLU* 3.3 6.8 - - - +
95L ASP 3.0 20.8 + - - +
96L ALA 4.0 1.3 - - - +
98L GLN* 1.3 79.2 + - - +
100L ASP* 1.3 57.5 + - - +
102L THR* 3.6 6.2 + - - -
103L ILE* 2.9 35.6 + - - +
132L GLU* 3.1 18.7 - - - +
135L HIS* 3.2 14.2 - - + +
136L LEU* 3.9 20.9 - - + -
139L TYR* 3.7 16.8 - - + -
200L FE 2.2 30.8 - - - -
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Residues in contact with ASP 100 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ALA 3.2 16.6 + - - +
97L ASP* 3.5 6.9 - - - +
98L GLN 3.1 0.4 - - - -
99L GLU* 1.3 76.9 - - - +
101L ALA* 1.3 68.2 + - - +
103L ILE* 3.4 10.5 + - - +
104L GLU* 3.0 31.0 + - - +
136L LEU* 4.3 16.6 - - + +
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Residues in contact with ALA 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L MET* 4.8 5.4 - - + -
97L ASP 2.9 17.0 + - - +
98L GLN* 3.7 7.2 - - + +
100L ASP* 1.3 79.3 + - - +
102L THR* 1.3 57.8 + - - +
104L GLU* 3.1 9.4 + - - +
105L ALA* 2.9 29.7 + - - +
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Residues in contact with THR 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L MET* 4.0 21.1 - - + +
23L GLU* 4.7 0.7 - - - +
98L GLN* 2.8 37.3 + - - +
99L GLU* 3.6 8.8 + - - -
100L ASP 3.2 0.2 - - - -
101L ALA* 1.3 73.7 - - - +
103L ILE* 1.3 63.7 + - - +
105L ALA 3.2 0.7 + - - -
106L TYR* 2.9 57.1 + - + +
132L GLU* 3.1 26.3 + - - +
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Residues in contact with ILE 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L GLU 2.9 22.3 + - - +
100L ASP* 3.8 6.5 - - - +
102L THR* 1.3 76.0 - - - +
104L GLU* 1.3 57.2 + - + +
106L TYR* 3.4 5.9 + - - +
107L SER* 2.5 43.3 + - - +
129L ILE* 4.2 22.6 - - + +
132L GLU* 3.6 24.2 - - + +
133L GLN* 3.8 36.3 - - + +
136L LEU* 4.0 20.2 - - + -
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L ASP* 3.0 22.3 + - - +
101L ALA* 3.2 12.8 - - - +
103L ILE* 1.3 80.8 - - + +
105L ALA* 1.3 58.3 + - - +
107L SER* 3.3 21.7 + - - -
108L GLN* 2.5 41.2 + - - +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L MET* 3.7 25.4 - - + -
101L ALA 2.9 16.0 + - - +
102L THR 3.8 0.4 - - - +
104L GLU* 1.3 75.4 - - - +
106L TYR* 1.3 58.9 + - - +
108L GLN* 2.9 32.4 + - - +
109L PHE* 3.0 31.8 + - + -
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Residues in contact with TYR 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L ALA* 3.4 26.0 + - + -
22L MET* 4.1 11.7 - - - +
23L GLU* 2.6 41.3 + - - +
63L PHE* 3.6 10.0 - + - -
102L THR* 2.9 43.2 + - + +
103L ILE 3.9 0.9 - - - +
105L ALA* 1.3 76.3 - - + +
107L SER* 1.3 57.3 + - - +
109L PHE* 3.7 19.3 - + - +
110L LEU* 2.9 28.9 + - - +
125L PHE* 4.0 14.1 - + + -
128L ILE* 3.8 24.5 - - + -
129L ILE* 3.6 29.1 - - + +
132L GLU* 4.2 5.8 - - + -
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Residues in contact with SER 107 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ILE* 2.5 30.6 + - - +
104L GLU* 3.4 18.2 + - - -
105L ALA 3.1 0.2 - - - -
106L TYR* 1.3 78.1 - - - +
108L GLN* 1.3 61.8 + - - +
110L LEU* 3.5 6.2 - - - +
111L LYS* 3.2 21.1 + - - +
129L ILE* 4.1 11.8 - - - +
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Residues in contact with GLN 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L GLU* 2.5 45.4 + - - +
105L ALA* 2.9 13.4 + - - +
107L SER* 1.3 78.2 - - - +
109L PHE* 1.3 72.3 + - + +
111L LYS* 3.0 35.4 + - + +
112L VAL* 3.0 13.2 + - + +
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Residues in contact with PHE 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L VAL* 3.5 32.5 - - + +
18L LYS* 3.9 34.1 - - + -
19L ALA* 4.0 15.9 - - + -
22L MET* 4.2 7.2 - - - -
105L ALA* 3.0 32.1 + - + -
106L TYR* 3.4 23.1 + + - +
108L GLN* 1.3 82.9 - - + +
110L LEU* 1.3 56.1 + - - +
112L VAL* 3.0 6.5 + - + +
113L CYS* 3.0 31.6 + - - -
125L PHE* 3.5 31.9 - + + -
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L TYR 2.9 16.3 + - - +
107L SER* 3.5 7.6 - - - +
109L PHE* 1.3 75.6 - - - +
111L LYS* 1.3 63.1 + - - +
113L CYS* 3.2 7.7 + - - +
114L LYS* 3.0 58.1 + - + +
122L ALA* 3.8 17.3 - - + +
125L PHE* 4.1 9.1 - - + -
126L GLU* 3.3 37.5 - - + +
129L ILE* 3.8 21.8 - - + -
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Residues in contact with LYS 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L SER 3.2 11.2 + - - +
108L GLN* 3.0 27.9 + - + +
110L LEU* 1.3 81.2 - - - +
112L VAL* 1.3 60.8 + - + +
114L LYS* 3.4 11.0 + - + +
115L GLU* 3.0 41.8 + - - +
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Residues in contact with VAL 112 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L LYS* 4.1 23.6 - - + +
12L VAL* 5.1 0.9 - - - +
15L VAL* 4.3 21.3 - - + -
108L GLN* 3.0 17.7 + - + +
109L PHE* 3.0 7.4 + - + +
111L LYS* 1.3 75.2 - - + +
113L CYS* 1.3 61.8 + - - +
115L GLU* 3.1 17.2 + - - +
116L GLN* 2.9 45.4 + - + +
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Residues in contact with CYS 113 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L VAL* 4.1 15.5 - - - -
15L VAL* 4.6 3.6 - - - -
109L PHE 3.0 17.3 + - - -
110L LEU 3.2 9.1 + - - +
112L VAL* 1.3 76.9 - - - +
114L LYS* 1.3 61.2 + - - +
116L GLN 3.1 2.9 + - - -
117L GLY 3.1 4.0 + - - -
118L ASP* 2.9 37.3 + - + +
121L THR* 3.5 32.5 - - - -
122L ALA* 3.7 18.2 - - + -
125L PHE* 3.7 17.5 - - - -
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Residues in contact with LYS 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L LEU* 3.0 42.8 + - + +
111L LYS* 3.6 12.2 - - + +
113L CYS* 1.3 77.6 - - - +
115L GLU* 1.3 62.8 + - + +
117L GLY* 3.0 15.0 + - - +
118L ASP 4.8 1.1 - - - +
119L ILE* 5.5 11.1 - - + +
122L ALA* 4.5 9.0 - - + -
126L GLU* 4.3 9.0 + - - -
2204L SO4 2.0 45.9 + - - +
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Residues in contact with GLU 115 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ARG* 5.5 0.5 - - - +
111L LYS* 3.0 32.0 + - + +
112L VAL* 3.1 26.1 + - - +
114L LYS* 1.3 76.7 - - + +
116L GLN* 1.3 71.9 + - - +
117L GLY 3.3 0.9 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L GLY 4.8 3.7 + - - +
7L ASP 4.5 0.5 - - - -
8L ARG* 2.7 71.2 + - + +
11L LYS* 3.4 51.4 + - + +
12L VAL* 3.7 20.2 - - + -
112L VAL* 2.9 25.7 + - + +
113L CYS 3.7 4.0 - - - +
114L LYS 3.1 0.6 - - - -
115L GLU* 1.3 90.4 + - - +
117L GLY* 1.3 60.8 + - - +
118L ASP* 3.2 2.3 + - - +
----------------------------------------------------------
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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