Contacts of the helix formed by residues 87 - 116 (chain P) in PDB entry 1NF4
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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P MET* 6.2 0.4 - - - -
85P GLY 3.6 3.6 + - - -
86P GLN* 1.3 74.0 - - - +
88P VAL* 1.3 68.0 + - - +
89P PRO* 3.8 13.2 - - + -
90P VAL* 3.0 18.6 + - + +
91P ILE* 2.8 20.4 + - - +
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Residues in contact with VAL 88 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 4.5 9.4 - - + -
40P MET* 3.8 32.7 - - + +
42P TYR* 4.8 8.7 - - + -
45P LEU* 4.9 3.8 - - + -
87P ALA* 1.3 69.6 - - - +
89P PRO* 1.3 71.2 - - + +
91P ILE* 3.1 16.7 + - + +
92P TYR* 3.2 31.6 - - + -
146P ILE* 3.8 24.9 - - + -
154P LEU* 4.6 22.2 - - + -
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Residues in contact with PRO 89 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 5.5 6.5 - - - +
87P ALA* 3.4 12.8 - - + -
88P VAL* 1.3 96.4 - - + +
90P VAL* 1.3 59.1 + - + +
92P TYR* 3.4 1.7 + - - +
93P GLU* 3.0 30.9 + - - +
143P GLY* 6.0 1.0 - - - -
146P ILE* 4.4 28.3 - - + -
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Residues in contact with VAL 90 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P VAL* 6.0 0.7 - - + -
86P GLN* 4.1 19.5 - - + +
87P ALA* 3.0 26.5 + - + +
89P PRO* 1.3 77.7 - - + +
91P ILE* 1.3 58.7 + - - +
93P GLU* 4.3 20.0 - - - +
94P SER* 2.3 49.5 + - - +
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Residues in contact with ILE 91 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P GLN* 3.9 34.1 - - + +
36P SER* 5.2 5.6 - - - -
37P LEU* 4.3 19.7 - - + -
40P MET* 5.3 1.8 - - + -
49P MET* 3.8 13.2 - - + -
86P GLN* 3.9 28.0 - - + +
87P ALA 2.8 15.0 + - - +
88P VAL* 3.1 17.0 + - + +
90P VAL* 1.3 76.9 - - - +
92P TYR* 1.3 77.7 + - + +
94P SER* 4.0 2.4 + - - -
95P ASP* 2.9 48.6 + - - +
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Residues in contact with TYR 92 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 3.3 25.1 - - + +
45P LEU* 3.4 24.5 + - + +
49P MET* 3.8 16.8 - - + +
88P VAL* 3.2 31.6 + - + +
89P PRO 4.3 1.3 - - - +
91P ILE* 1.3 91.6 - - + +
93P GLU* 1.3 61.1 + - - +
95P ASP* 3.8 2.1 - - - +
96P ALA* 2.9 31.5 + - - +
138P TYR* 4.4 5.7 + + - -
139P TYR* 3.6 38.3 - + - +
142P ILE* 3.7 33.2 - - + -
143P GLY* 4.0 15.7 - - - +
146P ILE* 3.6 11.4 - - + -
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Residues in contact with GLU 93 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P PRO 3.0 18.9 + - - +
90P VAL* 3.8 19.1 - - - +
92P TYR* 1.3 78.9 - - - +
94P SER* 1.3 76.8 + - - +
96P ALA* 3.4 3.9 + - - +
97P ASP* 3.1 36.0 + - - +
143P GLY* 5.6 1.2 - - - -
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Residues in contact with SER 94 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P GLN* 3.5 16.1 + - - -
90P VAL* 2.3 48.0 + - - +
91P ILE 4.0 1.2 + - - -
93P GLU* 1.3 80.2 + - - +
95P ASP* 1.3 62.4 + - - +
97P ASP* 3.3 7.6 + - - +
98P GLN* 2.8 31.0 + - - +
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Residues in contact with ASP 95 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P GLN* 4.8 2.4 - - - +
30P TYR* 3.5 17.7 - - - -
33P GLN* 2.6 41.2 + - - +
49P MET* 3.5 18.2 - - - +
91P ILE* 2.9 23.0 + - - +
92P TYR 3.8 1.1 - - - +
94P SER* 1.3 76.0 - - - +
96P ALA* 1.3 64.8 + - - +
98P GLN* 3.4 6.2 + - - +
99P GLU* 2.9 28.9 + - - +
139P TYR* 3.5 29.4 - - + -
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Residues in contact with ALA 96 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P TYR 2.9 18.3 + - - +
93P GLU* 3.8 4.5 - - - +
95P ASP* 1.3 75.8 - - - +
97P ASP* 1.3 65.8 + - - +
99P GLU 3.2 0.9 + - - -
100P ASP* 3.0 20.3 + - - +
136P LEU* 3.3 16.5 - - + +
139P TYR* 3.9 12.0 - - + +
140P GLU* 4.0 29.8 - - + +
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Residues in contact with ASP 97 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P GLU* 3.1 35.7 + - - +
94P SER* 3.7 8.6 - - - +
96P ALA* 1.3 78.9 - - - +
98P GLN* 1.3 57.5 + - - +
100P ASP* 3.3 7.2 + - - +
101P ALA* 3.0 28.5 + - - +
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Residues in contact with GLN 98 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P HIS* 2.9 42.0 + - - -
26P ALA* 4.2 10.3 - - + +
29P GLN* 4.1 8.4 + - - +
30P TYR* 3.9 27.6 + - - +
79P GLU* 5.1 3.0 - - - +
94P SER 2.8 21.0 + - - +
95P ASP* 3.8 7.8 + - - +
97P ASP* 1.3 70.3 - - - +
99P GLU* 1.3 65.6 + - - +
101P ALA* 3.4 7.5 + - + +
102P THR* 3.1 31.6 + - - +
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Residues in contact with GLU 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 2.7 25.1 + - - +
56P GLU* 3.1 3.6 - - - +
95P ASP 2.9 21.8 + - - +
96P ALA 3.9 1.8 - - - +
98P GLN* 1.3 75.1 - - - +
100P ASP* 1.3 65.8 + - - +
102P THR* 3.2 7.4 + - - -
103P ILE* 3.1 28.4 + - - +
132P GLU* 3.0 24.3 - - - +
135P HIS* 3.3 16.0 + - + +
136P LEU* 3.8 20.0 - - + +
139P TYR* 3.7 15.2 - - + -
201P FE2 2.2 31.2 - - - -
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Residues in contact with ASP 100 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 2.6 44.2 + - - -
9F LYS* 5.1 0.5 + - - -
96P ALA 3.0 16.8 + - - +
97P ASP* 3.3 7.2 + - - +
99P GLU* 1.3 79.4 - - - +
101P ALA* 1.3 63.6 + - - +
103P ILE* 3.3 6.8 + - - +
104P GLU* 3.1 20.6 + - - +
136P LEU* 4.1 23.1 - - + +
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Residues in contact with ALA 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P MET* 5.2 2.2 - - + -
97P ASP 3.0 16.8 + - - +
98P GLN* 3.7 8.5 - - + +
99P GLU 3.2 0.2 - - - -
100P ASP* 1.3 77.9 + - - +
102P THR* 1.3 58.3 + - - +
104P GLU* 3.1 11.2 + - - +
105P ALA* 2.8 30.0 + - - +
----------------------------------------------------------
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Residues in contact with THR 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P MET* 3.8 21.1 - - - +
98P GLN* 3.1 19.9 + - - +
99P GLU* 3.2 13.7 + - - -
101P ALA* 1.3 77.0 - - - +
103P ILE* 1.3 55.4 + - - +
105P ALA 3.2 0.7 + - - -
106P TYR* 2.6 74.1 + - + +
132P GLU* 4.0 20.0 - - + +
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Residues in contact with ILE 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 6.4 0.2 - - + -
120F VAL* 5.6 2.2 - - + -
99P GLU 3.1 14.1 + - - +
100P ASP* 3.6 9.0 - - - +
101P ALA 3.2 0.2 - - - -
102P THR* 1.3 80.7 - - - +
104P GLU* 1.3 60.1 + - - +
106P TYR* 4.1 4.8 - - - +
107P SER* 2.5 46.5 + - - +
129P ILE* 4.2 20.4 - - + +
132P GLU* 3.7 22.2 - - + +
133P GLN* 3.9 33.4 - - + +
136P LEU* 4.0 24.9 - - + -
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Residues in contact with GLU 104 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 3.5 40.4 + - - +
8F ARG* 3.2 34.8 + - - -
117F GLY 5.3 0.5 - - - +
100P ASP 3.1 16.6 + - - +
101P ALA* 3.2 12.6 - - - +
103P ILE* 1.3 80.1 - - - +
105P ALA* 1.3 65.7 - - - +
107P SER* 3.2 13.6 + - - -
108P GLN* 3.2 18.8 + - - +
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Residues in contact with ALA 105 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P MET* 4.0 26.0 - - + -
101P ALA 2.8 18.3 + - - +
102P THR 3.5 3.8 - - - +
104P GLU* 1.3 72.9 - - - +
106P TYR* 1.3 64.8 + - + +
108P GLN* 3.0 13.1 + - - +
109P PHE* 2.9 34.1 + - + -
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Residues in contact with TYR 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P ALA* 3.2 37.5 + - + -
22P MET* 4.0 18.0 - - + +
23P GLU* 2.6 35.9 + - - +
63P PHE* 3.7 3.8 - + - -
102P THR* 2.6 46.9 + - + +
103P ILE 4.1 0.2 - - - +
105P ALA* 1.3 75.3 - - + +
107P SER* 1.3 62.5 + - - +
109P PHE* 3.6 19.0 - + - +
110P LEU* 2.9 24.9 + - - +
125P PHE* 4.0 14.5 - + + -
128P ILE* 3.9 19.3 - - + -
129P ILE* 3.6 26.5 - - + +
132P GLU* 3.6 7.9 - - + -
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Residues in contact with SER 107 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ARG* 6.0 1.6 - - - -
117F GLY* 4.5 14.8 + - - -
119F ILE* 3.6 30.2 + - - +
103P ILE* 2.5 34.4 + - - +
104P GLU* 3.6 7.8 + - - -
105P ALA 3.1 0.4 - - - -
106P TYR* 1.3 78.0 - - - +
108P GLN* 1.3 62.2 + - - +
110P LEU* 3.6 3.7 - - - +
111P LYS* 3.3 19.2 + - - +
129P ILE* 3.9 10.9 - - - +
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Residues in contact with GLN 108 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P GLU 3.2 13.9 + - - +
105P ALA* 3.0 13.1 + - - +
107P SER* 1.3 77.4 - - - +
109P PHE* 1.3 69.8 + - + +
111P LYS* 3.1 18.2 + - + +
112P VAL* 3.1 25.5 + - + +
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Residues in contact with PHE 109 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P VAL* 3.5 42.9 - - + +
18P LYS* 3.8 28.0 - - + -
19P ALA* 3.8 15.7 - - + -
22P MET* 4.2 8.7 - - - -
105P ALA* 2.9 29.2 + - + -
106P TYR* 3.2 26.4 + + - +
108P GLN* 1.3 79.9 - - + +
110P LEU* 1.3 56.8 + - - +
112P VAL* 3.2 11.5 + - + +
113P CYS* 3.0 32.1 + - - -
125P PHE* 3.7 22.4 - + + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 4.2 20.0 - - + -
106P TYR 2.9 15.0 + - - +
107P SER* 3.6 7.0 - - - +
108P GLN 3.2 0.2 - - - -
109P PHE* 1.3 73.0 - - - +
111P LYS* 1.3 66.1 + - - +
113P CYS* 2.9 10.4 + - - +
114P LYS* 2.9 52.2 + - + +
122P ALA* 3.5 32.1 - - + +
125P PHE* 3.9 11.3 - - + -
126P GLU* 3.6 29.6 - - + +
129P ILE* 4.1 9.9 - - + -
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Residues in contact with LYS 111 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P SER 3.3 10.3 + - - +
108P GLN* 3.1 21.9 + - + +
110P LEU* 1.3 80.2 - - - +
112P VAL* 1.3 62.9 + - + +
114P LYS* 3.1 19.4 + - - +
115P GLU* 2.9 47.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P LYS* 4.2 15.5 - - + +
12P VAL* 5.1 0.7 - - - +
15P VAL* 4.1 28.3 - - + -
108P GLN* 3.1 15.6 + - + +
109P PHE* 3.3 9.4 - - + +
111P LYS* 1.3 75.5 - - + +
113P CYS* 1.3 64.8 + - - +
115P GLU* 3.3 16.5 + - - +
116P GLN* 2.9 38.9 + - + +
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Residues in contact with CYS 113 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P VAL* 3.8 19.3 - - - -
15P VAL* 4.5 4.3 - - - -
109P PHE 3.0 18.3 + - - -
110P LEU 2.9 9.2 + - - +
112P VAL* 1.3 76.9 - - - +
114P LYS* 1.3 61.8 + - - +
116P GLN 3.2 2.4 + - - -
117P GLY 3.1 3.6 + - - -
118P ASP* 2.9 32.1 + - + +
121P THR* 3.6 32.8 - - - -
122P ALA* 3.7 20.0 - - - +
125P PHE* 3.9 15.3 - - - -
----------------------------------------------------------
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Residues in contact with LYS 114 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LYS* 3.7 15.2 - - - +
119F ILE* 5.1 7.9 - - - +
114K LYS* 3.9 12.8 - - - +
110P LEU* 2.9 41.7 + - + +
111P LYS* 3.1 16.1 + - - +
113P CYS* 1.3 74.4 - - - +
115P GLU* 1.3 58.5 + - + +
117P GLY* 2.9 20.1 + - - -
118P ASP 4.7 2.7 - - - +
119P ILE* 5.5 8.0 - - + +
122P ALA* 4.3 9.9 - - + -
1504P SO4 3.0 48.8 + - - +
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Residues in contact with GLU 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P LYS* 2.9 44.6 + - + +
112P VAL* 3.5 23.0 + - - +
113P CYS 3.3 0.2 - - - -
114P LYS* 1.3 77.1 - - - +
116P GLN* 1.3 67.0 + - - +
117P GLY 3.3 3.5 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLY 4.9 5.1 + - - -
7P ASP* 4.4 0.7 - - - +
8P ARG* 3.0 58.5 + - + +
11P LYS* 3.5 49.2 + - + +
12P VAL* 3.7 23.8 - - + -
112P VAL* 2.9 27.9 + - + +
113P CYS 3.2 1.0 + - - +
115P GLU* 1.3 84.5 + - - +
117P GLY* 1.3 62.4 + - - +
118P ASP* 3.3 2.6 + - - +
----------------------------------------------------------
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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