Contacts of the helix formed by residues 90 - 114 (chain D) in PDB entry 2FRV
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 GLU 90 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE 3.8 0.8 + - - -
89D PRO* 1.3 72.5 - - - +
91D ASN* 1.3 57.4 + - - +
93D THR* 3.0 10.9 + - + -
94D LEU* 2.9 40.7 + - + +
431D LYS* 5.2 13.7 - - - +
435D ASN* 2.9 30.2 + - - +
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Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D PRO 3.2 0.6 - - - -
90D GLU* 1.3 76.9 - - - +
92D ALA* 1.3 62.8 + - - +
94D LEU* 4.0 2.5 - - - +
95D MET* 3.1 25.8 + - - +
234D LEU* 4.7 3.8 - - - +
432D LEU* 3.7 21.6 - - + +
435D ASN* 2.8 33.6 + - - +
436D VAL* 4.1 10.5 - - - +
440D LYS* 2.8 28.2 + - - -
441D ASP* 3.5 15.4 - - - +
442D ASP 3.1 20.1 + - - +
443D LEU* 3.8 10.5 - - + +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ILE* 4.2 7.0 - - + -
89D PRO* 2.6 17.5 + - + +
91D ASN* 1.3 73.2 - - - +
93D THR* 1.3 65.9 + - - +
96D ARG* 3.0 33.8 + - - -
227D GLY* 3.7 18.4 - - - -
228D CYS* 3.8 14.5 - - - -
443D LEU* 3.2 31.5 - - - +
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Residues in contact with THR 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ILE* 3.3 17.1 + - - +
89D PRO 3.0 7.3 + - - -
90D GLU* 3.0 13.2 + - + +
92D ALA* 1.3 80.3 - - - +
94D LEU* 1.3 65.4 + - + +
96D ARG* 3.4 2.4 + - - +
97D ASN* 3.2 27.2 + - - +
287D PRO 3.2 27.8 - - - +
288D THR* 4.4 11.4 + - + +
290D GLU* 2.8 35.4 + - - +
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 2.9 30.0 + - + +
91D ASN* 4.0 7.2 - - - +
92D ALA 3.4 0.2 - - - -
93D THR* 1.3 78.6 - - + +
95D MET* 1.3 51.4 + - - +
97D ASN* 3.2 9.9 + - - +
98D LEU* 2.9 39.8 + - - +
428D TRP* 4.0 39.5 - - + +
431D LYS* 3.9 22.4 - - + -
432D LEU* 3.8 30.7 - - + +
435D ASN* 3.9 20.6 - - - +
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Residues in contact with MET 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN 3.1 17.0 + - - +
92D ALA 4.3 1.8 - - - +
94D LEU* 1.3 73.9 - - - +
96D ARG* 1.3 60.8 + - - +
98D LEU* 3.5 10.7 + - + +
99D THR* 2.9 29.5 + - - -
213D PHE* 4.1 21.8 - - + +
222D PHE* 3.7 22.0 - - + -
228D CYS* 4.1 15.5 - - - -
230D ASN* 3.9 27.6 - - - +
233D SER* 3.7 16.8 - - - +
234D LEU* 3.5 31.6 - - + -
432D LEU* 4.4 5.6 - - + +
443D LEU* 4.2 8.5 - - + -
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Residues in contact with ARG 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D TYR* 2.6 32.2 + - - +
74D LEU* 4.1 13.9 - - + +
77D VAL* 3.5 24.9 - - - +
78D ARG* 4.1 18.4 - - - +
81D ASP* 2.8 26.4 + - - -
88D ILE* 3.7 17.3 - - - +
92D ALA* 3.0 27.2 + - - +
93D THR* 3.7 5.2 - - - +
95D MET* 1.3 75.0 - - - +
97D ASN* 1.3 58.3 + - - +
100D MET* 3.3 19.2 + - - +
222D PHE* 4.6 2.0 - - + -
223D THR* 4.1 12.9 - - + +
224D VAL 3.3 12.5 + - - -
227D GLY* 2.9 33.3 + - - -
228D CYS* 3.6 18.8 - - - -
290D GLU* 4.3 6.8 + - - +
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 4.2 7.1 + - - -
93D THR* 3.2 19.6 + - - +
94D LEU* 3.4 12.6 - - - +
96D ARG* 1.3 77.2 - - - +
98D LEU* 1.3 65.2 + - - +
99D THR 3.2 0.4 - - - -
100D MET* 3.3 1.7 + - - +
101D GLY 2.9 18.4 + - - -
285D GLU* 4.8 0.5 - - - +
286D PHE* 3.6 28.2 + - + +
287D PRO* 3.4 39.9 + - - +
290D GLU* 4.9 0.5 - - - +
428D TRP* 3.3 39.3 - - + +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU 2.9 22.1 + - - +
95D MET* 3.8 11.0 - - - +
96D ARG 3.5 0.2 - - - -
97D ASN* 1.3 79.2 - - - +
99D THR* 1.3 56.8 + - - +
101D GLY* 3.8 0.5 - - - -
102D ALA* 3.0 28.6 + - - +
213D PHE* 3.8 32.3 - - + -
242D PHE* 4.2 12.3 - - + -
425D VAL* 3.6 42.5 - - + +
428D TRP* 3.8 26.2 - - + +
429D LEU* 4.0 17.0 - - + +
432D LEU* 4.5 9.2 - - + -
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Residues in contact with THR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D TYR* 3.8 36.0 - - + -
95D MET 2.9 19.9 + - - -
96D ARG 4.0 0.2 - - - -
97D ASN 3.2 0.4 - - - -
98D LEU* 1.3 79.1 - - - +
100D MET* 1.3 57.7 + - - +
102D ALA* 3.7 6.8 + - - +
103D GLN* 3.2 23.2 + - - +
210D MET* 4.0 29.1 - - + +
213D PHE* 3.3 23.2 - - - +
214D GLY* 4.7 0.7 - - - -
220D THR* 4.3 3.6 - - + -
222D PHE* 3.5 14.5 - - + -
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Residues in contact with MET 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D TYR* 3.8 8.9 - - + -
71D VAL* 3.6 29.8 - - + -
74D LEU* 3.6 17.7 - - + -
96D ARG 3.3 17.6 + - - +
97D ASN* 3.9 4.9 - - - +
98D LEU 3.2 0.6 - - - -
99D THR* 1.3 74.1 - - - +
101D GLY* 1.3 66.0 + - - +
103D GLN* 3.1 7.4 + - - +
104D TYR* 3.0 57.3 + - + -
285D GLU* 4.1 10.3 - - + +
286D PHE* 3.7 18.6 - - + -
459D VAL* 3.3 34.8 - - + -
460D ASN 4.5 3.1 - - - +
462D PRO* 4.8 0.2 - - - -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASN 2.9 17.1 + - - -
98D LEU 3.8 1.8 - - - -
100D MET* 1.3 77.7 - - - +
102D ALA* 1.3 56.4 + - - +
104D TYR* 3.1 7.2 + - - +
105D MET* 3.0 31.4 + - - +
286D PHE* 3.9 13.0 - - - -
421D ALA* 4.7 4.7 - - - +
425D VAL* 3.8 20.4 - - - -
428D TRP* 4.4 1.1 - - - -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU 3.0 16.3 + - - +
99D THR* 3.9 5.8 - - - +
100D MET 3.3 0.2 - - - -
101D GLY* 1.3 77.7 - - - +
103D GLN* 1.3 58.5 + - - +
105D MET* 3.5 13.8 + - - +
106D HIS* 3.3 23.7 + - - +
206D ALA* 4.3 8.0 - - - +
209D ALA* 5.0 2.7 - - + -
210D MET* 4.0 30.9 - - + +
242D PHE* 4.8 13.2 - - + -
425D VAL* 4.4 2.4 - - - +
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Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL 3.2 17.8 + - - +
68D CYS* 3.7 3.8 - - - +
69D THR* 3.7 22.8 - - - +
70D TYR* 4.8 1.8 - - + -
71D VAL* 4.1 11.7 - - + -
99D THR 3.2 14.0 + - - +
100D MET* 3.1 15.0 + - - +
102D ALA* 1.3 72.8 - - - +
104D TYR* 1.3 61.1 + - - +
106D HIS* 4.7 7.6 + - - +
107D ASP* 2.8 69.1 + - - +
210D MET* 3.5 27.3 - - + +
217D ASN* 4.3 2.1 - - - +
462D PRO* 4.0 12.8 - - + -
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Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D MET* 3.0 45.2 + - + -
101D GLY 3.1 7.2 + - - +
103D GLN* 1.3 72.8 - - - +
105D MET* 1.3 71.5 + - - +
106D HIS 3.2 0.7 + - - -
107D ASP* 4.6 0.2 - - - -
108D HIS* 3.2 35.1 + + - +
285D GLU* 3.9 10.6 - - - +
286D PHE* 4.2 16.2 - + - -
298D THR* 5.4 1.0 + - + -
417D GLN* 3.7 40.0 + - + -
418D CYS* 4.1 1.7 - - - -
421D ALA* 3.7 25.6 - - + -
460D ASN* 2.6 40.8 + - - -
461D ALA 4.1 1.6 + - - -
462D PRO* 4.0 20.2 - - + -
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D GLY 3.0 14.0 + - - +
102D ALA* 3.5 16.2 - - - +
103D GLN 3.3 0.2 - - - -
104D TYR* 1.3 82.6 - - + +
106D HIS* 1.3 58.1 + - - +
109D LEU* 3.4 25.1 + - - +
206D ALA* 5.0 3.4 - - + -
246D TYR* 4.0 30.1 - - + -
249D VAL* 3.4 31.9 - - + -
250D ARG* 3.7 17.9 - - - +
253D ILE* 3.4 19.2 - - + +
418D CYS* 4.0 15.0 - - - +
422D ALA* 4.1 26.9 - - + +
425D VAL* 4.5 5.4 - - - -
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Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 4.0 6.7 - - - -
26C ARG* 3.4 35.4 + - - -
67D VAL 5.6 2.8 + - - -
102D ALA 3.3 13.6 + - - +
103D GLN* 3.9 13.5 + - - +
104D TYR 3.3 0.4 - - - -
105D MET* 1.3 73.8 - - - +
107D ASP* 1.3 71.2 + - - +
109D LEU* 3.4 6.2 + - - +
110D VAL* 2.9 35.9 + - + +
203D GLN* 3.1 49.1 + - + +
206D ALA* 3.6 20.8 - - + +
207D ALA* 3.8 10.5 - - + +
210D MET* 5.8 1.6 - - - -
217D ASN* 5.1 4.3 + - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 3.9 9.7 - - - +
68D CYS* 3.8 4.7 - - - -
103D GLN* 2.8 39.9 + - - +
104D TYR 4.2 0.4 - - - +
106D HIS* 1.3 84.0 + - - +
108D HIS* 1.3 53.1 + - - +
110D VAL* 3.2 5.0 + - - +
111D HIS* 2.8 32.8 + - - +
462D PRO* 3.4 21.5 - - + +
463D ARG* 2.8 45.5 + - - -
528D ASP* 4.5 1.5 - - - +
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Residues in contact with HIS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TYR* 3.2 25.2 + + + +
107D ASP* 1.3 73.5 - - + +
109D LEU* 1.3 61.2 + - - +
111D HIS* 3.4 4.5 + - - +
112D PHE* 3.0 30.3 + - - +
257D TYR* 3.7 9.3 + - + +
371D PRO* 4.1 1.6 - - - +
414D ARG* 3.5 32.6 + - + +
417D GLN* 2.8 47.5 + - + -
418D CYS* 3.1 36.8 - - + +
462D PRO* 3.6 20.2 + - + +
528D ASP* 4.8 4.7 - - - -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D MET 3.4 18.9 + - - +
106D HIS* 3.5 5.8 - - - +
108D HIS* 1.3 74.2 - - - +
110D VAL* 1.3 67.6 + - + +
112D PHE* 3.4 1.4 + - - -
113D TYR* 3.3 47.0 + - + +
114D HIS* 4.8 1.2 - - - -
199D ALA* 4.6 4.5 - - + +
202D VAL* 3.8 32.3 - - + -
203D GLN* 4.4 15.7 - - + +
206D ALA* 5.3 0.7 - - + -
249D VAL* 4.8 9.4 - - + -
252D PHE* 3.4 30.5 - - + -
253D ILE* 4.3 11.2 - - + -
257D TYR* 4.2 16.5 - - + -
418D CYS* 4.8 0.4 - - - -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 4.6 16.6 - - - +
25C LEU* 5.4 9.2 - - + -
67D VAL* 6.4 1.1 - - + -
106D HIS* 2.9 32.9 + - + +
107D ASP* 3.8 4.3 - - - +
109D LEU* 1.3 77.5 - - - +
111D HIS* 1.3 64.4 + - - +
114D HIS* 3.1 44.3 + - + +
115D LEU* 3.5 16.4 + - + -
203D GLN* 3.5 37.5 - - + +
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Residues in contact with HIS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG 5.4 0.9 - - - -
107D ASP* 2.8 20.8 + - - +
108D HIS* 3.7 5.8 - - - +
109D LEU 3.3 0.2 - - - -
110D VAL* 1.3 74.5 - - - +
112D PHE* 1.3 67.0 + - - +
115D LEU* 3.2 27.2 + - + +
116D HIS* 2.9 50.0 + + - +
414D ARG* 3.5 34.8 - - - -
525D HIS* 2.9 34.8 + - - +
528D ASP* 3.3 36.4 - - - +
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Residues in contact with PHE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D HIS 3.0 13.7 + - - +
109D LEU 3.4 2.4 + - - +
110D VAL 3.3 0.2 - - - -
111D HIS* 1.3 80.0 - - - +
113D TYR* 1.3 88.9 + + - +
116D HIS* 3.4 12.7 - + + +
117D ALA* 2.8 44.3 + - + +
120D TRP* 6.1 3.6 - + - -
257D TYR* 3.1 46.7 - + + +
260D ASP* 4.2 12.6 - - + -
261D LEU* 3.9 36.3 - - + -
264D VAL* 5.3 12.3 - - + -
411D THR* 5.0 10.3 - - + -
414D ARG* 6.0 0.4 - - - -
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.3 34.6 + - + +
112D PHE* 1.3 105.4 - + - +
114D HIS* 1.3 78.1 + - + +
117D ALA* 3.5 18.6 + - + +
118D LEU* 4.8 1.2 + - - +
192D ALA* 4.7 6.3 - - + -
195D HIS* 3.6 21.1 - - + -
196D TYR* 2.9 38.8 - - + -
199D ALA* 3.5 17.5 - - + -
252D PHE* 3.9 9.0 - + - -
256D VAL* 3.4 10.7 + - + +
257D TYR* 3.4 21.7 - - + -
260D ASP* 2.9 22.3 + - + +
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Residues in contact with HIS 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 6.3 1.0 - - + +
47C THR 4.6 1.2 - - - +
48C LEU* 4.5 21.6 - - + +
16D ARG* 3.6 18.6 - - - +
109D LEU 5.4 0.2 - - - -
110D VAL* 3.1 41.7 + - + +
113D TYR* 1.3 82.1 - - + +
115D LEU* 1.3 66.1 + - + +
117D ALA 5.3 0.2 - - - -
118D LEU* 4.9 2.6 - - - +
196D TYR* 3.2 54.0 + + + +
199D ALA* 3.7 33.2 - - + +
200D LEU* 3.5 25.2 - - + +
203D GLN* 4.5 1.5 - - + +
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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