Contacts of the helix formed by residues 85 - 109 (chain H) in PDB entry 3I6A
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 85 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLY 3.6 1.0 - - - -
84H LYS* 1.3 102.0 - - + +
86H ILE* 1.3 66.0 + - + +
87H LYS* 3.0 11.5 + - - +
88H GLU* 2.8 24.5 + - - +
89H ARG* 3.0 35.1 + - - +
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Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G TYR* 3.4 38.1 - - + +
77G SER* 3.8 16.4 - - - +
78G LYS* 3.4 40.4 - - + +
85H ASP* 1.3 77.4 - - + +
87H LYS* 1.3 72.5 + - + +
89H ARG* 3.3 23.5 + - - +
90H ALA* 3.1 22.3 + - - +
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Residues in contact with LYS 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 3.9 24.4 + - - +
63G MET* 4.5 14.9 - - + +
74G TYR* 4.2 21.3 - - + -
85H ASP* 3.0 9.9 + - - +
86H ILE* 1.3 86.2 - - + +
88H GLU* 1.3 66.6 + - + +
90H ALA* 3.3 15.4 + - - +
91H LEU* 3.3 18.0 + - - +
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLY* 3.4 10.0 - - - -
84H LYS* 3.0 51.8 + - - +
85H ASP* 2.8 27.0 + - - +
87H LYS* 1.3 72.8 - - + +
89H ARG* 1.3 58.3 + - - +
91H LEU* 3.3 10.3 + - + +
92H ILE* 2.9 33.3 + - - +
149H VAL* 3.9 17.1 - - + +
150H GLY* 3.4 30.6 - - - +
152H LYS* 5.9 2.1 - - - +
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Residues in contact with ARG 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G SER* 3.1 27.1 + - - -
77H SER* 5.6 1.1 - - - -
82H TYR* 2.9 51.6 + - + +
83H GLY 5.4 1.2 + - - -
84H LYS 4.7 2.4 + - - -
85H ASP* 3.0 33.3 + - - +
86H ILE* 3.3 29.2 - - + +
87H LYS 3.2 0.2 - - - -
88H GLU* 1.3 77.2 - - - +
90H ALA* 1.3 55.8 + - - +
92H ILE* 3.8 7.3 - - - +
93H ASP* 2.9 41.0 + - - +
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Residues in contact with ALA 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G MET* 4.0 15.9 - - + -
65G LEU* 4.0 28.7 - - + +
70G ALA* 4.1 6.6 - - - +
74G TYR* 4.2 10.1 - - + +
86H ILE 3.1 13.2 + - - +
87H LYS 3.6 9.4 - - - +
88H GLU 3.3 0.4 - - - -
89H ARG* 1.3 75.2 - - - +
91H LEU* 1.3 59.0 + - - +
93H ASP* 4.0 5.6 - - - +
94H MET* 3.0 32.7 + - - +
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Residues in contact with LEU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G MET* 5.0 13.0 - - + -
87H LYS 3.3 12.5 + - - +
88H GLU* 3.3 11.3 + - + +
90H ALA* 1.3 80.2 - - - +
92H ILE* 1.3 63.0 + - - +
94H MET* 3.7 21.9 - - + +
95H TYR* 3.1 49.8 + - + +
149H VAL* 4.0 25.1 - - + -
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Residues in contact with ILE 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TYR* 3.4 44.2 - - + +
83H GLY* 3.5 9.9 - - - +
88H GLU 2.9 22.4 + - - +
89H ARG* 3.8 4.5 - - - +
91H LEU* 1.3 75.3 - - - +
93H ASP* 1.3 58.0 + - - +
95H TYR* 3.2 4.8 + - - +
96H ILE* 3.0 43.7 + - + +
149H VAL* 3.9 24.5 - - + -
154H SER* 4.0 18.2 - - - +
155H ARG* 3.7 32.3 - - + -
156H ALA* 4.5 3.6 - - + -
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Residues in contact with ASP 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG 4.9 0.2 - - - -
70G ALA* 3.7 22.3 - - + +
73G ASN* 3.0 35.0 + - - +
74G TYR 5.3 0.2 + - - -
73H ASN* 5.0 0.3 - - - +
82H TYR* 2.5 34.3 + - - -
89H ARG* 2.9 32.2 + - - +
90H ALA* 4.0 2.3 + - - +
92H ILE* 1.3 70.6 - - - +
94H MET* 1.3 66.8 + - - +
96H ILE* 3.8 12.0 - - - +
97H GLU* 3.0 33.1 + - + +
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Residues in contact with MET 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G MET* 3.7 23.3 - - - +
52G PHE* 3.2 19.6 - - - -
63G MET* 6.1 0.4 - - + -
64G LYS 3.9 11.7 - - - +
65G LEU* 3.7 21.3 - - + -
66G VAL* 3.6 48.0 - - + +
67G GLN* 3.7 4.9 - - - +
70G ALA* 3.5 10.7 - - + +
90H ALA 3.0 14.2 + - - +
91H LEU* 3.7 25.8 - - + +
93H ASP* 1.3 78.2 - - - +
95H TYR* 1.3 72.3 + - + +
98H GLY 3.4 6.4 + - - -
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Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G MET* 3.4 35.2 - - + -
52G PHE* 4.2 1.6 - - - -
91H LEU* 3.1 41.9 + - + +
92H ILE 3.6 3.4 - - - +
93H ASP 3.2 0.2 - - - -
94H MET* 1.3 87.9 - - + +
96H ILE* 1.3 65.5 + - + +
98H GLY* 3.3 2.4 + - - -
99H ILE* 3.3 11.3 + - + +
136H PHE* 3.2 36.0 - + + -
139H VAL* 3.1 36.7 - - + +
148H LEU* 4.3 17.7 + - + -
149H VAL* 3.5 28.7 - - + -
156H ALA* 4.5 7.4 - - + -
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Residues in contact with ILE 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ASN* 5.3 0.4 - - - +
92H ILE* 3.0 27.6 + - + +
93H ASP* 3.6 16.4 - - - +
95H TYR* 1.3 74.1 - - - +
97H GLU* 1.3 71.3 + - + +
98H GLY 3.3 0.2 - - - -
99H ILE* 3.3 14.9 + - + +
100H ALA* 2.8 28.1 + - - +
155H ARG* 3.3 46.7 - - - +
156H ALA* 3.7 33.0 - - + -
159H HIS* 3.9 16.8 - - + -
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Residues in contact with GLU 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLN* 3.4 31.8 - - + +
69G ARG* 3.5 33.9 + - + +
70G ALA 4.8 0.4 - - - +
5107G GSH 5.1 0.5 + - - -
69H ARG* 2.9 47.5 + - - +
93H ASP* 3.0 28.7 + - + +
96H ILE* 1.3 81.8 - - + +
98H GLY* 1.3 61.6 + - - +
100H ALA* 3.6 4.1 - - - +
101H ASP* 2.9 35.7 + - - +
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Residues in contact with GLY 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PHE* 3.7 21.1 - - - -
67G GLN* 3.4 15.6 - - - +
94H MET 3.4 4.2 + - - -
95H TYR 3.3 4.2 + - - -
96H ILE 3.3 0.4 - - - -
97H GLU* 1.3 78.8 - - - +
99H ILE* 1.3 60.8 + - - +
101H ASP* 3.3 2.8 + - - +
102H LEU* 3.2 16.8 + - - +
132H TYR* 3.2 25.6 - - - -
136H PHE* 4.9 0.4 - - - -
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Residues in contact with ILE 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TYR* 3.3 18.7 + - + +
96H ILE* 3.4 17.7 - - + +
98H GLY* 1.3 75.8 - - - +
100H ALA* 1.3 52.1 + - - +
102H LEU* 3.3 7.0 + - - +
103H GLY* 2.6 33.6 + - - -
132H TYR* 5.5 0.2 - - - -
136H PHE* 3.6 22.2 - - + -
148H LEU* 5.6 0.9 - - + -
156H ALA 4.3 4.7 - - - +
159H HIS* 3.7 28.0 - - + +
160H LEU* 3.7 36.6 - - + +
163H LEU* 4.2 18.5 - - + +
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Residues in contact with ALA 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ARG* 3.7 27.4 - - - +
96H ILE 2.8 16.4 + - - +
97H GLU* 3.6 11.4 - - - +
98H GLY 3.2 0.2 - - - -
99H ILE* 1.3 73.4 - - - +
101H ASP* 1.3 61.8 + - - +
103H GLY* 4.3 1.8 - - - +
104H GLU* 2.8 34.0 + - - +
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Residues in contact with ASP 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLN* 3.8 10.6 + - - +
67G GLN* 3.2 12.1 + - - -
5107G GSH 2.9 37.3 + - - +
69H ARG* 5.4 2.6 + - - -
97H GLU* 2.9 19.1 + - - +
98H GLY 3.5 8.1 - - - +
100H ALA* 1.3 80.1 - - - +
102H LEU* 1.3 61.4 + - - +
104H GLU* 3.5 10.4 - - - +
105H MET* 3.3 20.3 - - - +
132H TYR* 3.5 14.7 + - - +
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLY 3.2 8.5 + - - +
99H ILE* 3.6 7.4 - - - +
101H ASP* 1.3 77.0 - - - +
103H GLY* 1.3 66.6 + - - +
105H MET* 3.0 26.6 + - - +
106H ILE* 3.3 13.4 + - + +
124H ILE* 3.8 30.1 - - + +
127H LYS* 5.1 0.7 - - + -
128H ILE* 4.0 21.8 - - + +
132H TYR* 3.7 44.6 + - + -
133H PHE* 5.4 1.6 - - + -
136H PHE* 6.2 0.2 - - + -
163H LEU* 3.5 35.7 - - + -
167H VAL* 5.3 0.2 - - + -
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Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ILE* 2.6 22.1 + - - -
100H ALA* 3.7 2.5 - - - -
102H LEU* 1.3 73.6 - - - +
104H GLU* 1.3 55.9 + - - +
106H ILE* 3.2 14.4 + - - +
107H ILE* 3.0 41.1 + - - +
163H LEU* 5.1 4.0 - - - +
166H TYR* 6.3 1.3 - - - -
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Residues in contact with GLU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ARG* 2.8 45.3 + - - -
100H ALA 2.8 18.9 + - - +
101H ASP* 3.5 9.6 - - - +
102H LEU 3.1 0.2 - - - -
103H GLY* 1.3 78.3 - - - +
105H MET* 1.3 61.2 + - + +
107H ILE* 3.4 9.9 + - - +
108H MET* 3.1 34.6 + - + +
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Residues in contact with MET 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ASP 3.3 18.8 - - - +
102H LEU* 3.0 21.3 + - - +
104H GLU* 1.3 74.7 - - + +
106H ILE* 1.3 64.1 + - + +
108H MET* 3.7 3.2 + - - +
109H LEU* 3.1 22.9 + - - +
120H LYS* 3.3 33.5 + - - +
123H LEU* 4.7 9.9 - - + -
124H ILE* 4.0 25.0 - - + +
127H LYS* 4.2 32.5 - - + -
132H TYR* 5.4 3.4 - - - -
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ARG* 6.4 0.2 - - - +
102H LEU* 3.7 16.2 - - + +
103H GLY* 3.4 10.5 - - - +
104H GLU 3.2 0.2 - - - -
105H MET* 1.3 78.1 - - - +
107H ILE* 1.3 66.1 + - + +
109H LEU* 3.2 25.9 + - + +
110H PRO* 3.3 7.3 - - - +
124H ILE* 4.4 20.9 - - + -
128H ILE* 5.8 0.7 - - + -
163H LEU* 3.7 31.0 - - + -
166H TYR* 4.3 29.8 - - + -
167H VAL* 5.1 4.5 - - + -
170H LEU* 5.8 10.3 - - + -
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Residues in contact with ILE 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ARG* 6.5 0.2 - - + -
14H GLY* 3.8 39.0 - - - +
15H ARG* 4.6 23.1 - - + +
103H GLY* 3.0 28.1 + - - +
104H GLU* 3.7 13.2 - - - +
105H MET 3.3 0.2 - - - -
106H ILE* 1.3 80.8 - - + +
108H MET* 1.3 70.1 + - - +
110H PRO* 3.1 16.7 - - - +
111H PHE* 4.0 12.7 - - + -
166H TYR* 6.4 1.8 - - + -
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ARG* 3.9 22.9 - - - -
104H GLU* 3.1 30.1 + - + +
105H MET* 4.3 4.0 - - - +
107H ILE* 1.3 81.8 - - - +
109H LEU* 1.3 57.9 + - - +
110H PRO* 3.3 0.2 - - - -
111H PHE* 2.8 49.9 + - + +
112H CYS* 3.6 7.4 + - - -
120H LYS* 5.5 5.8 - - - -
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Residues in contact with LEU 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H MET 3.1 12.6 + - - +
106H ILE* 3.2 19.7 - - + +
108H MET* 1.3 75.6 - - - +
110H PRO* 1.4 58.6 - - + +
111H PHE 3.1 0.2 - - - -
112H CYS* 3.2 31.6 + - + +
117H LYS* 3.5 22.0 - - - +
120H LYS* 3.7 31.2 - - + +
121H LEU* 3.3 35.7 - - + -
124H ILE* 4.2 14.8 - - + -
170H LEU* 4.6 14.4 - - + -
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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