Contacts of the helix formed by residues 86 - 111 (chain H) in PDB entry 1GUM
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 LEU 86 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G TYR* 3.8 28.7 - - + -
77G ASP* 4.2 29.8 - - + +
78G LYS* 4.0 21.1 - - + +
85H ASN* 1.3 75.9 + - - +
87H LYS* 1.3 61.3 + - - +
89H ARG* 3.2 16.5 - - + +
90H THR* 2.5 53.0 + - - +
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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* 4.8 4.8 + - - +
63G MET* 3.6 29.0 - - + +
74G TYR* 3.2 34.5 + - - -
78G LYS* 5.6 3.9 - - - +
85H ASN* 2.7 15.8 + - - +
86H LEU* 1.3 85.0 - - + +
88H GLU* 1.3 66.4 + - + +
90H THR* 3.4 3.7 + - - +
91H LEU* 3.1 28.3 + - + +
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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* 3.6 9.2 - - - -
84H LYS* 3.0 37.1 + - - +
85H ASN* 3.0 35.6 + - - +
87H LYS* 1.3 75.5 - - + +
89H ARG* 1.3 55.2 + - - +
91H LEU* 2.7 30.4 + - + +
92H ILE* 3.0 15.7 + - - +
149H VAL* 4.0 18.5 - - + +
150H GLY* 4.1 25.0 - - - +
152H GLN* 5.2 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 ASP* 4.6 2.2 + - - -
89G ARG* 3.1 38.5 - - - +
73H HIS* 5.1 4.6 + - - +
77H ASP* 3.0 42.2 + - - -
82H PHE* 3.5 56.3 + - + +
85H ASN 2.7 21.6 + - - +
86H LEU* 3.2 22.4 - - + +
88H GLU* 1.3 72.7 - - - +
90H THR* 1.3 65.3 + - - +
92H ILE* 3.3 5.5 + - - +
93H ASP* 2.9 26.0 + - + +
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Residues in contact with THR 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G MET* 3.9 22.2 - - + -
65G LEU* 4.1 18.8 - - + -
70G SER* 5.4 4.3 - - - +
74G TYR* 3.9 19.4 - - + +
86H LEU* 2.5 43.6 + - - +
87H LYS* 3.5 7.8 - - - -
88H GLU 3.0 0.2 + - - -
89H ARG* 1.3 75.0 - - - +
91H LEU* 1.3 61.7 + - + +
93H ASP* 3.3 9.2 - - - +
94H MET* 3.1 26.6 + - + +
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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* 5.6 6.7 - - + -
87H LYS* 3.1 20.4 - - + +
88H GLU* 2.7 13.1 + - + +
90H THR* 1.3 71.4 - - + +
92H ILE* 1.3 70.0 + - - +
93H ASP 3.0 2.2 - - - -
94H MET* 3.0 11.6 + - - -
95H TYR* 2.7 53.7 + - + +
149H VAL* 3.8 26.2 - - + -
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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
----------------------------------------------------------
81H LEU 4.1 0.2 - - - +
82H PHE* 4.0 18.6 - - + -
83H GLY* 3.9 22.7 - - - +
88H GLU 3.2 18.6 - - - +
89H ARG* 3.5 7.9 - - - +
91H LEU* 1.3 76.6 - - - +
93H ASP* 1.3 54.1 - - - +
95H TYR* 3.2 3.2 + - - +
96H VAL* 2.7 44.8 + - + +
149H VAL* 4.0 22.0 - - + +
154H SER* 3.2 29.8 - - - +
155H LEU* 4.1 8.1 - - + -
156H ALA* 3.7 29.4 - - + +
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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
----------------------------------------------------------
70G SER* 3.0 31.9 + - - +
73G HIS* 3.3 29.6 + - - +
73H HIS* 4.3 4.7 + - - -
82H PHE* 4.4 15.9 - - + -
89H ARG* 2.9 18.3 + - + +
90H THR* 3.3 9.4 - - - +
92H ILE* 1.3 78.5 - - - +
94H MET* 1.3 64.3 + - - +
96H VAL* 3.0 7.2 + - - +
97H GLU* 2.8 39.0 + - - +
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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 LEU* 4.3 22.7 - - + -
52G PHE* 3.6 7.2 - - - -
64G LYS 3.6 4.9 - - - +
65G LEU* 2.7 39.7 - - + -
66G VAL* 2.5 54.7 - - + +
67G GLN* 4.0 4.2 - - + +
70G SER* 3.6 15.2 + - - -
90H THR* 3.1 16.9 + - + +
91H LEU* 3.0 15.0 + - - +
93H ASP* 1.3 79.4 - - - +
95H TYR* 1.3 64.9 + - + +
97H GLU* 3.8 0.7 - - - +
98H GLY 2.9 20.8 + - - -
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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 LEU* 4.0 25.6 - - + +
52G PHE* 4.2 6.3 - + - -
91H LEU* 2.7 49.9 + - + +
92H ILE 3.5 5.6 - - - +
94H MET* 1.3 74.9 - - + +
96H VAL* 1.3 65.4 + - - +
98H GLY* 3.8 0.5 - - - -
99H THR* 2.7 29.8 + - - -
136H PHE* 4.0 19.5 - + + -
139H ILE* 3.4 34.1 - - + +
148H LEU* 4.2 15.9 - - + -
149H VAL* 3.5 28.4 - - + +
156H ALA* 3.7 21.1 - - + +
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Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H LEU* 5.4 3.1 - - + -
73H HIS* 5.8 4.3 - - + +
92H ILE* 2.7 26.7 + - + +
93H ASP* 3.4 6.1 - - - +
95H TYR* 1.3 78.4 - - - +
97H GLU* 1.3 69.5 + - - +
99H THR* 3.1 5.2 + - - -
100H LEU* 2.9 39.2 + - + +
155H LEU* 4.1 21.5 - - + +
156H ALA* 3.5 31.9 - - - +
159H ILE* 4.2 17.5 - - + -
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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* 3.1 30.5 - - + +
69G ARG* 4.0 15.6 - - + +
70G SER* 3.0 28.5 - - - +
69H ARG* 3.0 39.3 + - - +
73H HIS* 3.8 17.8 + - - -
93H ASP* 2.8 26.2 + - - +
96H VAL* 1.3 78.4 - - - +
98H GLY* 1.3 65.1 + - - +
100H LEU* 3.2 6.9 + - - +
101H ASP* 3.0 26.3 + - - +
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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* 3.8 19.5 - - - -
67G GLN* 3.5 20.2 - - - -
94H MET 2.9 10.7 + - - -
95H TYR 3.8 0.2 - - - -
97H GLU* 1.3 77.7 - - - +
99H THR* 1.3 64.9 + - - +
101H ASP* 2.9 18.6 + - - +
102H LEU 3.3 1.2 + - - -
132H TYR* 3.3 19.0 - - - -
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Residues in contact with THR 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PHE* 5.1 0.4 - - - -
95H TYR* 2.7 19.9 + - - +
96H VAL* 3.7 4.3 - - - -
98H GLY* 1.3 75.8 - - - +
100H LEU* 1.3 59.1 + - - +
102H LEU* 2.8 12.4 + - + +
103H LEU* 2.7 26.6 + - - +
132H TYR* 4.5 4.0 - - - -
136H PHE* 3.7 19.0 - - + -
156H ALA 5.3 1.4 + - - -
159H ILE* 4.0 18.8 - - + +
160H LEU* 4.1 17.6 - - + +
163H THR* 3.4 32.1 - - + +
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H SER* 4.6 7.6 - - - +
68H THR* 6.1 2.5 - - + -
69H ARG* 3.9 48.0 - - + +
72H LEU* 4.6 13.7 - - + -
96H VAL* 2.9 33.9 + - + +
97H GLU* 3.4 9.2 - - - +
99H THR* 1.3 78.2 - - - +
101H ASP* 1.3 64.5 + - - +
103H LEU* 3.6 27.9 - - + +
104H GLU* 3.1 28.5 + - - +
159H ILE* 4.0 13.0 - - + -
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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* 4.4 7.4 + - - +
67G GLN* 3.5 26.5 + - - +
69H ARG* 4.8 10.4 + - - -
97H GLU 3.0 15.9 + - - +
98H GLY 2.9 9.3 + - - +
99H THR 2.9 0.8 - - - -
100H LEU* 1.3 80.8 - - - +
102H LEU* 1.3 60.3 + - - +
104H GLU* 3.3 16.5 - - - +
105H LEU* 4.2 7.3 - - - +
132H TYR* 3.7 14.5 + - - +
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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 3.3 2.8 + - - +
99H THR* 2.8 14.7 + - + +
101H ASP* 1.3 73.6 - - - +
103H LEU* 1.3 66.2 + - - +
104H GLU 2.9 5.9 + - - -
105H LEU* 3.0 31.9 + - + +
106H LEU* 3.9 3.1 + - - +
124H MET* 4.2 7.6 - - + +
127H LYS* 4.1 9.6 - - + -
128H ALA* 4.1 22.2 - - + +
132H TYR* 4.0 45.5 + - + -
133H PHE* 4.5 7.2 - - + -
160H LEU* 6.1 1.3 - - + -
163H THR* 4.0 13.9 - - + -
167H LEU* 3.9 25.8 - - + -
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H SER* 3.9 6.3 - - - +
99H THR 2.7 14.2 + - - +
100H LEU* 3.6 27.4 - - + +
102H LEU* 1.3 77.4 - - - +
104H GLU* 1.3 62.6 + - - +
106H LEU* 2.8 39.7 + - + +
107H ILE* 3.0 26.5 + - + +
159H ILE* 4.8 1.1 - - + -
162H GLN* 3.7 35.0 - - + +
163H THR* 3.7 29.3 - - + +
166H ALA* 4.8 3.6 - - + -
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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* 2.7 43.2 + - - -
69H ARG* 5.7 3.1 + - - -
100H LEU* 3.1 14.4 + - - +
101H ASP* 3.3 19.1 - - - +
103H LEU* 1.3 79.2 - - - +
105H LEU* 1.3 61.3 + - + +
107H ILE* 3.3 8.8 - - - +
108H MET* 2.8 55.9 + - + +
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ASP 4.2 10.3 - - - +
102H LEU* 3.3 26.2 - - + +
104H GLU* 1.3 81.8 - - + +
106H LEU* 1.3 62.6 + - + +
108H MET* 3.9 25.2 - - + +
109H HIS* 3.2 23.6 + - - +
120H GLU* 4.9 9.6 - - - +
123H ASN* 4.5 9.0 - - - +
124H MET* 3.5 45.9 - - + +
127H LYS* 4.4 14.4 - - + -
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LEU 4.8 2.7 - - - +
103H LEU* 2.8 27.5 + - + +
105H LEU* 1.3 82.0 - - + +
107H ILE* 1.3 63.4 + - + +
109H HIS* 3.2 4.2 - - - +
110H PRO* 3.1 20.6 - - - +
124H MET* 3.7 28.0 - - + -
163H THR* 4.2 4.9 - - + +
166H ALA* 3.5 38.4 - - + +
167H LEU* 3.8 23.3 - - + -
170H LYS* 4.2 21.2 + - + +
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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
----------------------------------------------------------
14H GLY* 3.6 28.9 - - - +
15H ARG* 4.0 51.6 - - + +
18H SER* 6.0 0.7 - - - +
103H LEU* 3.3 30.5 - - + +
104H GLU* 3.3 15.0 - - - +
106H LEU* 1.3 80.4 - - + +
108H MET* 1.3 60.7 + - + +
110H PRO* 3.5 11.1 - - - +
111H PHE* 4.1 10.6 - - - -
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H GLU* 2.8 48.8 + - + +
105H LEU* 3.9 28.9 - - + +
107H ILE* 1.3 74.8 - - + +
109H HIS* 1.3 67.1 + - - +
110H PRO* 3.2 2.0 - - - -
111H PHE* 2.9 23.2 + - - +
112H LEU* 3.8 19.9 - - + +
120H GLU* 5.3 8.5 - - - +
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Residues in contact with HIS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H LEU 3.2 11.9 + - - +
106H LEU* 3.2 11.2 - - - +
108H MET* 1.3 78.3 - - - +
110H PRO* 1.3 70.3 - - + +
111H PHE 2.9 1.9 + - - -
112H LEU* 3.0 19.0 + - + +
117H GLN* 2.9 68.5 + - + +
120H GLU* 4.2 11.9 - - + -
121H VAL* 3.6 11.0 - - + +
124H MET* 3.7 20.9 - - + -
170H LYS* 2.6 33.3 + - + +
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Residues in contact with PRO 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU 3.1 11.7 - - - +
107H ILE 3.5 9.4 - - - +
108H MET 3.2 4.5 - - - -
109H HIS* 1.3 101.1 - - + +
111H PHE* 1.3 71.4 + - + +
112H LEU 3.2 5.1 + - - +
117H GLN* 3.7 12.6 + - - +
170H LYS* 5.2 2.2 - - - +
208H PRO* 4.0 30.5 - - + +
212H TYR* 5.8 0.4 - - + -
213H VAL* 4.2 26.1 - - + +
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Residues in contact with PHE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H ILE 4.1 11.0 - - - -
108H MET* 2.9 17.2 + - - +
110H PRO* 1.3 97.0 - - + +
112H LEU* 1.3 66.6 + - + +
113H LYS* 4.0 6.1 + - - +
212H TYR* 4.2 21.3 - + - -
213H VAL* 3.9 22.7 - - + -
216H VAL* 3.7 32.8 - - + -
217H TYR* 3.5 40.2 + + - +
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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