Contacts of the helix formed by residues 90 - 114 (chain C) in PDB entry 4GTU
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR* 1.3 73.2 - - - +
91C GLU* 1.3 64.4 + - - +
93C LYS* 3.0 14.9 + - - +
94C ILE* 3.1 23.9 + - + +
67D HIS* 5.1 5.6 - - - +
78D TYR* 4.2 9.2 - - + -
81D ARG* 3.0 48.9 + - - +
82D LYS* 4.2 19.8 - - - +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR* 3.6 10.5 + - - +
90C GLU* 1.3 79.3 - - - +
92C GLU* 1.3 70.8 + - - +
94C ILE* 3.0 23.4 + - + +
95C ARG* 3.2 34.4 + - + +
148C VAL 5.9 0.4 - - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLY* 3.4 16.4 - - - -
88C GLU* 3.6 4.7 + - - +
89C THR* 2.7 52.3 + - - +
91C GLU* 1.3 86.5 - - - +
93C LYS* 1.3 58.9 + - - +
95C ARG* 3.0 4.4 + - - +
96C VAL* 2.8 34.7 + - - +
148C VAL* 3.3 34.0 - - + +
149C GLY* 5.9 0.2 - - - -
151C LYS* 3.9 32.8 - - + +
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C CYS* 6.4 0.4 - - - -
87C GLY* 3.2 29.4 + - - +
88C GLU* 3.6 15.6 + - - +
89C THR 3.0 13.1 + - - +
90C GLU* 3.0 12.6 + - - +
92C GLU* 1.3 75.4 - - - +
94C ILE* 1.3 56.0 + - - +
96C VAL* 4.2 6.3 - - - -
97C ASP* 2.8 35.1 - - - +
81D ARG* 3.5 41.8 + - + +
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 3.3 29.4 - - + +
91C GLU* 3.0 16.3 + - - +
93C LYS* 1.3 77.3 - - - +
95C ARG* 1.3 65.9 + - + +
97C ASP* 3.9 3.9 - - - +
98C ILE* 3.0 39.6 + - + +
67D HIS* 3.6 23.1 - - + -
68D LYS 5.2 2.0 - - - +
69D ILE* 3.2 27.4 - - + +
78D TYR* 3.6 30.7 - - + -
81D ARG* 5.0 1.3 - - - +
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU* 3.2 33.6 + - + +
92C GLU* 3.0 4.0 + - - +
94C ILE* 1.3 81.9 - - + +
96C VAL* 1.3 65.2 - - - +
97C ASP 3.3 0.2 - - - -
98C ILE* 3.8 0.8 + - + -
99C LEU* 3.4 28.6 + - - +
140C PHE* 2.8 61.2 + - + +
144C ARG* 2.7 33.1 - - - +
147C PHE 2.5 29.3 + - - -
148C VAL* 3.5 23.6 - - + +
55D ASP* 4.8 4.6 + - - -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C CYS* 4.5 2.9 - - + -
87C GLY* 3.8 26.2 - - - +
92C GLU 2.8 25.1 + - - +
93C LYS* 4.5 2.2 - - - -
95C ARG* 1.3 71.9 - - - +
97C ASP* 1.3 71.5 + - - +
100C GLU* 3.0 19.3 + - + +
148C VAL* 3.6 24.5 - - + -
153C THR* 4.6 4.9 - - + +
154C PHE* 3.5 34.5 - - + -
155C VAL* 3.2 16.5 - - + +
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LYS* 2.8 26.8 - - - +
94C ILE* 3.9 5.6 - - - +
96C VAL* 1.3 78.9 - - - +
98C ILE* 1.3 68.2 + - - +
100C GLU* 2.7 29.3 + - - +
101C ASN* 3.0 11.6 + - - +
69D ILE* 6.0 0.2 - - + -
74D ALA* 3.6 21.2 - - + +
77D CYS* 3.3 32.4 - - - +
81D ARG* 3.4 8.9 + - - -
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 3.0 31.1 + - + +
95C ARG* 4.0 4.3 - - + +
97C ASP* 1.3 78.7 - - - +
99C LEU* 1.3 56.0 + - - +
101C ASN* 3.1 1.6 + - - +
102C GLN* 2.6 46.1 + - + +
140C PHE* 4.0 22.0 - - + -
55D ASP* 4.6 10.1 - - + +
56D PHE* 4.1 27.6 - - + -
68D LYS 4.7 11.0 - - - +
69D ILE* 4.6 3.1 - - + -
70D THR* 4.3 29.2 - - - +
71D GLN* 4.3 2.6 - - + +
74D ALA* 4.0 10.3 - - + +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG 3.4 13.9 + - - +
96C VAL 4.0 2.0 - - - +
97C ASP 3.3 0.4 - - - -
98C ILE* 1.3 77.6 - - - +
100C GLU* 1.3 65.7 + - - +
102C GLN* 4.1 4.0 - - - -
103C ALA* 2.7 32.3 + - + +
137C PHE* 4.7 17.3 - - + -
140C PHE* 3.7 22.9 - - + -
147C PHE* 3.3 55.2 - - + -
148C VAL* 4.7 2.0 - - + -
155C VAL* 3.7 30.3 - - + +
158C LEU* 5.4 1.1 - - + -
159C ALA* 5.2 5.8 - - + -
56D PHE* 4.8 6.1 - - + -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 2.9 43.8 + - + +
77C CYS* 5.9 4.5 - - - -
96C VAL* 3.0 15.5 + - + +
97C ASP* 2.7 23.0 + - - +
99C LEU* 1.3 74.6 - - - +
101C ASN* 1.3 83.6 + - - +
104C MET* 3.4 16.3 + - - +
154C PHE* 4.3 22.7 - - + -
155C VAL* 4.2 5.3 - - + +
158C LEU* 4.1 17.6 - - + +
73D ASN* 5.7 0.9 - - - +
100D GLU* 5.2 6.9 - - - +
101D ASN* 4.7 1.8 + - - +
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Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 5.2 1.8 + - - +
97C ASP* 3.0 17.8 + - - +
98C ILE 3.9 1.1 - - - +
100C GLU* 1.3 100.9 + - - +
102C GLN* 1.3 66.9 + - - +
104C MET* 2.8 9.5 + - - +
105C ASP* 2.7 20.8 + - - +
71D GLN* 3.0 28.9 - - + +
73D ASN* 3.5 28.1 + - - +
74D ALA* 3.7 22.3 - - - +
77D CYS* 6.0 0.8 - - - -
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 2.6 30.3 + - + +
99C LEU* 3.9 4.3 - - - +
101C ASN* 1.3 71.1 - - - +
103C ALA* 1.3 57.6 + - - +
105C ASP* 3.0 21.5 + - - +
106C VAL* 2.9 29.9 + - - +
133C MET* 3.7 22.2 - - - +
137C PHE* 4.6 7.0 - - + -
56D PHE* 3.7 48.7 - - + +
58D ASN* 5.0 2.7 + - - +
70D THR* 4.3 4.3 - - - +
71D GLN* 3.3 27.6 + - + +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 2.7 26.3 + - + +
100C GLU 4.1 1.8 - - - +
102C GLN* 1.3 72.9 - - - +
104C MET* 1.3 55.8 + - - +
106C VAL* 3.1 12.2 - - - +
107C SER* 2.9 30.8 + - - -
137C PHE* 4.8 8.7 - - + -
158C LEU* 4.4 20.9 - - + -
159C ALA* 4.8 4.7 - - + +
162C VAL* 3.5 22.5 - - + +
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Residues in contact with MET 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.2 19.3 - - + +
72C SER* 4.1 25.4 - - - +
73C ASN* 3.6 33.0 - - - +
76C LEU* 5.5 0.2 - - + -
100C GLU 3.4 10.9 + - - +
101C ASN* 2.8 11.9 + - - +
103C ALA* 1.3 74.7 - - - +
105C ASP* 1.3 57.9 + - - +
107C SER* 3.7 10.2 - - - -
108C ASN* 2.9 54.1 + - - +
158C LEU* 4.1 21.7 - - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN 2.7 10.7 + - - +
102C GLN* 3.1 25.1 + - - +
104C MET* 1.3 78.5 - - - +
106C VAL* 1.3 57.0 + - - +
108C ASN* 3.4 4.6 + - - +
109C GLN* 3.0 37.1 + - - +
58D ASN* 5.4 1.4 + - - -
71D GLN* 3.6 23.5 + - - +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 2.9 18.1 + - - +
103C ALA* 3.1 15.7 - - - +
105C ASP* 1.3 74.3 + - - +
107C SER* 1.3 56.6 + - - +
109C GLN* 3.0 22.5 + - - +
110C LEU* 2.9 27.5 + - - +
126C TYR* 3.9 19.2 + - - +
130C LEU* 6.1 0.4 - - + -
133C MET* 4.4 26.2 - - + -
137C PHE* 3.8 18.6 - - + -
162C VAL* 3.5 22.2 - - + -
166C HIS* 4.1 9.4 - - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 5.6 4.0 - - - +
103C ALA 2.9 19.5 + - - -
104C MET* 3.7 17.0 - - - -
106C VAL* 1.3 78.6 - - - +
108C ASN* 1.3 57.1 + - - +
110C LEU* 3.1 11.6 + - - +
111C ALA* 3.0 27.4 + - - +
161C ASP* 5.2 4.5 + - - -
162C VAL* 4.5 14.8 - - - +
165C LEU* 4.8 13.4 - - - +
166C HIS* 5.7 1.1 - - - -
208C TYR* 4.7 1.6 + - - -
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Residues in contact with ASN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 5.2 8.9 - - - +
104C MET* 2.9 43.2 + - - +
105C ASP* 3.9 4.7 - - - +
107C SER* 1.3 73.4 - - - +
109C GLN* 1.3 62.9 + - - +
110C LEU 3.3 0.2 - - - -
111C ALA* 4.0 9.4 - - - +
112C ARG* 3.2 30.8 + - - +
112D ARG* 5.2 12.5 + - - +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASP* 3.0 21.9 + - - +
106C VAL* 3.0 27.0 - - - +
108C ASN* 1.3 78.2 - - - +
110C LEU* 1.3 60.7 + - - +
112C ARG* 3.2 24.3 - - - +
113C VAL* 3.7 10.7 + - - +
126C TYR* 3.3 30.9 - - + -
129C GLU* 6.2 0.2 - - - +
133C MET* 4.7 16.2 - - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL 2.9 11.9 + - - +
107C SER* 3.3 10.5 - - - +
109C GLN* 1.3 73.1 - - - +
111C ALA* 1.3 65.0 + - - +
112C ARG 3.0 1.1 - - - -
113C VAL* 2.8 31.9 + - + +
114C CYS* 3.2 4.1 + - - +
126C TYR* 3.7 26.2 + - + +
165C LEU* 4.1 20.9 - - + -
166C HIS* 3.2 33.0 - - + +
169C PHE* 3.7 36.3 - - + -
208C TYR* 3.3 22.0 - - + +
214C TRP* 6.5 0.2 - - + -
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SER 3.0 14.6 + - - +
108C ASN* 4.5 11.0 - - - +
110C LEU* 1.3 76.0 - - - +
112C ARG* 1.3 62.5 + - - +
114C CYS* 4.1 2.0 - - - -
115C TYR* 2.9 40.4 + - + +
208C TYR* 3.5 32.1 - - + -
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASN* 3.2 24.0 + - - +
109C GLN* 3.2 19.4 - - - +
110C LEU 3.0 0.6 + - - -
111C ALA* 1.3 77.3 - - - +
113C VAL* 1.3 57.1 + - + +
115C TYR* 3.7 4.5 + - - +
116C SER* 2.7 31.6 + - - +
108D ASN* 5.1 7.1 + - - +
111D ALA* 6.2 0.6 - - - +
112D ARG* 3.1 65.8 - - - +
115D TYR* 6.0 3.4 - - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLN 3.9 10.1 - - - +
110C LEU* 2.8 39.5 + - + +
112C ARG* 1.3 76.4 - - + +
114C CYS* 1.3 56.8 + - - +
115C TYR 3.0 4.5 - - - -
116C SER* 2.9 28.3 + - - +
119C PHE* 3.2 33.3 - - + -
122C LEU* 5.0 24.0 - - + +
123C LYS* 5.8 0.7 - - - -
126C TYR* 4.9 21.1 - - + -
169C PHE* 4.7 4.0 - - + -
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Residues in contact with CYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.2 12.4 + - - +
111C ALA 3.1 7.4 + - - +
113C VAL* 1.3 76.3 - - - +
115C TYR* 1.3 59.9 + - + +
116C SER 3.4 0.4 - - - -
119C PHE* 4.0 9.0 - - - -
169C PHE* 4.0 18.2 - - - -
208C TYR* 3.4 45.5 - - + -
212C ALA* 3.3 3.8 - - - +
213C VAL* 2.8 31.6 + - - +
214C TRP* 3.5 28.6 + - - +
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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