Contacts of the helix formed by residues 86 - 111 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASN* 1.3 76.5 - - - +
87C LYS* 1.3 60.0 + - - +
89C ARG* 3.2 14.8 - - + +
90C THR* 2.5 52.8 + - - +
74D TYR* 3.7 28.9 - - + -
77D ASP* 4.0 34.5 - - + +
78D LYS* 3.7 23.6 - - + +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASN* 2.7 16.3 + - - +
86C LEU* 1.3 81.8 - - - +
88C GLU* 1.3 65.5 + - + +
90C THR* 3.4 3.6 + - - -
91C LEU* 3.1 27.7 + - + +
61D ASP* 4.5 5.5 + - - +
63D MET* 3.6 29.4 - - + +
74D TYR* 2.8 41.5 + - + -
78D LYS* 5.3 4.2 - - - +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 3.6 9.2 - - - -
84C LYS* 3.0 38.6 + - - +
85C ASN* 3.0 36.4 + - - +
87C LYS* 1.3 75.9 - - + +
89C ARG* 1.3 53.6 + - - +
91C LEU* 2.7 30.8 + - + +
92C ILE* 3.0 16.3 + - - +
149C VAL* 4.0 18.5 - - + +
150C GLY* 4.1 25.6 - - - +
152C GLN* 5.2 1.9 + - - -
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 5.1 5.1 + - - +
77C ASP* 3.0 41.6 + - - -
82C PHE* 3.5 56.0 + - + +
85C ASN 2.7 22.8 + - - +
86C LEU* 3.2 22.0 - - + +
88C GLU* 1.3 72.3 - - - +
90C THR* 1.3 64.5 + - - +
92C ILE* 3.3 5.5 + - - +
93C ASP* 2.9 26.4 + - + +
77D ASP* 4.4 2.6 + - - -
89D ARG* 2.9 39.8 - - - +
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 2.5 35.9 + - - +
87C LYS* 3.5 8.1 - - - -
89C ARG* 1.3 75.0 - - - +
91C LEU* 1.3 62.8 + - + +
93C ASP* 3.3 8.3 - - - +
94C MET* 3.1 25.6 + - + +
63D MET* 4.0 12.1 - - + -
65D LEU* 3.9 29.6 - - + -
70D SER* 5.2 5.3 - - - +
74D TYR* 3.6 28.9 - - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS* 3.1 19.5 - - + +
88C GLU* 2.7 14.3 + - + +
90C THR* 1.3 69.4 - - + +
92C ILE* 1.3 70.0 + - - +
93C ASP 3.0 1.3 - - - -
94C MET* 3.0 10.5 + - - +
95C TYR* 2.7 54.2 + - + +
149C VAL* 3.8 25.8 - - + -
63D MET* 5.4 10.1 - - + -
65D LEU* 6.5 0.4 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU 4.4 0.2 - - - +
82C PHE* 4.0 17.5 - - + -
83C GLY* 3.9 22.9 - - - +
88C GLU 3.2 18.8 - - - +
89C ARG* 3.5 7.2 - - - +
91C LEU* 1.3 76.4 - - - +
93C ASP* 1.3 53.5 + - - +
95C TYR* 3.2 2.8 + - - +
96C VAL* 2.7 45.3 + - + +
149C VAL* 4.0 20.9 - - + +
154C SER* 3.2 29.4 - - - +
155C LEU* 4.1 9.0 - - + -
156C ALA* 3.7 28.7 - - + +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 4.3 3.9 + - - -
82C PHE* 4.4 14.1 - - + -
89C ARG* 2.9 19.2 + - + +
90C THR* 3.3 9.4 - - - +
92C ILE* 1.3 78.9 - - - +
94C MET* 1.3 63.6 + - - +
96C VAL* 3.0 7.1 + - - +
97C GLU* 2.8 37.6 + - - +
70D SER* 2.9 34.7 + - - +
73D HIS* 3.2 31.6 + - - +
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Residues in contact with MET 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 3.1 15.0 + - + +
91C LEU* 3.0 14.6 + - - +
93C ASP* 1.3 79.1 - - - +
95C TYR* 1.3 67.1 + - + +
97C GLU* 3.8 0.7 - - - +
98C GLY 2.9 20.6 + - - -
51D LEU* 4.3 17.9 - - + -
52D PHE* 3.6 6.8 - - - -
64D LYS 3.5 4.5 - - - +
65D LEU* 2.5 42.8 - - + -
66D VAL* 2.3 59.7 - - + +
67D GLN* 3.8 4.8 - - + +
70D SER* 3.4 14.8 - - - -
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 2.7 48.8 + - + +
92C ILE 3.5 5.2 - - - +
94C MET* 1.3 73.6 - - + +
96C VAL* 1.3 64.3 + - - +
98C GLY* 3.4 0.5 + - - -
99C THR* 2.7 30.6 + - - +
136C PHE* 4.0 18.9 - + + -
139C ILE* 3.4 33.0 - - + +
148C LEU* 4.2 15.3 - - + -
149C VAL* 3.5 29.7 - - + +
156C ALA* 3.7 21.8 - - + -
51D LEU* 3.8 27.4 - - + +
52D PHE* 4.2 5.8 - + - -
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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
----------------------------------------------------------
72C LEU* 5.4 3.1 - - + -
73C HIS* 5.8 3.8 - - + +
82C PHE* 6.5 0.2 - - + -
92C ILE* 2.7 26.7 + - + +
93C ASP* 3.4 6.1 - - - +
95C TYR* 1.3 78.8 - - - +
97C GLU* 1.3 70.2 + - - +
99C THR* 3.1 5.0 + - - -
100C LEU* 2.9 39.2 + - + +
155C LEU* 4.1 19.7 - - + +
156C ALA* 3.5 31.9 - - - +
159C ILE* 4.2 17.3 - - + -
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 3.0 38.8 + - - +
73C HIS* 3.8 17.5 + - - -
93C ASP* 2.8 26.0 + - - +
96C VAL* 1.3 78.4 - - - +
98C GLY* 1.3 64.6 + - - +
100C LEU* 3.2 7.3 + - - +
101C ASP* 3.0 26.0 + - - +
67D GLN* 3.0 32.1 - - + +
69D ARG* 3.9 14.8 - - + +
70D SER* 3.0 28.3 - - - +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C MET 2.9 11.3 + - - -
97C GLU* 1.3 76.6 - - - +
99C THR* 1.3 64.4 + - - +
101C ASP* 2.9 18.8 + - - +
102C LEU 3.3 1.2 + - - -
132C TYR* 3.3 18.7 - - - -
52D PHE* 3.7 19.3 - - - -
67D GLN* 3.3 19.6 - - - -
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Residues in contact with THR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR 2.7 19.5 + - - -
96C VAL* 3.7 4.0 - - - -
98C GLY* 1.3 76.2 - - - +
100C LEU* 1.3 58.4 + - - +
102C LEU* 2.8 13.5 + - + +
103C LEU* 2.7 26.3 + - - +
132C TYR* 4.9 3.6 - - - -
136C PHE* 3.7 18.6 - - + -
156C ALA 5.3 1.6 + - - -
159C ILE* 4.0 19.3 - - + +
160C LEU* 4.1 18.3 - - + +
163C THR* 3.4 31.6 - - + +
52D PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 4.6 7.4 - - - +
68C THR* 6.1 1.8 - - + -
69C ARG* 3.9 46.6 + - + +
72C LEU* 4.6 12.8 - - + -
96C VAL* 2.9 33.7 + - + +
97C GLU* 3.4 9.4 - - - +
99C THR* 1.3 76.9 - - - +
101C ASP* 1.3 64.3 + - - +
103C LEU* 3.6 27.0 - - + +
104C GLU* 3.1 28.5 + - - +
159C ILE* 4.0 13.2 - - + -
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 4.8 9.7 + - - -
97C GLU 3.0 14.4 + - - +
98C GLY 2.9 9.3 + - - +
99C THR 2.9 0.8 - - - -
100C LEU* 1.3 81.8 - - - +
102C LEU* 1.3 60.4 + - - +
104C GLU* 3.3 16.4 - - - +
105C LEU* 4.2 7.3 - - - +
132C TYR* 3.7 14.6 + - - +
54D GLN* 4.3 7.6 + - - +
67D GLN* 3.5 24.6 + - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLY 3.3 2.6 + - - +
99C THR* 2.8 15.8 + - + +
101C ASP* 1.3 71.5 - - - +
103C LEU* 1.3 65.7 + - - +
104C GLU 2.9 6.0 + - - -
105C LEU* 3.0 31.7 + - + +
106C LEU* 3.9 3.3 + - + +
124C MET* 4.2 7.6 - - - +
127C LYS* 4.1 9.9 - - + -
128C ALA* 4.1 22.7 - - + +
132C TYR* 4.0 45.3 + - + -
133C PHE* 4.5 6.5 - - + -
160C LEU* 6.1 1.6 - - + -
163C THR* 4.0 14.1 - - + -
167C LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.9 5.8 - - - +
99C THR 2.7 15.0 + - - +
100C LEU* 3.6 27.4 - - + +
102C LEU* 1.3 76.7 - - - +
104C GLU* 1.3 63.9 + - - +
106C LEU* 2.8 39.1 + - + +
107C ILE* 3.0 25.7 + - + +
159C ILE* 4.8 0.7 - - + -
162C GLN* 3.7 35.7 - - + +
163C THR* 3.7 29.6 - - + +
166C ALA* 4.8 3.4 - - + -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 2.7 43.7 + - - -
69C ARG* 5.7 3.1 + - - -
100C LEU* 3.1 14.3 + - - +
101C ASP* 3.3 19.1 - - - +
103C LEU* 1.3 79.8 - - - +
105C LEU* 1.3 61.3 + - + +
107C ILE* 3.0 8.7 + - - +
108C MET* 2.8 57.0 + - + +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASP 4.2 9.9 - - - +
102C LEU* 3.3 26.2 - - + +
104C GLU* 1.3 82.6 - - + +
106C LEU* 1.3 62.4 + - + +
108C MET* 3.9 25.1 - - + +
109C HIS* 3.2 23.7 + - - +
120C GLU* 4.9 9.9 - - - +
123C ASN* 4.5 7.6 - - - +
124C MET* 3.5 46.2 - - + +
127C LYS* 4.4 15.3 - - + -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.8 3.4 - - + +
103C LEU* 2.8 26.4 + - + +
105C LEU* 1.3 82.4 - - + +
107C ILE* 1.3 64.0 + - + +
109C HIS* 3.2 4.0 - - - +
110C PRO* 3.1 20.8 - - - +
124C MET* 3.7 28.0 - - + -
163C THR* 4.2 5.4 - - + +
166C ALA* 3.5 37.2 - - + +
167C LEU* 3.8 23.8 - - + +
170C LYS* 4.2 21.4 + - + -
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLY* 3.6 29.6 - - - +
15C ARG* 4.0 51.6 - - + +
18C SER* 6.0 0.4 - - - +
103C LEU* 3.3 31.0 - - + +
104C GLU* 3.3 15.9 - - - +
106C LEU* 1.3 80.1 - - + +
108C MET* 1.3 60.4 + - + +
110C PRO* 3.5 11.0 - - - +
111C PHE* 4.1 10.6 - - - -
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Residues in contact with MET 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 2.8 49.1 + - + +
105C LEU* 3.9 29.4 - - + +
107C ILE* 1.3 73.4 - - + +
109C HIS* 1.3 68.1 + - - +
110C PRO* 3.2 2.2 - - - -
111C PHE* 2.9 23.8 + - - +
112C LEU* 3.8 19.0 - - + +
120C GLU* 5.3 8.5 - - - +
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Residues in contact with HIS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU 3.2 12.5 + - - +
106C LEU* 3.2 11.0 - - - +
108C MET* 1.3 77.7 - - - +
110C PRO* 1.3 70.3 - - + +
111C PHE 2.9 2.1 + - - -
112C LEU* 3.0 18.6 + - + +
117C GLN* 2.9 69.6 + - + +
118C GLN* 6.1 0.2 - - - -
120C GLU* 4.2 11.9 - - + -
121C VAL* 3.6 9.9 - - + +
124C MET* 3.7 20.9 - - + -
170C LYS* 2.7 31.3 + - - +
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Residues in contact with PRO 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU 3.1 11.4 - - - +
107C ILE 3.5 9.0 - - - +
108C MET 3.2 4.7 - - - -
109C HIS* 1.3 101.1 - - + +
111C PHE* 1.3 74.0 + - + +
112C LEU 3.2 4.7 + - - +
117C GLN* 3.7 13.1 + - - +
170C LYS* 5.2 3.1 - - - +
208C PRO* 4.0 29.8 - - + +
212C TYR* 5.8 0.2 - - + -
213C VAL* 4.2 26.1 - - + +
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ILE 4.1 10.1 - - - -
108C MET* 2.9 16.1 + - - +
110C PRO* 1.3 96.3 - - + +
112C LEU* 1.3 66.5 + - + +
113C LYS* 4.0 5.7 + - - +
212C TYR* 4.2 21.3 - + - -
213C VAL* 3.9 22.9 - - + -
216C VAL* 3.7 32.3 - - + -
217C TYR* 3.5 40.3 + + + +
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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