Contacts of the helix formed by residues 86 - 111 (chain A) in PDB entry 1GUL
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 1.3 73.9 - - - +
87A LYS* 1.3 62.4 - - + +
89A ARG* 4.0 15.7 - - + +
90A THR* 2.5 53.5 + - - +
74B TYR* 3.9 18.8 - - + -
77B ASP* 4.1 28.9 - - + +
78B LYS* 3.8 33.9 - - + +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 2.8 18.2 + - - +
86A LEU* 1.3 88.7 - - + +
88A GLU* 1.3 60.6 - - + +
90A THR* 3.3 5.6 + - - +
91A LEU* 3.2 28.0 + - + +
61B ASP* 5.1 3.2 + - - +
63B MET* 3.9 26.6 - - + +
74B TYR* 3.3 36.0 + - - -
78B LYS* 5.0 6.0 - - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 3.5 14.5 - - - -
84A LYS* 2.8 32.7 + - - +
85A ASN* 3.0 31.6 + - - +
87A LYS* 1.3 71.8 - - + +
89A ARG* 1.3 68.2 + - - +
90A THR 3.0 1.3 - - - -
91A LEU* 2.8 17.6 + - + +
92A ILE* 2.9 19.6 + - - +
149A VAL* 3.9 20.3 - - + +
150A GLY* 4.0 24.1 - - - -
152A GLN* 5.5 2.3 - - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 5.3 2.6 - - - +
77A ASP* 2.7 43.4 + - - -
82A PHE* 3.6 57.2 + - + +
85A ASN 2.8 19.7 + - - +
86A LEU* 3.4 21.3 - - + +
88A GLU* 1.3 72.6 - - - +
90A THR* 1.3 65.4 + - - +
92A ILE* 3.4 1.5 + - - +
93A ASP* 2.9 27.3 + - + +
77B ASP* 4.8 1.8 - - - -
89B ARG* 3.6 36.0 - - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 2.5 45.5 + - - +
87A LYS* 3.4 6.9 - - - -
89A ARG* 1.3 76.1 - - - +
91A LEU* 1.3 62.7 + - + +
93A ASP* 3.3 6.7 + - + +
94A MET* 3.0 29.6 + - + +
63B MET* 4.2 12.6 - - + -
65B LEU* 4.0 32.5 - - + -
70B SER* 5.5 4.7 - - - +
74B TYR* 3.9 15.3 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.2 19.0 + - + +
88A GLU* 2.8 14.0 + - + +
90A THR* 1.3 71.3 - - + +
92A ILE* 1.3 66.9 + - - +
94A MET* 3.2 11.3 + - - +
95A TYR* 2.8 56.8 + - + +
149A VAL* 4.0 21.5 - - + -
51B LEU* 6.2 0.7 - - + -
63B MET* 6.0 4.5 - - + -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 4.3 0.4 - - - +
82A PHE* 3.7 23.3 - - + -
83A GLY* 3.5 31.0 - - - +
88A GLU 3.1 14.6 - - - +
89A ARG 3.6 3.6 - - - +
91A LEU* 1.3 75.3 - - - +
93A ASP* 1.3 64.5 + - - +
95A TYR* 3.3 2.2 + - - +
96A VAL* 2.9 30.7 + - + +
149A VAL* 3.9 23.8 - - + +
154A SER* 3.5 24.5 - - - +
155A LEU* 4.2 10.5 - - + -
156A ALA* 3.9 26.7 - - - +
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 4.6 4.4 + - - -
82A PHE* 4.3 17.3 - - + -
89A ARG* 2.9 20.1 + - + +
90A THR* 3.4 7.7 - - - +
92A ILE* 1.3 78.1 - - - +
94A MET* 1.3 63.3 + - - +
96A VAL* 3.1 7.5 + - - +
97A GLU* 2.8 35.5 + - - +
70B SER* 2.9 30.0 + - - +
73B HIS* 2.8 36.4 + - - +
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.0 18.8 + - + +
91A LEU* 3.6 15.0 - - - +
93A ASP* 1.3 77.3 - - - +
95A TYR* 1.3 70.5 + - + +
97A GLU* 3.2 2.0 + - - +
98A GLY 2.9 19.6 + - - -
51B LEU* 4.4 13.7 - - + -
52B PHE* 3.5 9.5 - - + -
64B LYS 4.2 3.4 - - - +
65B LEU* 3.4 25.6 - - + -
66B VAL* 2.5 69.1 - - + +
67B GLN* 4.1 4.0 - - + +
70B SER* 3.8 15.3 - - - -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.8 47.7 + - + +
92A ILE 3.6 3.6 - - - +
94A MET* 1.3 78.4 - - + +
96A VAL* 1.3 61.4 + - - +
98A GLY* 3.8 0.7 - - - -
99A THR* 2.6 34.7 + - - +
135A VAL* 5.3 0.2 - - + -
136A PHE* 4.0 19.9 - + + -
139A ILE* 3.2 34.4 - - + +
148A LEU* 4.3 14.5 + - + -
149A VAL* 3.4 33.0 - - + -
156A ALA* 3.8 19.7 - - + +
51B LEU* 4.0 27.9 - - + +
52B PHE* 4.2 6.3 - + - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.4 3.6 - - + -
73A HIS* 5.8 3.6 - - - +
92A ILE 2.9 23.2 + - - +
93A ASP* 3.3 7.0 - - - +
95A TYR* 1.3 80.2 - - - +
97A GLU* 1.3 71.3 + - - +
99A THR* 3.2 5.5 + - - -
100A LEU* 2.8 41.7 + - + +
155A LEU* 3.9 24.9 - - + +
156A ALA* 3.7 29.2 - - - +
159A ILE* 4.5 13.7 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 2.7 44.3 + - - +
73A HIS* 4.2 13.9 + - - -
93A ASP* 2.8 26.1 + - - +
96A VAL* 1.3 76.5 - - - +
98A GLY* 1.3 65.4 + - - +
100A LEU* 3.2 6.9 + - - +
101A ASP* 3.1 26.6 + - - +
67B GLN* 3.3 29.0 - - + +
69B ARG* 3.5 21.1 + - + +
70B SER* 3.2 23.1 - - - +
73B HIS* 5.1 0.2 - - - -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A MET 2.9 14.6 + - - -
95A TYR 3.8 0.9 - - - -
97A GLU* 1.3 76.1 - - - +
99A THR* 1.3 63.8 + - - +
101A ASP* 2.9 20.0 + - - +
102A LEU 3.4 1.2 + - - -
132A TYR* 3.3 22.2 - - - -
52B PHE* 3.8 11.7 - - - -
67B GLN* 3.4 20.2 - - - +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 2.6 25.1 + - - +
96A VAL* 3.6 3.6 - - - -
98A GLY* 1.3 77.4 - - - +
100A LEU* 1.3 53.7 + - - +
102A LEU* 2.8 31.1 + - + +
103A LEU* 2.9 11.9 + - - +
132A TYR* 4.5 3.9 - - - -
136A PHE* 3.6 18.8 - - + -
156A ALA 5.3 1.4 + - - -
159A ILE* 3.8 20.4 - - + +
160A LEU* 4.1 17.9 - - + +
163A THR* 3.4 31.2 - - + +
52B PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 4.6 6.7 - - - +
68A THR* 5.6 5.4 - - + -
69A ARG* 3.8 50.2 + - + +
72A LEU* 4.8 14.1 - - + -
96A VAL* 2.8 38.4 + - + +
97A GLU* 3.2 7.2 + - - +
99A THR* 1.3 70.7 - - - +
101A ASP* 1.3 63.4 + - - +
103A LEU* 3.7 27.3 - - + +
104A GLU* 3.0 26.2 + - - +
159A ILE* 3.9 13.2 - - + -
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.6 9.5 + - - -
97A GLU 3.1 13.9 + - - +
98A GLY 2.9 11.9 + - - +
100A LEU* 1.3 81.4 - - - +
102A LEU* 1.3 60.3 + - - +
104A GLU* 3.6 14.2 - - - +
105A LEU* 4.2 9.0 + - - +
132A TYR* 3.7 14.5 + - - +
54B GLN* 4.2 4.8 + - - +
67B GLN* 3.4 18.0 + - - +
301B IBG 3.4 33.6 + - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 3.4 1.7 + - - +
99A THR* 2.8 16.0 + - + +
101A ASP* 1.3 77.7 - - - +
103A LEU* 1.3 66.5 + - - +
104A GLU 3.0 3.0 + - - -
105A LEU* 3.0 32.6 + - + +
106A LEU* 3.9 3.5 + - + +
124A MET* 4.4 6.5 - - + +
127A LYS* 4.2 18.2 - - + -
128A ALA* 4.2 12.6 - - + +
132A TYR* 3.7 48.0 + - + -
133A PHE* 4.5 6.3 - - + -
136A PHE* 6.3 0.4 - - + -
160A LEU* 6.0 1.3 - - + -
163A THR* 4.0 20.9 - - + -
167A LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.8 22.0 - - - +
99A THR 2.9 14.2 + - - +
100A LEU* 3.7 22.7 - - + +
102A LEU* 1.3 77.7 - - - +
104A GLU* 1.3 63.4 + - - +
106A LEU* 2.8 34.6 + - + +
107A ILE* 3.0 29.0 + - + +
159A ILE* 4.8 0.9 - - + -
162A GLN* 3.8 23.6 - - + +
163A THR* 3.8 31.8 - - + +
166A ALA* 5.0 4.0 - - + -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 2.9 42.2 + - - -
100A LEU 3.0 18.7 + - - +
101A ASP* 3.6 12.6 - - - +
103A LEU* 1.3 77.3 - - - +
105A LEU* 1.3 65.4 + - + +
107A ILE* 3.0 12.4 + - - +
108A MET* 2.8 52.3 + - - +
301A IBG 5.0 0.7 - - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP 4.3 9.0 - - - +
102A LEU* 3.3 22.0 - - + +
104A GLU* 1.3 80.2 - - + +
106A LEU* 1.3 64.8 + - + +
108A MET* 4.0 25.2 - - + +
109A HIS* 3.1 24.8 + - - +
120A GLU* 5.0 7.9 - - - +
123A ASN* 4.1 20.2 - - - +
124A MET* 3.8 44.8 - - + +
127A LYS* 4.2 11.9 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.1 11.0 - - + +
103A LEU* 2.8 26.1 + - + +
105A LEU* 1.3 83.8 - - + +
107A ILE* 1.4 62.5 + - + +
109A HIS* 3.3 17.4 - - - +
110A PRO* 3.3 7.1 - - - +
124A MET* 3.8 24.2 - - + -
163A THR* 4.8 1.6 - - + -
166A ALA* 4.1 30.1 - - + +
167A LEU* 3.9 30.1 - - + -
170A LYS* 4.2 21.4 + - + -
208A PRO* 5.9 0.5 - - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 3.9 28.3 - - - +
15A ARG* 4.0 32.1 - - + +
18A SER* 6.0 0.2 - - - +
100A LEU 6.0 0.2 - - - +
103A LEU* 3.0 32.1 + - + +
104A GLU* 3.0 23.5 + - - +
106A LEU* 1.4 77.4 - - + +
108A MET* 1.3 60.2 + - - +
110A PRO* 3.5 10.4 - - - +
111A PHE* 3.6 14.4 - - - -
301A IBG 3.6 26.0 - - + -
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.8 45.4 + - - +
105A LEU* 4.0 29.2 - - + +
107A ILE* 1.3 73.0 - - - +
109A HIS* 1.3 66.5 + - - +
110A PRO* 3.3 0.7 - - - -
111A PHE* 2.9 24.2 + - - +
112A LEU* 3.7 20.4 + - + +
120A GLU* 5.4 7.0 - - - +
301A IBG 4.6 11.2 - - + -
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 3.1 11.1 + - - +
106A LEU* 3.3 11.7 - - - +
108A MET* 1.3 75.8 - - - +
110A PRO* 1.3 69.6 - - + +
111A PHE 3.0 1.4 + - - -
112A LEU* 3.1 21.6 + - + +
117A GLN* 2.8 66.6 + - + -
118A GLN* 5.7 0.7 - - - -
120A GLU* 3.9 12.1 - - + -
121A VAL* 3.7 14.3 - - + +
124A MET* 3.6 20.6 - - + -
170A LYS* 2.7 32.0 + - + +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.3 10.8 - - - +
107A ILE 3.5 8.7 - - - +
108A MET 3.3 4.5 - - - -
109A HIS* 1.3 97.9 - - + +
111A PHE* 1.3 70.6 + - + +
112A LEU 3.3 3.9 + - - +
117A GLN* 3.6 13.4 + - - +
170A LYS* 5.5 1.6 - - - +
208A PRO* 3.8 29.8 - - + +
212A TYR* 5.4 1.1 - - + -
213A VAL* 3.8 32.8 - - + +
217A TYR* 5.1 0.3 + - - -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE 3.6 24.2 - - - -
108A MET* 2.9 11.1 + - + +
110A PRO* 1.3 86.3 - - + +
112A LEU* 1.3 65.6 + - - +
113A LYS* 4.6 6.2 + - - +
212A TYR* 3.9 19.1 - + - -
213A VAL* 3.8 18.8 - - + -
216A VAL* 3.0 37.5 - - + -
217A TYR* 3.7 37.9 + + + +
301A IBG 4.1 32.3 - + + -
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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