Contacts of the helix formed by residues 83 - 110 (chain A) in PDB entry 5GUF
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 MET 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.4 39.3 - - + +
78A LEU* 3.9 22.0 - - + -
81A GLY* 3.6 11.2 + - - +
82A ASN* 1.3 72.4 + - - +
84A LEU* 1.3 63.1 + - - +
85A LEU 3.1 0.4 - - - -
86A ALA* 3.0 23.2 + - - +
87A VAL* 3.8 6.5 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.8 30.7 - - + +
82A ASN* 2.8 17.9 + - - +
83A MET* 1.3 77.5 - - - +
85A LEU* 1.3 57.6 + - - +
87A VAL* 2.9 23.4 + - + +
88A HIS* 2.8 51.2 + - + +
139A TYR* 5.0 0.4 - - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 16.4 - - + -
19A ILE* 3.9 17.5 - - + +
20A LEU* 4.1 11.7 - - + -
73A GLY 3.8 3.0 - - - +
76A ALA* 3.5 25.4 - - + +
77A ALA* 3.7 10.8 - - - +
80A SER* 3.4 20.4 - - - +
82A ASN* 3.0 30.8 + - + +
84A LEU* 1.3 77.0 - - - +
86A ALA* 1.3 55.6 + - - +
88A HIS* 4.4 3.6 - - + +
89A SER* 2.6 38.4 + - - +
139A TYR* 3.6 24.0 - - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 5.4 2.1 - - - +
73A GLY 3.8 11.4 - - - +
74A VAL* 4.6 16.2 - - + +
77A ALA* 3.6 14.7 - - + +
83A MET* 3.0 16.2 + - - +
85A LEU* 1.3 79.9 - - - +
87A VAL* 1.3 60.8 + - + +
90A PRO* 3.3 20.4 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET 4.4 8.1 - - - +
84A LEU* 2.9 23.9 + - + +
86A ALA* 1.3 82.1 - - + +
88A HIS* 1.3 72.1 + - + +
90A PRO* 3.3 12.6 - - - +
91A ALA* 4.6 4.2 + - - +
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Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.5 29.6 - + - -
20A LEU* 5.6 0.9 - - + -
84A LEU* 2.8 42.3 + - + +
85A LEU* 4.4 4.0 - - + +
87A VAL* 1.3 84.6 - - + +
89A SER* 1.3 65.0 + - - +
91A ALA* 3.0 8.8 + - - +
92A ILE* 3.0 28.6 + - + +
137A LEU* 3.6 35.8 + - + +
139A TYR* 2.7 34.8 + + - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 5.1 2.6 + - - +
23A PRO* 3.3 23.0 - - - +
69A GLY 4.0 4.0 - - - -
70A SER 5.2 0.2 - - - -
73A GLY* 3.2 28.6 - - - -
76A ALA* 4.7 0.7 - - - +
85A LEU* 2.6 28.5 + - - +
88A HIS* 1.3 78.7 - - - +
90A PRO* 1.3 61.5 - - - +
92A ILE* 3.7 9.7 - - - +
93A ALA* 2.7 31.4 + - - +
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Residues in contact with PRO 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.6 20.9 - - + -
70A SER* 3.9 29.8 - - - +
86A ALA 3.3 22.7 - - - +
87A VAL* 3.3 12.1 - - - +
89A SER* 1.3 92.0 - - - +
91A ALA* 1.3 62.5 + - - +
93A ALA* 3.3 5.9 + - + +
94A LEU* 2.9 26.8 + - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL 4.6 2.8 + - - +
88A HIS* 3.0 11.4 + - - +
90A PRO* 1.3 78.8 - - - +
92A ILE* 1.3 57.4 + - - +
94A LEU* 3.1 14.9 + - - +
95A GLY 3.0 22.5 + - - -
133A VAL* 3.5 21.7 - - + +
137A LEU* 4.5 15.9 - - + -
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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
----------------------------------------------------------
20A LEU* 3.8 39.9 - - + +
21A MET* 4.1 8.5 - - + -
23A PRO* 5.4 0.7 - - + -
24A ALA* 4.0 13.7 - - + +
88A HIS* 3.0 23.2 + - + +
89A SER* 3.7 11.2 - - - +
91A ALA* 1.3 72.3 - - - +
93A ALA* 1.3 61.2 + - - +
95A GLY* 3.1 2.4 + - - -
96A ALA* 2.8 27.2 + - - +
130A ALA* 3.7 22.9 - - + +
133A VAL* 4.0 11.2 - - + -
134A SER* 4.1 19.1 - - - +
137A LEU* 4.0 16.8 - - + -
139A TYR* 5.1 0.7 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO 4.6 1.1 - - - +
24A ALA* 4.7 4.0 - - - +
27A ALA* 3.9 23.7 - - + +
65A GLY 4.7 2.2 - - - +
66A PHE* 4.5 11.0 - - + -
69A GLY* 4.1 16.8 - - - -
89A SER 2.7 21.1 + - - +
90A PRO* 3.4 9.0 - - + +
92A ILE* 1.3 74.1 - - - +
94A LEU* 1.3 56.9 + - - +
96A ALA* 3.2 4.6 + - - +
97A LEU* 2.9 34.9 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.6 35.4 - - + -
90A PRO 2.9 16.2 + - - +
91A ALA* 3.1 14.8 + - - +
93A ALA* 1.3 73.8 - - - +
95A GLY* 1.3 58.9 + - - +
97A LEU* 3.1 13.8 + - + +
98A ALA* 2.7 32.4 + - - +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.0 11.9 + - - -
92A ILE 3.1 3.5 + - - -
94A LEU* 1.3 75.5 - - - +
96A ALA* 1.3 57.5 + - - +
98A ALA* 3.8 5.9 - - - +
99A GLY 2.9 24.6 + - - -
129A GLY* 3.3 21.0 - - - -
133A VAL* 3.6 26.2 - - - +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.6 42.8 - - + +
27A ALA* 4.6 3.6 - - + -
28A ASN* 5.0 2.7 - - - +
92A ILE 2.8 7.6 + - - +
93A ALA* 3.2 8.5 + - - +
95A GLY* 1.3 75.6 - - - +
97A LEU* 1.3 63.3 + - - +
100A ASP* 3.1 20.8 + - - +
126A PHE* 3.3 32.5 - - + +
130A ALA 3.8 1.0 - - - +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 3.6 27.6 - - + +
28A ASN* 4.9 2.7 - - - +
31A PRO* 4.6 10.1 - - + -
62A LEU* 3.5 47.6 - - + +
65A GLY* 4.0 6.7 - - - -
66A PHE* 3.6 22.7 - - + +
93A ALA 2.9 23.2 + - - +
94A LEU* 3.7 13.5 - - + +
96A ALA* 1.3 77.7 - - - +
98A ALA* 1.3 61.8 + - - +
100A ASP* 3.4 8.8 + - + +
101A MET* 3.1 30.7 + - + +
201A CTP 5.1 2.6 + - + +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU 2.7 22.1 + - - +
95A GLY* 3.9 6.5 - - - +
97A LEU* 1.3 72.7 - - - +
99A GLY* 1.3 53.2 + - - +
101A MET* 3.2 16.9 + - + +
102A ALA* 2.7 35.3 + - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 2.9 17.1 + - - -
96A ALA 3.9 0.7 - - - -
98A ALA* 1.3 75.4 - - - +
100A ASP* 1.3 58.3 + - - +
102A ALA* 3.7 7.8 - - - +
103A GLY 2.9 22.9 + - - -
125A ASP* 3.2 31.6 - - - +
129A GLY* 4.3 7.2 - - - -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 4.1 18.2 - - - +
57A LYS* 2.6 31.9 + - - +
96A ALA 3.1 18.1 + - - +
97A LEU* 3.8 9.4 - - + +
99A GLY* 1.3 75.3 - - - +
101A MET* 1.3 62.6 + - - +
103A GLY 3.3 0.9 + - - -
104A SER* 3.0 21.5 + - - -
125A ASP* 3.4 14.5 - - - +
126A PHE* 4.0 3.9 - - + +
201A CTP 3.3 12.6 + - - -
205A K 2.7 28.2 - - - -
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Residues in contact with MET 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.1 12.8 - - + -
53A LEU* 3.6 28.7 - - + +
57A LYS* 4.1 20.4 - - + -
62A LEU* 4.0 38.6 - - + -
97A LEU* 3.1 19.5 + - + +
98A ALA* 3.6 16.2 - - + +
100A ASP* 1.3 75.6 - - - +
102A ALA* 1.3 59.0 + - - +
104A SER* 3.1 7.9 + - - +
105A PHE* 2.8 29.8 + - - +
201A CTP 4.9 0.9 - - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 2.7 20.0 + - - +
99A GLY* 3.7 9.6 - - - +
101A MET* 1.3 72.9 - - - +
103A GLY* 1.3 56.7 + - - +
105A PHE* 3.4 10.6 - - + +
106A VAL* 3.0 33.4 + - + +
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY 2.9 14.5 + - - -
100A ASP 3.3 3.8 + - - -
101A MET 3.1 0.2 - - - -
102A ALA* 1.3 74.4 - - - +
104A SER* 1.3 59.3 + - - +
106A VAL* 3.2 5.7 + - - +
107A LYS* 2.9 35.9 + - - +
121A LEU* 4.0 15.6 - - - +
125A ASP* 3.9 17.0 - - - -
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.9 13.5 - - - -
57A LYS* 2.9 31.5 + - - -
100A ASP 3.0 6.9 + - - -
101A MET 3.1 6.9 + - - -
103A GLY* 1.3 71.2 - - - +
105A PHE* 1.3 67.2 + - - +
107A LYS* 3.2 7.1 + - - +
108A ARG* 3.0 30.7 + - - +
125A ASP* 4.7 0.4 + - - -
201A CTP 2.3 34.9 + - - -
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.6 4.5 - - + -
52A LEU* 3.5 33.7 - - + -
53A LEU* 3.9 9.9 - - + +
101A MET 2.8 17.9 + - - +
102A ALA* 3.4 15.7 - - + +
104A SER* 1.3 73.6 - - - +
106A VAL* 1.3 73.0 + - + +
108A ARG 3.3 0.2 + - - -
109A ARG* 3.1 73.4 + - + +
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.0 20.5 + - + +
103A GLY* 3.2 7.1 + - - +
105A PHE* 1.3 88.2 - - + +
107A LYS* 1.3 63.2 + - - +
109A ARG* 3.4 6.5 + - - +
110A LEU* 3.2 39.9 + - + +
121A LEU* 4.2 17.0 - - + -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 2.9 21.6 + - - +
104A SER* 3.2 6.5 + - - +
106A VAL* 1.3 77.1 - - - +
108A ARG* 1.3 76.8 + - - +
110A LEU* 3.2 6.9 + - - -
112A ILE* 2.8 48.0 + - + +
116A ARG 2.8 29.2 + - - +
118A ALA* 3.8 15.0 - - + -
121A LEU* 4.0 14.4 - - + -
122A ASP* 3.0 31.2 + - - +
201A CTP 3.0 31.4 + - - +
202A MG 4.5 3.0 - - - -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.3 21.1 - - + +
51A ARG* 3.2 28.3 - - - +
52A LEU 4.1 1.6 - - - +
53A LEU 2.9 31.5 + - - +
54A GLY* 4.6 2.5 - - - +
104A SER 3.0 21.6 + - - +
105A PHE 3.3 0.2 + - - -
107A LYS* 1.3 92.0 - - - +
109A ARG* 1.3 67.7 + - - +
111A GLY* 2.9 17.3 + - - -
112A ILE 2.8 30.7 + - - -
113A GLU* 3.3 9.3 + - - +
114A ARG* 3.6 17.9 - - - +
201A CTP 2.7 44.4 + - - -
204A MG 3.8 20.6 - - - -
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.7 17.7 - - - +
48A ASP* 2.7 37.6 + - - +
50A ARG* 3.3 24.4 + - - +
51A ARG 2.8 22.0 + - - -
52A LEU* 3.2 27.1 + - - +
105A PHE* 3.1 60.0 + - + +
106A VAL* 3.8 6.5 - - - +
107A LYS 3.4 0.4 - - - -
108A ARG* 1.3 76.4 - - - +
110A LEU* 1.3 63.0 + - + +
111A GLY 3.3 0.9 + - - -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.2 33.5 + - + +
107A LYS* 3.7 5.2 - - - +
108A ARG 3.1 1.4 - - - -
109A ARG* 1.3 79.2 - - + +
111A GLY* 1.3 61.5 + - - +
112A ILE* 3.3 23.9 + - + +
121A LEU* 5.9 1.8 - - + -
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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