Contacts of the helix formed by residues 83 - 107 (chain A) in PDB entry 4JUY
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A HIS 3.7 0.4 + - - -
82A GLY* 1.3 74.6 - - - -
84A PRO* 1.3 74.2 - - + +
85A ARG* 4.2 14.9 - - + +
86A ASN* 2.9 23.7 + - + +
87A TYR* 3.1 14.9 + - - -
86B ASN* 3.9 18.6 - - - +
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLY 4.3 1.8 - - - +
83A GLU* 1.3 84.7 - - + +
85A ARG* 1.3 62.6 + - - +
86A ASN 2.9 1.0 + - - -
87A TYR* 3.3 33.2 - - + +
88A LEU* 3.0 47.9 + - + +
193A LEU* 4.1 17.3 - - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 4.2 15.7 - - + +
84A PRO* 1.3 78.0 - - - +
86A ASN* 1.3 63.4 + - - +
89A ASN* 2.8 30.8 + - - +
183A LEU* 3.8 12.8 - - + +
86B ASN* 4.9 2.7 - - - +
89B ASN* 4.2 3.7 + - + +
90B THR* 5.4 7.4 - - - +
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Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A HIS 5.0 3.4 - - - +
82A GLY* 6.0 0.8 - - - -
83A GLU* 2.9 18.0 + - - +
85A ARG* 1.3 80.9 - - - +
87A TYR* 1.3 61.1 + - - +
88A LEU 3.2 1.8 - - - -
89A ASN* 2.9 21.3 + - - +
90A THR* 3.0 14.8 + - - +
85B ARG* 4.5 8.9 - - - +
86B ASN* 2.8 54.0 + - - +
89B ASN* 3.6 17.2 + - - +
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.7 8.1 - - + -
79A ASN* 3.2 23.4 - - - +
80A ALA* 3.7 30.4 - - + +
81A HIS* 3.4 26.7 - - + +
82A GLY 3.7 8.5 - - - -
83A GLU 3.1 21.2 + - - -
84A PRO* 3.3 36.2 - - + +
86A ASN* 1.3 79.2 - - - +
88A LEU* 1.3 79.4 + - + +
90A THR* 3.6 10.7 - - - -
91A LEU* 2.7 35.6 + - + +
193A LEU* 4.2 15.8 - - + +
197A LEU* 4.4 8.9 - - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 6.1 2.5 - - + -
84A PRO* 3.0 44.9 + - + +
87A TYR* 1.3 93.0 - - + +
89A ASN* 1.3 52.9 + - - +
91A LEU* 3.8 6.0 - - + +
92A SER* 2.6 38.0 + - - -
179A LEU* 3.9 30.3 - - + +
182A LEU* 4.0 27.6 - - + -
183A LEU* 4.1 23.8 - - + +
193A LEU* 4.6 18.2 - - + -
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG 2.8 23.0 + - - -
86A ASN 2.9 10.6 + - - +
88A LEU* 1.3 76.5 - - - +
90A THR* 1.3 58.6 + - - +
92A SER* 3.2 7.4 + - - -
93A THR* 2.9 36.0 + - - +
183A LEU* 3.6 25.7 - - - +
89B ASN* 3.4 43.2 + - - +
93B THR* 4.5 8.7 + - - -
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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
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79A ASN* 5.9 2.2 - - + +
86A ASN* 3.0 14.2 + - - +
87A TYR* 3.6 13.8 - - + +
89A ASN* 1.3 75.2 - - - +
91A LEU* 1.3 63.1 + - - +
93A THR* 3.5 6.8 + - - +
94A ALA* 3.2 20.4 + - - +
127A THR 5.0 1.0 - - - +
130A ALA* 4.7 13.0 - - + +
131A VAL* 3.8 22.2 - - + +
89B ASN* 5.8 0.5 + - - -
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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
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75A LEU* 3.3 47.6 - - + +
76A VAL* 3.7 15.0 - - + +
79A ASN* 4.8 4.9 - - + +
87A TYR* 2.7 24.6 + - + +
88A LEU* 5.6 3.6 - - + -
90A THR* 1.3 76.3 - - - +
92A SER* 1.3 56.3 + - - +
94A ALA* 3.1 5.6 + - + +
95A LEU* 2.8 46.3 + - + +
131A VAL* 4.3 25.8 - - + -
175A LEU* 5.4 2.2 - - + -
179A LEU* 3.5 25.8 - - + -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU 2.6 29.5 + - - -
89A ASN* 3.2 11.4 + - - -
91A LEU* 1.3 72.4 - - - +
93A THR* 1.3 53.0 - - - +
95A LEU* 3.7 6.6 - - - +
96A ASN* 2.8 36.3 + - - +
176A ARG* 3.7 16.3 + - - -
179A LEU* 3.8 19.3 - - - +
180A SER* 4.8 3.5 + - - -
183A LEU* 4.2 7.9 - - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 2.9 17.7 + - - +
90A THR* 3.6 7.8 - - - +
92A SER* 1.3 76.9 - - - +
94A ALA* 1.3 61.4 + - - +
96A ASN* 3.4 6.3 + - - +
97A ILE* 3.2 25.3 + - + +
126A SER 5.5 0.7 - - - +
127A THR* 4.0 27.4 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR 3.2 7.6 + - - +
91A LEU* 3.1 10.8 + - + +
93A THR* 1.3 77.1 - - - +
95A LEU* 1.3 60.9 + - + +
97A ILE* 3.1 4.2 + - - +
98A LEU* 2.8 36.9 + - + +
127A THR* 3.5 30.9 + - - +
128A VAL* 4.0 5.5 - - + +
131A VAL* 3.6 24.5 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 5.2 1.1 - - + -
75A LEU* 4.9 10.8 - - + -
91A LEU* 2.8 28.0 + - + +
92A SER 3.7 4.3 - - - +
94A ALA* 1.3 75.6 - - - +
96A ASN* 1.3 58.1 + - - +
98A LEU* 4.2 14.1 - - + -
99A GLU* 2.9 27.4 + - - +
172A VAL* 3.2 30.0 - - + +
175A LEU* 3.9 22.2 - - + -
176A ARG* 3.6 43.5 - - + +
179A LEU* 3.8 22.9 - - + -
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A SER 2.8 19.1 + - - +
93A THR* 3.5 8.7 - - - +
94A ALA 3.2 0.2 - - - -
95A LEU* 1.3 79.4 - - - +
97A ILE* 1.3 70.6 + - - +
99A GLU* 3.3 8.3 + - - +
100A LYS* 3.3 29.1 + - - +
176A ARG* 3.6 31.6 + - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.2 15.0 + - + +
94A ALA 3.1 7.0 + - - +
96A ASN* 1.3 84.8 - - - +
98A LEU* 1.3 63.2 + - - +
100A LYS* 3.1 25.5 + - + +
101A TYR* 3.1 43.7 + - + -
123A VAL* 4.2 21.5 - - + -
127A THR* 3.5 35.2 - - + +
128A VAL* 3.8 3.8 - - + -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 5.6 2.2 - - + -
94A ALA* 2.8 28.1 + - + +
95A LEU* 3.2 18.1 + - + +
97A ILE* 1.3 76.4 - - - +
99A GLU* 1.3 57.8 + - - +
101A TYR* 3.2 5.0 + - + +
102A GLY 3.1 10.2 + - - -
128A VAL* 3.9 19.1 - - + -
131A VAL* 5.9 0.9 - - + -
134A GLY* 3.9 21.8 - - - +
137A VAL* 3.9 42.4 - - + -
138A LEU* 4.0 19.1 - - + -
141A TYR* 2.6 28.2 + - + +
172A VAL* 4.1 8.1 - - + -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU 2.9 12.6 + - - +
96A ASN* 3.4 12.9 - - - +
97A ILE 3.2 0.2 - - - -
98A LEU* 1.3 73.0 - - - +
100A LYS* 1.3 61.5 + - + +
102A GLY* 3.2 1.4 + - - -
103A ARG* 2.7 73.5 + - - +
141A TYR* 4.0 5.8 - - - -
169A THR* 3.9 15.8 - - + +
172A VAL* 3.8 6.4 - - + +
173A LEU* 4.0 18.5 - - + +
176A ARG* 2.7 39.7 + - - -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN* 3.3 20.1 + - - +
97A ILE* 3.1 27.9 + - + +
99A GLU* 1.3 76.2 - - + +
101A TYR* 1.3 64.7 + - + +
103A ARG* 4.5 9.4 - - - +
104A ASN* 2.9 41.2 + - - +
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.1 46.0 + - + +
98A LEU* 3.2 12.7 + - + +
100A LYS* 1.3 76.3 - - - +
102A GLY* 1.3 61.2 + - - +
104A ASN* 3.8 10.7 - - + +
105A LEU* 3.4 27.1 + - - +
117A VAL* 3.8 41.2 - - + +
121A ASN* 4.1 9.7 + - - -
123A VAL* 5.3 1.9 - - - +
124A PHE* 3.9 20.5 + + + +
128A VAL* 4.3 9.0 - - + -
138A LEU* 4.0 19.1 - - + -
141A TYR* 4.1 12.6 - - + -
143A TYR* 4.8 9.8 + - + -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 3.1 11.1 + - - -
99A GLU 3.2 2.4 + - - -
101A TYR* 1.3 73.9 - - - +
103A ARG* 1.3 64.7 + - - +
105A LEU* 3.1 11.4 + - - +
106A LEU* 3.4 3.7 + - - +
141A TYR* 3.5 21.0 - - - -
165A VAL* 3.4 18.1 - - - +
169A THR* 3.3 22.7 - - - -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.4 22.0 - - + +
44A SER* 2.6 52.3 + - - +
45A GLY* 3.4 11.0 - - - -
46A GLN 2.9 29.0 + - - -
47A ALA* 4.7 3.2 - - - +
48A PHE* 4.7 1.6 - - - +
99A GLU* 2.7 54.1 + - - +
100A LYS* 4.0 7.9 - - - +
102A GLY* 1.3 72.7 - - - +
104A ASN* 1.3 66.6 + - - +
106A LEU* 3.0 18.4 + - - -
107A SER* 3.1 10.2 + - - -
169A THR* 4.0 11.4 - - + +
173A LEU* 4.1 14.6 - - - +
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 2.9 36.2 + - - +
101A TYR* 3.8 11.5 - - + +
103A ARG* 1.3 78.2 - - - +
105A LEU* 1.3 62.5 + - + +
107A SER* 3.3 21.4 + - - -
110A ARG* 3.5 11.6 - - - +
111A PRO* 3.6 31.8 - - + +
114A TRP* 6.3 0.2 - - + -
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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
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101A TYR 3.4 16.4 - - - +
102A GLY 3.1 7.8 + - - +
104A ASN* 1.3 77.3 - - + +
106A LEU* 1.3 62.0 + - - +
107A SER 3.4 0.2 - - - -
110A ARG* 3.6 22.2 + - - +
114A TRP* 3.6 38.4 - - + +
141A TYR* 3.7 38.6 - - + +
143A TYR* 3.7 24.5 - - + +
153A PHE* 4.2 4.9 - - + -
160A PRO* 3.8 21.8 - - + +
165A VAL* 4.0 14.4 - - + -
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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
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40A LEU* 4.1 28.3 - - + +
41A ARG* 4.6 11.6 - - + +
44A SER* 3.7 16.2 + - - -
102A GLY 3.7 14.4 - - - +
103A ARG* 3.0 14.7 + - - +
105A LEU* 1.3 78.3 - - - +
107A SER* 1.3 64.0 + - - +
108A PRO* 3.6 2.6 - - - +
160A PRO* 6.4 0.2 - - + -
162A GLU* 3.8 41.3 - - + +
165A VAL* 3.8 13.0 - - + -
166A ALA* 4.1 20.9 - - + -
169A THR* 4.5 5.6 - - - +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 3.4 11.0 - - - -
103A ARG 3.1 7.2 + - - -
104A ASN* 3.3 20.5 + - - -
105A LEU 4.6 0.3 - - - +
106A LEU* 1.3 80.1 - - - +
108A PRO* 1.4 75.6 - - - +
109A GLN* 2.8 26.3 + - - +
110A ARG* 3.8 18.7 + - - +
111A PRO* 5.2 0.9 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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