Contacts of the helix formed by residues 87 - 112 (chain A) in PDB entry 1RXV
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 LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ASP* 5.3 3.6 + - - -
83A PRO* 3.8 19.3 - - + +
84A PRO* 3.0 16.1 + - + +
85A GLU 2.9 0.8 + - - -
86A PHE* 1.3 76.7 - - - +
88A LYS* 1.3 65.9 + - - +
89A ALA 3.2 3.4 - - - -
90A GLU* 2.9 33.1 + - - +
91A ILE* 3.0 21.9 + - + +
151A GLU* 2.7 38.9 + - - +
235A ASP* 3.6 29.6 + - - +
236A TYR* 3.5 23.3 + - + +
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Residues in contact with LYS 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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83A PRO* 6.0 3.1 - - + -
84A PRO 4.0 1.5 + - - +
85A GLU* 2.9 60.7 + - - +
87A LYS* 1.3 77.4 - - - +
89A ALA* 1.3 63.4 + - - +
91A ILE* 3.1 13.4 + - + +
92A GLU* 2.9 27.6 + - + +
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Residues in contact with ALA 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 GLU 4.9 0.2 + - - -
86A PHE 4.7 6.6 + - - +
87A LYS 3.0 1.6 + - - -
88A LYS* 1.3 78.0 - - - +
90A GLU* 1.3 57.1 + - - +
92A GLU* 3.2 6.7 + - - +
93A GLU* 2.9 29.7 + - - +
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Residues in contact with GLU 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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86A PHE 5.4 0.2 + - - -
87A LYS* 2.9 26.3 + - - +
89A ALA* 1.3 78.7 - - - +
91A ILE* 1.3 68.6 + - - +
93A GLU* 3.9 6.9 - - + +
94A ARG* 2.5 67.6 + - + +
234A THR 4.9 1.8 - - - +
235A ASP* 3.2 46.3 - - - +
236A TYR* 5.1 3.1 - - - -
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Residues in contact with ILE 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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83A PRO* 3.7 35.2 - - + -
87A LYS* 3.0 28.8 + - + +
88A LYS* 3.1 12.5 + - + +
90A GLU* 1.3 90.1 - - - +
92A GLU* 1.3 63.2 + - + +
94A ARG* 3.4 6.6 + - - +
95A LYS* 3.2 28.7 + - + +
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Residues in contact with GLU 92 (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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88A LYS* 2.9 17.7 + - + +
89A ALA* 3.6 6.5 - - - +
91A ILE* 1.3 77.5 - - + +
93A GLU* 1.3 66.2 + - - +
94A ARG 3.1 0.2 - - - -
95A LYS* 3.1 37.0 + - - +
96A LYS* 3.1 14.8 + - - +
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Residues in contact with GLU 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 ALA 2.9 17.0 + - - +
90A GLU* 3.9 7.7 - - - +
91A ILE 3.4 0.2 - - - -
92A GLU* 1.3 76.2 - - - +
94A ARG* 1.3 64.3 + - - +
96A LYS* 3.4 21.7 + - - +
97A ARG* 3.0 69.2 + - - +
238A GLU* 6.1 1.1 - - - +
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Residues in contact with ARG 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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29A PHE* 4.9 16.8 - - - -
90A GLU* 2.5 38.9 + - + +
91A ILE* 3.7 7.2 - - - +
92A GLU 3.1 0.6 - - - -
93A GLU* 1.3 83.5 - - - +
95A LYS* 1.3 64.8 + - - +
97A ARG* 3.9 5.3 - - + +
98A ARG* 3.0 26.3 + - - +
235A ASP* 3.2 23.3 + - - -
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Residues in contact with LYS 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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91A ILE* 3.2 20.4 + - + +
92A GLU* 3.1 27.1 + - - +
94A ARG* 1.3 75.7 - - - +
96A LYS* 1.3 58.4 + - - +
98A ARG* 3.3 44.7 + - - +
99A ALA* 2.9 25.7 + - - +
125A ARG* 5.6 14.2 - - - +
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Residues in contact with LYS 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 GLU* 3.1 12.6 + - - +
93A GLU* 3.5 27.9 + - - +
95A LYS* 1.3 75.5 - - - +
97A ARG* 1.3 94.6 + - - +
99A ALA* 3.2 6.1 + - - +
100A GLU* 3.0 53.1 + - + +
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Residues in contact with ARG 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 GLU* 3.0 46.5 + - - +
94A ARG* 3.9 6.1 - - + +
96A LYS* 1.3 98.9 - - - +
98A ARG* 1.3 57.5 + - - +
100A GLU* 3.2 14.3 + - - +
101A ALA* 2.9 29.6 + - - +
122A ALA 5.0 1.8 - - - +
17B GLU* 4.9 14.5 + - - -
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Residues in contact with ARG 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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94A ARG 3.0 18.3 + - - +
95A LYS* 3.4 47.9 + - - +
97A ARG* 1.3 78.7 - - - +
99A ALA* 1.3 73.2 + - - +
101A ALA* 3.3 2.6 + - - +
102A GLU* 2.9 27.6 + - + +
122A ALA 3.9 13.2 - - - +
123A ALA* 3.3 32.6 - - - +
124A GLY 4.5 4.3 - - - +
125A ARG* 3.6 43.1 - - - +
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Residues in contact with ALA 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 LYS 2.9 18.0 + - - +
96A LYS* 3.2 6.0 + - - +
98A ARG* 1.3 88.6 - - - +
100A GLU* 1.3 63.9 + - + +
102A GLU* 3.7 8.1 - - - +
103A GLU* 3.2 23.4 + - - +
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Residues in contact with GLU 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 LYS* 3.0 51.5 + - + +
97A ARG* 3.2 12.9 + - - +
99A ALA* 1.3 75.8 - - + +
101A ALA* 1.3 59.3 + - - +
103A GLU* 3.5 9.9 + - - +
104A MET* 2.9 38.0 + - - +
15B GLU* 3.8 34.3 - - + +
17B GLU* 3.7 19.0 - - - +
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Residues in contact with ALA 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 ARG 2.9 16.8 + - - +
98A ARG 3.4 5.6 - - - +
100A GLU* 1.3 76.0 - - - +
102A GLU* 1.3 60.1 + - - +
104A MET* 3.1 7.0 + - - -
105A TRP* 2.8 31.5 + - - +
119A TYR* 3.4 29.3 - - + +
122A ALA* 3.7 15.0 - - + -
123A ALA 3.7 12.8 - - - +
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Residues in contact with GLU 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 ARG* 2.9 17.0 + - + +
99A ALA* 3.7 10.3 - - - +
101A ALA* 1.3 74.7 - - - +
103A GLU* 1.3 64.2 + - - +
105A TRP* 3.2 23.5 + - - +
106A ILE* 3.1 50.3 + - + +
123A ALA* 3.6 18.0 - - + +
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Residues in contact with GLU 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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99A ALA 3.2 13.8 + - - +
100A GLU* 3.6 9.2 - - - +
102A GLU* 1.3 81.8 - - - +
104A MET* 1.3 60.0 + - - +
106A ILE* 3.3 11.6 + - - +
107A ALA* 3.2 20.4 + - - +
12B GLU* 5.4 0.5 - - - +
13B GLU* 3.0 39.9 - - + +
14B VAL* 3.6 11.9 - - - -
15B GLU* 3.1 26.8 + - - +
205B LYS* 3.0 23.0 + - - -
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Residues in contact with MET 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 GLU* 2.9 23.4 + - - +
101A ALA* 3.1 4.0 + - - +
103A GLU* 1.3 74.2 - - - +
105A TRP* 1.3 59.9 + - - +
107A ALA* 3.8 6.4 - - - +
108A ALA* 2.9 29.3 + - - +
119A TYR* 3.0 49.2 - - + +
14B VAL* 4.1 15.7 - - + -
15B GLU* 4.2 13.5 - - - +
17B GLU* 4.1 24.2 - - + +
18B TYR* 3.1 48.7 - - + +
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Residues in contact with TRP 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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40A ARG* 5.2 1.8 - - - -
43A ASP 3.0 19.6 + - - -
44A GLY 3.8 2.9 - - - -
45A THR* 3.7 38.8 - - + -
46A PRO* 4.3 11.4 - - + -
48A LYS* 6.5 0.2 - - - -
101A ALA 2.8 16.6 + - - +
102A GLU* 3.2 29.1 + - - +
104A MET* 1.3 73.9 - - - +
106A ILE* 1.3 64.3 + - + +
108A ALA* 3.3 1.7 + - - +
109A LEU* 2.9 55.5 + - + +
116A ALA* 3.0 29.2 - - + -
119A TYR* 3.6 14.1 - - + +
120A ALA* 3.5 21.5 - - + +
123A ALA* 5.6 1.1 - - + -
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Residues in contact with ILE 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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102A GLU* 3.1 39.3 + - + +
103A GLU* 3.5 11.9 - - - +
105A TRP* 1.3 83.5 - - + +
107A ALA* 1.3 64.2 + - - +
109A LEU* 3.6 10.9 + - + +
110A GLN* 3.3 21.8 + - + +
12B GLU* 4.3 17.0 - - + -
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Residues in contact with ALA 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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103A GLU 3.2 8.2 + - - +
104A MET 3.8 4.9 - - - +
105A TRP 3.3 0.2 - - - -
106A ILE* 1.3 77.6 - - - +
108A ALA* 1.3 63.2 - - - +
110A GLN* 2.9 15.2 + - - +
111A ALA* 2.9 13.5 + - - +
12B GLU* 3.8 18.8 - - + -
14B VAL* 3.3 33.9 - - + -
18B TYR* 4.5 3.6 - - + -
208B ILE* 3.5 20.8 - - + +
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Residues in contact with ALA 108 (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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104A MET 2.9 19.4 + - - +
105A TRP 3.6 3.1 - - - +
107A ALA* 1.3 75.8 - - - +
109A LEU* 1.3 62.6 + - - +
111A ALA 3.0 1.4 + - - -
112A GLY 2.9 4.5 + - - -
113A ASP* 2.9 44.4 + - + +
116A ALA* 3.3 30.5 - - + -
119A TYR* 4.0 10.1 - - + -
18B TYR* 4.0 7.3 + - + -
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Residues in contact with LEU 109 (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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43A ASP* 3.8 30.5 - - + +
45A THR* 5.4 2.5 - - - +
105A TRP* 2.9 61.3 + - + +
106A ILE* 3.8 10.8 - - + +
108A ALA* 1.3 75.8 - - - +
110A GLN* 1.3 65.7 + - - +
112A GLY* 3.3 12.2 + - - +
116A ALA* 4.3 5.8 - - + -
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Residues in contact with GLN 110 (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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106A ILE* 3.3 12.8 + - - +
107A ALA 2.9 11.6 + - - +
109A LEU* 1.3 81.9 - - - +
111A ALA* 1.3 57.0 - - - +
112A GLY 3.7 0.3 + - - -
12B GLU* 3.3 35.1 - - - +
210B ILE* 3.7 19.5 - - + +
213B SER* 3.4 37.4 + - - +
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Residues in contact with ALA 111 (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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107A ALA 2.9 14.1 + - - +
108A ALA 3.7 3.6 - - - +
110A GLN* 1.3 78.1 - - - +
112A GLY* 1.3 63.1 + - - +
113A ASP* 4.3 6.0 - - - +
18B TYR* 4.0 8.3 - - - +
166B GLU* 5.1 1.8 - - - +
167B TYR* 3.6 24.2 - - - +
182B ARG* 4.0 27.1 + - - +
208B ILE* 4.2 5.8 - - + -
210B ILE* 4.0 9.4 - - + -
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Residues in contact with GLY 112 (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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108A ALA 2.9 3.9 + - - -
109A LEU* 3.3 10.8 + - - -
110A GLN 3.4 1.2 + - - -
111A ALA* 1.3 78.6 - - - +
113A ASP* 1.3 58.1 + - - +
114A LYS* 3.1 19.9 + - - +
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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