Contacts of the helix formed by residues 80 - 104 (chain A) in PDB entry 1ALU
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.9 16.9 - - + -
79A ASN* 1.3 72.2 + - - +
81A GLU* 1.3 59.8 + - - +
83A CYS* 3.3 1.4 + - - +
84A LEU* 2.9 37.0 + - + +
129A LYS* 4.6 8.3 + - - -
184A MET* 3.8 52.8 - - + +
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Residues in contact with GLU 81 (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* 3.3 8.4 + - - +
80A GLU* 1.3 79.8 - - + +
82A THR* 1.3 66.7 + - + +
84A LEU* 3.6 0.4 + - - -
85A VAL* 3.2 28.0 + - - +
133A LEU* 3.6 27.4 - - + +
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Residues in contact with THR 82 (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 LYS 4.6 4.3 + - - +
71A ASP* 2.9 25.3 + - - +
72A GLY* 3.8 0.5 - - - -
79A ASN* 3.1 35.7 + - - +
81A GLU* 1.3 74.0 - - + +
83A CYS* 1.3 61.8 + - - +
85A VAL* 3.4 7.7 + - - +
86A LYS* 2.9 28.9 + - - +
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Residues in contact with CYS 83 (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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71A ASP 3.4 3.6 - - - -
72A GLY 3.4 11.4 - - - +
73A CYS* 2.0 51.4 - - - -
78A PHE* 4.9 0.7 - - + -
79A ASN 3.0 19.8 + - - +
80A GLU* 3.7 3.8 - - - +
82A THR* 1.3 78.4 + - - +
84A LEU* 1.3 55.3 + - - +
86A LYS* 3.0 4.2 + - - +
87A ILE* 2.8 36.8 + - - +
180A ALA* 3.5 19.1 - - - -
184A MET* 3.5 13.2 - - + -
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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
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80A GLU* 2.9 24.4 + - + +
81A GLU* 4.0 3.8 - - - +
83A CYS* 1.3 75.3 - - - +
85A VAL* 1.3 61.7 + - - +
87A ILE* 3.3 8.0 + - + +
88A ILE* 3.1 38.2 + - + +
126A LEU* 3.9 28.9 - - + +
129A LYS* 4.1 22.0 - - + +
130A ALA* 3.7 38.1 - - + +
133A LEU* 4.3 7.4 - - + -
181A LEU* 4.4 13.7 - - + -
184A MET* 4.6 7.0 - - + -
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Residues in contact with VAL 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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81A GLU 3.2 15.9 + - - +
82A THR* 3.6 10.3 - - - +
83A CYS 3.2 0.2 - - - -
84A LEU* 1.3 71.7 - - - +
86A LYS* 1.3 61.9 + - - +
88A ILE* 3.4 5.9 + - - +
89A THR* 2.8 44.2 + - - +
130A ALA* 6.0 0.2 - - + -
133A LEU* 3.6 24.9 - - + -
134A ASP* 5.9 1.6 - - + +
136A ILE* 4.7 17.7 - - + +
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Residues in contact with LYS 86 (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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65A PRO* 5.3 2.7 - - - +
66A LYS 3.2 29.6 + - - +
67A MET* 3.8 13.9 - - + -
71A ASP* 3.5 43.8 + - + +
73A CYS* 4.6 0.7 - - - -
82A THR 2.9 14.8 + - - +
83A CYS* 3.0 8.9 + - - +
85A VAL* 1.3 79.2 - - - +
87A ILE* 1.3 59.2 + - - +
89A THR* 4.3 8.7 - - + -
90A GLY* 2.8 34.5 + - - +
93A GLU* 5.5 3.8 + - - -
173A PHE* 3.7 16.3 - - - -
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Residues in contact with ILE 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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29A ILE* 6.2 0.7 - - + -
67A MET* 3.7 11.9 - - + -
83A CYS* 2.8 36.1 + - - +
84A LEU* 3.7 11.2 - - + +
85A VAL 3.3 0.2 - - - -
86A LYS* 1.3 76.9 - - - +
88A ILE* 1.3 62.0 + - - +
90A GLY 3.4 0.2 + - - -
91A LEU* 2.9 37.1 + - + +
126A LEU* 3.9 25.6 - - + -
173A PHE* 3.6 8.3 - - - -
177A SER* 3.6 37.9 - - - +
180A ALA* 4.7 0.2 - - + -
181A LEU* 4.0 31.4 - - + -
184A MET* 4.5 1.1 - - + -
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Residues in contact with ILE 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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84A LEU* 3.1 22.1 + - + +
85A VAL* 3.9 3.1 - - - +
87A ILE* 1.3 75.5 - - - +
89A THR* 1.3 56.8 + - - +
91A LEU* 3.2 7.6 + - - +
92A LEU* 2.8 45.9 + - + +
123A ILE* 4.5 8.5 - - + -
126A LEU* 3.8 47.1 - - + +
127A GLN* 4.2 16.4 - - + +
130A ALA* 4.0 19.1 - - + -
136A ILE* 3.9 27.6 - - + -
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Residues in contact with THR 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 VAL* 2.8 31.2 + - - +
86A LYS* 3.7 11.2 - - + -
88A ILE* 1.3 76.9 - - - +
90A GLY* 1.4 57.3 + - - +
92A LEU* 3.2 5.1 + - - +
93A GLU* 2.9 54.2 + - + +
136A ILE* 3.1 23.9 - - - +
137A THR* 4.7 13.2 - - + +
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Residues in contact with GLY 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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65A PRO* 3.7 7.8 - - - +
86A LYS* 2.8 22.7 + - - +
87A ILE 3.8 0.2 - - - -
89A THR* 1.4 70.3 - - - +
91A LEU* 1.3 64.7 + - - +
93A GLU* 3.1 16.3 + - - +
94A PHE* 2.9 27.8 + - - -
173A PHE* 3.7 19.7 - - - -
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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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87A ILE* 2.9 27.7 + - + +
88A ILE* 3.7 1.8 - - - +
90A GLY* 1.3 76.2 - - - +
92A LEU* 1.4 65.4 + - - +
94A PHE* 3.1 15.6 + - - +
95A GLU* 3.4 14.6 + - - +
119A THR* 4.5 6.7 - - + +
122A LEU* 3.6 21.5 - - + -
123A ILE* 3.6 24.8 - - + +
126A LEU* 3.6 31.0 - - + -
170A PHE* 3.8 19.7 - - + -
173A PHE* 4.1 12.3 - - + -
174A LEU* 3.8 26.0 - - + -
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Residues in contact with LEU 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 ILE* 2.8 28.0 + - + +
89A THR* 3.2 5.6 + - - +
91A LEU* 1.4 78.4 - - - +
93A GLU* 1.3 60.6 + - - +
95A GLU* 3.3 36.7 + - - +
96A VAL 4.8 0.7 + - - -
123A ILE* 4.0 22.7 - - + -
127A GLN* 4.8 5.6 - - - +
136A ILE* 3.8 27.4 - - + -
137A THR 4.1 2.9 - - - +
138A THR* 3.9 27.4 - - + -
139A PRO* 3.5 25.0 - - + +
144A ASN* 5.4 0.7 + - - -
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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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65A PRO* 3.8 21.4 - - + +
86A LYS* 5.5 4.2 + - - -
89A THR* 2.9 36.4 + - + +
90A GLY* 3.1 15.6 + - - +
92A LEU* 1.3 77.2 - - - +
94A PHE* 1.4 59.6 + - - +
95A GLU 3.4 0.5 + - - -
96A VAL* 4.0 8.9 - - - +
97A TYR* 3.6 18.8 - - + -
137A THR 6.2 0.4 - - - +
139A PRO* 4.0 18.6 - - + -
144A ASN* 5.9 0.6 + - - -
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Residues in contact with PHE 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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64A LEU* 4.5 7.0 - - + -
65A PRO* 3.6 34.8 - - + -
90A GLY 2.9 24.7 + - - -
91A LEU* 3.1 9.6 + - - +
93A GLU* 1.4 76.9 - - - +
95A GLU* 1.4 66.9 + - - +
96A VAL 3.3 0.7 - - - -
97A TYR* 2.9 28.5 + + + +
98A LEU* 3.0 18.0 + - + +
166A ILE* 4.4 7.0 - - + -
169A SER* 3.4 28.3 - - - -
170A PHE* 3.6 56.8 - + + -
173A PHE* 3.7 24.2 - + + -
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Residues in contact with GLU 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 LEU 3.4 15.9 - - - +
92A LEU* 3.6 30.9 - - - +
93A GLU 3.2 2.2 - - - -
94A PHE* 1.4 77.1 - - - +
96A VAL* 1.3 56.9 + - - +
98A LEU* 3.0 11.1 + - + +
99A GLU* 2.9 27.8 + - - +
116A GLN* 4.7 2.9 - - - +
119A THR* 4.8 8.7 - - + -
120A LYS* 2.5 46.9 + - - +
123A ILE* 4.0 14.4 - - + +
144A ASN* 5.9 1.6 - - - +
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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
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92A LEU 4.8 0.2 + - - -
93A GLU 4.0 6.2 + - - +
95A GLU* 1.3 77.9 - - - +
97A TYR* 1.3 76.0 + - + +
99A GLU* 3.2 10.5 + - - +
100A TYR 2.9 22.5 + - - -
144A ASN* 3.5 63.0 - - + +
147A LEU* 3.9 25.6 - - + -
148A LEU* 3.7 21.2 - - + +
151A LEU* 6.2 0.7 - - + -
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Residues in contact with TYR 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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62A LEU* 4.9 10.3 - - + -
63A ASN* 4.0 22.3 + - - +
64A LEU* 3.5 31.4 - - + -
65A PRO* 4.6 7.2 - - + -
93A GLU 3.6 21.5 - - - -
94A PHE* 2.9 18.6 + + + +
96A VAL* 1.3 83.6 - - + +
98A LEU* 1.4 59.4 + - - +
100A TYR* 3.3 7.5 + - - +
101A LEU* 3.0 29.7 + - - +
147A LEU* 3.6 29.7 - - + +
151A LEU* 4.2 16.2 - - + -
166A ILE* 3.8 34.9 - - + +
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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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94A PHE* 3.0 17.5 + - + +
95A GLU* 3.7 11.7 - - + +
97A TYR* 1.4 75.3 - - + +
99A GLU* 1.4 65.0 + - - +
101A LEU* 3.3 26.7 + - + +
102A GLN* 3.1 22.3 + - - +
112A ALA 4.8 2.1 - - - +
115A VAL* 4.1 6.3 - - + +
116A GLN* 4.0 28.5 - - + +
119A THR* 3.6 40.2 - - + +
166A ILE* 4.8 5.8 - - + -
170A PHE* 3.8 33.2 - - + -
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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 GLU 2.9 12.3 + - - +
96A VAL* 3.4 15.7 - - - +
98A LEU* 1.4 73.2 - - - +
100A TYR* 1.3 65.2 + - - +
102A GLN* 3.1 3.6 + - + +
103A ASN* 3.1 34.0 + - - +
116A GLN* 3.4 20.0 + - - +
144A ASN* 6.0 1.2 - - - +
148A LEU* 3.4 28.8 - - + +
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Residues in contact with TYR 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 VAL 2.9 10.3 + - - +
97A TYR* 3.3 11.9 + - - +
99A GLU* 1.3 74.2 - - - +
101A LEU* 1.3 62.3 + - + +
103A ASN* 3.2 3.6 + - - +
104A ARG* 2.9 38.5 + - + +
148A LEU* 3.5 17.1 - - + +
151A LEU* 3.9 37.2 - - + -
152A GLN* 4.1 17.5 - - + +
159A GLN* 2.8 57.2 + - - +
162A THR* 3.7 16.6 - - + -
163A THR* 3.6 18.8 - - - -
166A ILE* 3.6 19.7 - - + -
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Residues in contact with LEU 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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39A LEU* 4.5 11.2 - - + -
97A TYR 3.0 16.2 + - - +
98A LEU* 3.5 31.4 - - + +
99A GLU 3.3 0.2 - - - -
100A TYR* 1.3 87.8 - - + +
102A GLN* 1.3 58.4 + - - +
104A ARG* 4.3 2.9 - - + -
105A PHE* 2.9 44.8 + - + -
112A ALA* 3.7 8.6 - - + +
115A VAL* 5.4 3.6 - - + -
163A THR* 4.0 33.2 - - + +
166A ILE* 4.2 15.5 - - + -
167A LEU* 3.9 23.3 - - + -
170A PHE* 6.1 0.2 - - + -
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Residues in contact with GLN 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 10.0 + - - +
99A GLU* 3.1 8.5 + - + +
101A LEU* 1.3 75.6 - - - +
103A ASN* 1.3 82.1 + - - +
104A ARG 3.5 0.3 + - - -
105A PHE 3.6 5.2 - - - +
109A GLU* 3.5 42.7 + - - +
112A ALA* 3.6 10.1 - - + +
113A ARG* 3.7 35.6 - - + +
116A GLN* 3.2 32.1 - - - +
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Residues in contact with ASN 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 GLU* 3.1 29.9 + - - +
100A TYR 3.8 1.3 - - - +
102A GLN* 1.3 94.9 + - - +
104A ARG* 1.3 60.0 + - - +
105A PHE 4.8 1.3 - - - +
106A GLU* 5.0 8.0 - - - +
109A GLU* 5.7 0.8 - - - +
148A LEU* 4.1 4.5 - - - +
152A GLN* 2.9 36.1 + - - +
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Residues in contact with ARG 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 TYR* 2.9 30.0 + - + +
101A LEU* 3.1 4.5 + - - +
103A ASN* 1.3 80.1 - - - +
105A PHE* 1.3 68.7 + - + +
106A GLU* 3.4 10.7 + - - +
156A GLN* 2.7 50.1 + - - +
159A GLN* 3.5 36.1 + - - +
160A ASP* 3.0 29.1 + - - -
163A THR* 3.8 22.6 + - + +
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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