Contacts of the helix formed by residues 92 - 121 (chain A) in PDB entry 1YV5
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 ASP 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG 5.1 3.0 + - - +
90A LYS 3.2 4.6 + - - +
91A GLN* 1.3 78.4 - - - +
93A ALA* 1.3 66.6 + - - +
94A ASP* 4.0 12.0 + - - +
95A SER* 2.9 25.7 + - - -
96A LEU* 3.0 21.9 + - - +
98A ARG* 4.6 2.5 + - - -
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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
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92A ASP* 1.3 76.2 - - - +
94A ASP* 1.3 64.9 - - - +
96A LEU* 3.4 8.5 + - - +
97A GLN* 3.0 26.0 + - - +
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Residues in contact with ASP 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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92A ASP* 3.3 11.4 + - - +
93A ALA* 1.3 81.4 - - - +
95A SER* 1.3 62.1 + - - +
97A GLN* 3.4 19.8 + - - +
98A ARG* 3.1 47.1 + - - +
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Residues in contact with SER 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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82A PHE* 3.7 24.4 - - - -
90A LYS 3.1 20.6 + - - -
91A GLN* 3.5 4.9 - - - -
92A ASP* 2.9 28.7 + - - -
94A ASP* 1.3 77.0 - - - +
96A LEU* 1.3 59.8 + - - +
98A ARG* 3.4 27.3 + - - +
99A ALA 3.1 20.4 + - - -
166A TYR* 6.0 0.2 - - - -
230A MET* 4.6 0.3 - - - +
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Residues in contact with LEU 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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79A VAL* 5.9 2.9 - - + -
82A PHE* 4.3 16.4 - - + -
83A ARG* 4.0 42.0 - - + +
91A GLN* 4.2 16.6 - - + +
92A ASP 3.0 12.0 + - - +
93A ALA* 3.4 11.2 - - - +
95A SER* 1.3 77.4 + - - +
97A GLN* 1.3 64.0 + - - +
99A ALA* 3.1 8.0 + - + +
100A TRP* 2.9 55.2 + - + +
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Residues in contact with GLN 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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34A HIS* 3.8 22.3 - - + -
37A GLN* 4.8 7.7 - - - +
93A ALA 3.0 14.2 + - - +
94A ASP* 3.5 24.6 - - - +
96A LEU* 1.3 76.5 - - - +
98A ARG* 1.3 62.4 + - - +
100A TRP* 3.3 13.1 + - - +
101A THR* 3.0 26.7 + - - -
160A TYR* 3.7 33.4 + - + -
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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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92A ASP* 4.6 2.0 + - - -
94A ASP* 3.1 33.6 + - - +
95A SER* 3.4 34.9 - - - +
96A LEU 3.2 0.2 - - - -
97A GLN* 1.3 75.0 - - - +
99A ALA* 1.3 58.8 + - - +
101A THR* 3.7 6.2 - - - -
102A VAL* 2.9 34.0 + - - +
160A TYR* 3.3 39.4 + - + +
161A CYS* 4.2 4.9 - - - -
164A GLN* 3.1 35.1 + - - +
166A TYR* 3.3 20.6 + - - +
230A MET* 3.8 13.0 - - + -
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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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78A VAL* 3.8 6.7 - - + +
79A VAL* 3.7 19.4 - - + +
82A PHE* 3.6 43.7 - - + -
95A SER 3.1 8.9 + - - +
96A LEU* 3.1 10.0 + - + +
98A ARG* 1.3 77.3 - - - +
100A TRP* 1.3 60.4 + - - +
102A VAL 3.4 0.5 + - - -
103A GLY 3.0 18.2 + - - -
230A MET* 3.8 10.9 - - - +
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Residues in contact with TRP 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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27A GLU* 4.3 7.6 - - + -
30A ASP* 3.8 27.4 - - + -
31A PHE* 3.4 50.2 - + + -
34A HIS* 3.7 30.7 - + + -
76A LEU* 4.7 2.2 - - + -
79A VAL* 3.6 33.4 - - + -
83A ARG* 5.5 6.5 - - - -
96A LEU* 2.9 56.0 + - + +
97A GLN* 3.6 10.8 - - - +
99A ALA* 1.3 75.8 - - - +
101A THR* 1.3 58.7 + - - +
103A GLY 3.5 0.7 + - - -
104A TRP* 3.0 34.7 + - - -
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Residues in contact with THR 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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34A HIS* 3.5 14.2 + - - -
38A ILE* 4.3 11.1 - - + +
97A GLN 3.0 17.3 + - - -
98A ARG* 3.7 4.9 - - - -
100A TRP* 1.3 73.4 - - - +
102A VAL* 1.3 62.9 + - + +
104A TRP* 3.1 4.0 + - - +
105A CYS* 2.8 27.7 + - - -
156A LEU* 3.9 28.7 - - + +
157A LEU* 5.8 0.4 - - - -
160A TYR* 3.7 43.7 - - + -
161A CYS* 6.0 0.7 - - - -
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Residues in contact with VAL 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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78A VAL* 3.9 15.7 - - + -
98A ARG 2.9 21.3 + - - +
99A ALA 4.0 3.1 - - - +
101A THR* 1.3 76.8 - - + +
103A GLY* 1.3 63.0 + - - +
105A CYS* 3.2 8.5 + - - +
106A VAL* 3.1 21.7 + - - +
157A LEU* 3.9 15.0 - - + -
161A CYS* 4.2 9.4 - - - -
170A LEU* 3.9 23.3 - - + -
174A PHE* 4.4 14.1 - - + -
226A ALA* 4.0 20.4 - - + -
230A MET* 4.0 13.9 - - - -
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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
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31A PHE* 3.6 8.1 - - - -
75A GLY* 3.2 34.4 - - - -
78A VAL* 3.8 12.9 - - - +
99A ALA 3.0 13.3 + - - -
100A TRP 3.5 3.6 + - - -
101A THR 3.2 0.2 - - - -
102A VAL* 1.3 77.0 - - - +
104A TRP* 1.3 60.1 + - - +
106A VAL* 3.2 2.6 + - - +
107A GLU* 3.2 16.3 + - - +
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Residues in contact with TRP 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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31A PHE* 3.0 44.0 + + - -
32A VAL* 4.2 8.5 - - - -
34A HIS* 4.2 5.8 - + + -
35A PHE* 3.5 51.3 - + + +
38A ILE* 3.1 39.3 - - + -
67A ALA* 3.5 23.6 - - + -
68A ILE* 4.1 4.5 - - + -
72A TYR* 3.7 23.8 - + - -
100A TRP 3.0 21.9 + - - -
101A THR 3.5 3.8 - - - +
103A GLY* 1.3 73.6 - - - +
105A CYS* 1.3 54.0 + - - +
107A GLU* 3.0 25.1 + - + +
108A LEU* 2.8 43.4 + - + +
156A LEU* 5.1 2.0 - - + -
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Residues in contact with CYS 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 THR* 2.8 22.2 + - - -
102A VAL* 3.2 15.0 + - - +
104A TRP* 1.3 71.8 - - - +
106A VAL* 1.3 57.7 + - - +
108A LEU* 3.4 6.7 + - - -
109A LEU 3.1 22.2 + - - -
153A ILE* 3.6 35.8 - - + +
156A LEU* 3.8 21.3 - - - +
157A LEU* 4.2 11.4 - - - -
174A PHE* 3.6 26.2 - - + -
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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
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74A ARG* 3.7 34.5 - - + +
78A VAL* 3.8 19.3 - - + -
102A VAL* 3.1 18.8 + - + +
103A GLY 3.2 8.5 + - - +
105A CYS* 1.3 75.9 - - - +
107A GLU* 1.3 57.3 + - - +
109A LEU* 3.4 5.2 + - - +
110A GLN* 3.2 24.8 + - - +
174A PHE* 3.8 19.7 - - + -
218A TYR* 4.4 9.6 - - + +
222A LEU* 4.2 23.6 - - + -
223A PRO* 4.4 6.7 - - + -
226A ALA* 5.4 0.9 - - + -
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Residues in contact with GLU 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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31A PHE* 4.1 12.3 - - + -
67A ALA* 4.5 9.8 - - + +
70A GLY* 5.8 0.3 - - - -
72A TYR* 3.6 33.1 + - - -
73A ASN 4.2 0.2 + - - -
74A ARG* 3.6 13.7 + - - +
75A GLY* 3.1 26.4 + - - -
103A GLY 3.2 13.1 + - - +
104A TRP* 3.0 26.8 + - + +
106A VAL* 1.3 77.4 - - - +
108A LEU* 1.3 59.5 + - - +
110A GLN* 3.4 10.2 + - - +
111A ALA* 2.9 28.5 + - - +
127A ARG* 4.7 7.6 + - - -
1001A PO4 4.5 11.8 + - - -
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Residues in contact with LEU 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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35A PHE* 5.5 2.5 - - + -
38A ILE* 5.3 4.5 - - + -
42A LEU* 4.5 4.7 - - + -
63A LEU* 3.7 24.9 - - + -
67A ALA* 4.1 19.3 - - + -
104A TRP* 2.8 25.3 + - + +
105A CYS* 3.7 5.6 - - - +
106A VAL 3.4 0.2 - - - -
107A GLU* 1.3 71.8 - - - +
109A LEU* 1.3 58.1 + - - +
111A ALA* 3.6 3.6 - - + +
112A PHE* 2.9 28.4 + - - +
149A LEU* 3.9 17.2 - - + +
152A CYS* 3.7 27.4 - - + -
153A ILE* 3.9 16.2 - - + +
156A LEU* 3.8 26.0 - - + -
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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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105A CYS 3.1 10.3 + - - +
106A VAL* 3.6 10.1 - - - +
107A GLU 3.2 0.2 - - - -
108A LEU* 1.3 73.6 - - - +
110A GLN* 1.3 66.4 + - - +
112A PHE* 3.4 13.3 + - + +
113A PHE* 3.1 51.8 + - + -
150A GLU* 4.8 2.7 - - + -
153A ILE* 3.5 25.9 - - + +
154A TYR* 5.3 1.1 - - - +
174A PHE* 4.3 8.1 - - + +
177A SER* 3.7 13.0 - - - +
178A SER* 3.4 23.8 - - - +
218A TYR* 4.4 10.8 - - + -
222A LEU* 3.6 29.6 - - + -
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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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74A ARG* 2.9 35.3 - - - +
106A VAL 3.2 13.7 + - - +
107A GLU* 3.7 10.8 - - - +
108A LEU 3.3 0.2 - - - -
109A LEU* 1.3 79.8 - - - +
111A ALA* 1.3 56.9 + - - +
113A PHE* 3.3 3.3 + - - +
114A LEU* 3.0 50.8 + - + +
127A ARG* 3.9 14.4 - - - +
218A TYR* 2.5 43.2 + - + -
1001A PO4 3.5 8.7 + - - +
1002A PO4 2.7 28.5 + - - -
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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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66A ASN 3.5 28.3 - - - +
67A ALA* 4.3 7.4 - - + -
107A GLU 2.9 18.4 + - - +
108A LEU* 3.3 9.8 + - - +
110A GLN* 1.3 78.6 - - - +
112A PHE* 1.3 59.1 + - - +
114A LEU* 4.1 6.0 - - - +
115A VAL* 3.1 31.7 + - - +
127A ARG* 5.2 1.8 - - - +
149A LEU* 3.8 15.9 - - + -
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Residues in contact with PHE 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 LEU 2.9 16.7 + - - +
109A LEU* 3.5 14.1 - - + +
111A ALA* 1.3 76.0 - - - +
113A PHE* 1.3 105.0 + + - +
114A LEU 3.3 0.5 + - - -
115A VAL* 3.6 3.3 + - - +
116A ALA* 3.5 18.5 + - - +
146A ALA* 3.0 35.0 - - + +
147A ASN* 3.9 17.0 - - - -
149A LEU* 4.0 5.1 - - + +
150A GLU* 3.5 49.1 - - + +
178A SER* 4.9 0.7 - - - -
182A GLU* 4.0 12.1 - - - -
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Residues in contact with PHE 113 (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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109A LEU* 3.1 55.1 + - + +
110A GLN* 3.8 6.1 - - - +
112A PHE* 1.3 96.7 - + - +
114A LEU* 1.3 58.8 + - + +
116A ALA* 3.5 5.0 + - + +
117A ASP* 2.8 31.1 + - - +
178A SER* 3.7 18.8 - - - -
181A THR* 3.5 44.6 - - + -
182A GLU* 3.6 22.4 - - + -
185A GLN* 4.7 11.0 + - + -
218A TYR* 5.0 9.4 - + - +
901A RIS 4.3 13.4 - + + -
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Residues in contact with LEU 114 (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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110A GLN* 3.0 42.9 + - - +
111A ALA* 4.1 4.5 - - - +
112A PHE 3.3 0.2 - - - -
113A PHE* 1.3 75.3 - - + +
115A VAL* 1.3 63.4 + - + +
117A ASP* 3.6 2.1 - - - +
118A ASP* 2.8 36.6 + - - -
126A ARG* 3.7 48.2 - - + +
127A ARG* 3.6 28.7 - - - +
218A TYR* 4.5 0.4 - - - +
901A RIS 3.8 28.7 - - + -
1001A PO4 5.1 0.2 - - - +
1002A PO4 3.9 5.2 - - - +
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Residues in contact with VAL 115 (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 VAL* 6.1 0.2 - - + -
66A ASN* 3.5 34.1 - - + +
111A ALA 3.1 18.5 + - - +
112A PHE 3.8 4.9 - - - +
114A LEU* 1.3 80.4 - - + +
116A ALA* 1.3 60.7 + - - +
118A ASP* 3.3 13.2 + - - +
119A ILE* 3.5 14.8 + - + +
132A TRP* 4.4 11.4 - - + -
133A TYR* 5.0 2.2 - - + +
142A ALA* 3.8 35.0 - - + +
145A ASP 5.4 0.4 - - - -
146A ALA* 3.8 11.9 - - + +
149A LEU* 4.3 6.1 - - + -
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Residues in contact with ALA 116 (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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112A PHE* 3.5 18.2 + - + +
113A PHE* 4.0 5.6 - - + +
114A LEU 3.1 0.4 - - - -
115A VAL* 1.3 76.6 - - - +
117A ASP* 1.3 67.6 + - - +
119A ILE* 3.2 14.6 + - + +
120A MET* 3.1 39.3 + - + +
143A ILE* 6.5 0.4 - - - -
146A ALA* 4.7 9.9 - - + -
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE 2.8 20.4 + - - +
114A LEU* 3.7 5.4 - - - +
116A ALA* 1.3 77.7 - - - +
118A ASP* 1.3 60.7 + - - +
120A MET* 3.3 9.7 + - - +
121A ASP* 3.0 30.0 + - - +
126A ARG* 4.1 2.6 + - - -
185A GLN* 2.7 24.5 + - - +
901A RIS 2.9 24.0 + - + +
907A MG 2.1 28.3 - - - -
909A MG 2.1 23.7 - - - -
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU 2.8 22.4 + - - +
115A VAL* 3.8 6.8 - - - +
116A ALA 3.2 0.6 - - - -
117A ASP* 1.3 76.0 - - - +
119A ILE* 1.3 60.3 + - - +
122A SER 3.3 0.5 + - - -
123A SER* 3.0 42.9 + - - -
125A THR 5.1 0.5 - - - +
126A ARG* 2.8 46.1 + - - +
131A CYS* 3.2 35.0 - - + +
132A TRP 5.4 0.3 + - - -
133A TYR* 3.0 13.8 + - + -
901A RIS 4.4 0.2 + - - -
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Residues in contact with ILE 119 (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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115A VAL 3.5 13.9 - - - +
116A ALA* 3.2 13.6 + - - +
118A ASP* 1.3 77.9 - - - +
120A MET* 1.3 67.2 + - + +
122A SER* 3.3 15.8 + - - -
133A TYR* 3.7 32.2 + - + -
140A LEU* 4.0 23.1 - - + -
142A ALA* 3.9 27.6 - - + +
143A ILE* 4.1 24.0 - - + +
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Residues in contact with MET 120 (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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116A ALA* 3.1 32.6 + - + +
117A ASP* 4.0 4.0 - - - +
119A ILE* 1.3 81.1 - - + +
121A ASP* 1.3 64.6 + - - +
122A SER* 3.4 2.8 + - - -
185A GLN* 4.1 25.4 - - + +
189A LEU* 4.0 41.3 - - + +
278A ASP* 5.6 0.5 - - - -
280A LYS* 4.9 1.4 + - - -
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 3.0 16.5 + - - +
120A MET* 1.3 79.0 - - - +
122A SER* 1.3 71.7 + - - +
123A SER* 3.3 10.7 + - - +
188A ASP* 4.4 0.5 - - - +
189A LEU* 4.4 3.3 - - - +
274A THR* 3.6 7.1 + - - +
275A ASP* 5.7 1.2 - - - +
278A ASP* 2.5 30.7 - - - +
280A LYS* 2.7 37.6 + - - +
901A RIS 3.1 0.9 + - - -
907A MG 2.2 20.5 - - - -
909A MG 2.1 30.8 - - - -
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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
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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