Contacts of the helix formed by residues 87 - 113 (chain A) in PDB entry 1WD5
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 4.4 1.8 - - - -
86A ALA* 1.3 76.1 - - - +
88A GLN* 1.3 63.7 - - - +
89A SER* 2.3 40.6 + - - -
90A TYR* 3.3 23.0 + - - +
91A LEU* 3.3 14.4 + - - +
93A ARG* 4.9 2.6 + - - -
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Residues in contact with GLN 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 LEU* 4.6 2.4 - - - +
78A LEU* 4.3 17.4 - - - +
83A LEU* 3.7 26.9 - - + +
87A ASP* 1.3 73.4 + - - +
89A SER* 1.3 63.2 + - - +
91A LEU* 3.2 16.0 + - - +
92A GLU* 2.7 54.5 + - + +
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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
----------------------------------------------------------
87A ASP* 2.3 28.4 + - - -
88A GLN* 1.3 75.5 - - - +
90A TYR* 1.3 62.5 + - - +
92A GLU* 3.2 9.0 + - - +
93A ARG* 3.0 44.6 + - - +
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 2.8 28.7 + - - -
59A ALA* 3.3 11.8 + - - -
60A PRO* 3.6 34.7 - - + +
61A GLY 5.0 0.3 + - - -
67A LEU* 4.7 0.2 - - + -
86A ALA* 3.7 19.3 - - + -
87A ASP* 3.2 21.6 + - - +
88A GLN 3.2 0.4 - - - -
89A SER* 1.3 80.9 + - - +
91A LEU* 1.3 70.7 + - + +
93A ARG* 2.9 30.3 + - - +
94A GLU* 2.8 49.9 + - + -
97A ARG* 4.1 16.0 + - - -
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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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57A VAL* 4.6 10.7 - - + +
67A LEU* 4.0 36.1 - - + -
76A LEU* 4.4 3.4 - - + +
78A LEU* 3.9 36.1 - - + -
82A ALA* 4.2 9.4 - - + -
83A LEU* 3.8 29.2 - - + -
86A ALA* 4.3 3.8 - - + +
87A ASP 3.3 10.1 + - - +
88A GLN* 3.2 16.1 + - - +
90A TYR* 1.3 89.2 - - + +
92A GLU* 1.3 58.1 + - - +
94A GLU* 4.0 2.3 - - - +
95A ALA* 2.9 31.0 + - - +
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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
----------------------------------------------------------
76A LEU* 3.8 16.5 - - - +
88A GLN* 2.7 48.2 + - + +
89A SER* 3.6 10.8 - - - +
91A LEU* 1.3 75.8 - - - +
93A ARG* 1.3 64.2 + - + +
95A ALA* 3.6 4.2 + - - +
96A ALA* 3.1 22.5 + - - +
99A ARG* 4.7 11.4 + - - -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 4.9 2.0 + - - -
89A SER* 3.0 42.8 + - - +
90A TYR* 2.9 38.2 + - + +
92A GLU* 1.3 75.0 - - + +
94A GLU* 1.3 66.0 + - - +
96A ALA* 3.2 8.7 + - - +
97A ARG* 3.2 41.8 + - - +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.3 28.9 - - + -
58A GLY* 3.0 25.5 + - - +
63A PRO* 5.9 1.6 - - - +
90A TYR* 2.8 37.1 + - + +
91A LEU 4.0 3.1 - - - +
93A ARG* 1.3 72.7 - - - +
95A ALA* 1.3 63.8 + - - +
97A ARG* 2.7 46.1 + - - +
98A GLN* 3.1 47.8 + - + +
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Residues in contact with ALA 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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57A VAL* 4.4 5.4 - - - +
70A VAL* 3.9 22.9 - - + +
76A LEU* 4.0 18.4 - - + -
91A LEU 2.9 19.1 + - - +
92A GLU* 3.7 6.7 - - - +
93A ARG 3.3 0.2 - - - -
94A GLU* 1.3 77.9 - - - +
96A ALA* 1.3 56.3 + - - +
98A GLN* 3.2 3.3 + - - +
99A ARG* 2.9 48.8 + - - +
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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
----------------------------------------------------------
92A GLU 3.1 11.9 + - - +
93A ARG* 3.5 10.8 - - - +
94A GLU 3.2 0.2 - - - -
95A ALA* 1.3 79.4 - - - +
97A ARG* 1.3 61.6 + - + +
99A ARG* 3.3 18.7 + - - +
100A ASP* 3.1 28.5 + - - +
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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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90A TYR* 4.1 16.2 + - - -
93A ARG* 3.2 29.9 + - - +
94A GLU* 2.7 46.7 + - - +
96A ALA* 1.3 77.1 - - + +
98A GLN* 1.3 67.8 + - - +
100A ASP* 3.4 20.4 + - - +
101A VAL* 3.4 17.8 + - - +
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Residues in contact with GLN 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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55A ARG* 2.8 66.6 + - + +
56A LYS 3.3 24.2 + - - +
57A VAL* 4.5 2.7 - - + -
70A VAL* 3.9 9.4 - - + -
94A GLU* 3.1 42.4 + - + +
95A ALA* 3.2 7.2 + - - +
97A ARG* 1.3 78.1 - - - +
99A ARG* 1.3 65.3 + - - +
101A VAL* 3.2 13.1 + - - +
102A LEU* 3.3 9.5 + - - +
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Residues in contact with ARG 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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70A VAL* 4.5 14.5 - - + +
71A GLY 5.7 0.9 - - - +
74A GLY* 2.9 41.0 + - - -
76A LEU* 4.1 20.4 - - - +
92A GLU* 4.7 10.7 + - - -
95A ALA* 2.9 30.4 + - - +
96A ALA* 3.3 32.6 + - - +
98A GLN* 1.3 77.2 - - - +
100A ASP* 1.3 58.8 + - - +
102A LEU* 3.2 7.8 + - - +
103A ARG* 2.9 42.0 + - - +
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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
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96A ALA* 3.1 17.3 + - - +
97A ARG* 3.5 14.4 - - - +
98A GLN 3.2 0.6 - - - -
99A ARG* 1.3 79.5 - - - +
101A VAL* 1.3 63.9 + - + +
102A LEU 3.3 0.3 + - - -
103A ARG* 2.4 49.1 + - - +
104A LYS* 4.7 4.7 + - - +
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Residues in contact with VAL 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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55A ARG* 3.7 32.5 - - - +
97A ARG 3.4 15.5 - - - +
98A GLN* 3.2 17.6 + - - +
100A ASP* 1.3 76.5 - - + +
102A LEU* 1.3 58.7 + - - +
104A LYS 5.3 0.2 + - - -
105A ARG* 4.3 18.1 + - - +
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Residues in contact with LEU 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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53A LEU* 3.8 28.3 - - + +
54A VAL* 3.8 31.2 - - - +
55A ARG* 3.9 9.6 - - + -
70A VAL* 4.3 8.1 - - + +
71A GLY 3.8 7.9 - - - +
72A GLU* 3.7 33.9 - - - +
98A GLN 3.3 11.4 + - - +
99A ARG* 3.2 6.2 + - - +
100A ASP 3.2 0.4 - - - -
101A VAL* 1.3 82.4 - - - +
103A ARG* 1.3 63.5 + - - +
104A LYS 3.6 1.1 - - - -
105A ARG* 3.5 8.8 + - + +
106A ALA* 3.1 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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99A ARG* 2.9 28.0 + - - +
100A ASP* 2.4 44.7 + - - +
102A LEU* 1.3 77.2 - - - +
104A LYS* 1.3 69.6 + - + +
106A ALA* 3.3 4.7 + - - +
107A GLU* 3.0 47.6 + - + +
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Residues in contact with LYS 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 ASP 4.7 4.6 + - - +
101A VAL 5.3 0.4 + - - -
102A LEU 3.6 0.6 - - - -
103A ARG* 1.3 84.0 - - + +
105A ARG* 1.3 64.2 + - - +
107A GLU* 3.2 15.8 + - - +
108A ARG* 3.2 37.9 + - - +
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Residues in contact with ARG 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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31A PRO* 4.9 9.6 - - - -
32A ARG* 4.1 15.2 - - - +
53A LEU* 4.7 7.2 - - + -
101A VAL* 4.3 15.5 + - - +
102A LEU* 3.5 11.6 + - + +
103A ARG 3.3 0.6 - - - -
104A LYS* 1.3 77.0 - - - +
106A ALA* 1.3 63.9 + - - +
108A ARG* 3.1 32.5 - - - +
109A TYR* 3.1 55.2 + - + -
196A ASP* 2.8 35.3 + - - +
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Residues in contact with ALA 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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53A LEU* 3.9 27.3 - - + +
72A GLU* 4.4 19.3 - - + +
102A LEU* 3.1 23.8 + - + +
103A ARG* 3.7 4.9 - - - +
104A LYS 3.3 0.2 - - - -
105A ARG* 1.3 78.3 - - - +
107A GLU* 1.3 56.5 - - + +
109A TYR* 3.5 0.5 + - - +
110A ARG* 2.9 37.5 + - + +
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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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103A ARG* 3.0 37.4 + - + +
104A LYS* 3.2 14.4 + - - +
106A ALA* 1.3 77.2 - - + +
108A ARG* 1.3 62.0 + - - +
110A ARG* 3.5 4.9 + - - +
111A ARG* 3.1 42.5 + - - +
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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
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104A LYS* 3.2 18.1 + - - +
105A ARG* 3.1 69.5 - - - +
107A GLU* 1.3 76.2 - - - +
109A TYR* 1.3 74.7 + - + +
111A ARG* 3.4 27.5 + - - +
112A VAL* 3.7 12.5 + - - +
196A ASP* 3.6 16.7 + - - -
200A GLU* 4.0 22.9 - - - +
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Residues in contact with TYR 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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31A PRO* 4.4 10.3 - - + -
32A ARG* 3.8 10.0 - - - +
51A VAL* 4.1 13.5 - - + -
53A LEU* 3.8 30.7 - - + -
105A ARG* 3.1 39.0 + - + +
106A ALA 4.0 3.1 - - - +
108A ARG* 1.3 82.5 - - + +
110A ARG* 1.3 59.5 + - + +
112A VAL* 3.0 10.8 - - - +
113A ARG* 3.0 25.7 + - - +
196A ASP* 2.6 43.6 + - + -
199A VAL* 3.6 30.2 - - + +
200A GLU* 4.1 12.1 - - + -
203A LEU* 3.7 19.6 - - + +
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Residues in contact with ARG 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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50A ASP* 2.9 27.9 + - - -
51A VAL* 3.2 29.9 + - - +
53A LEU* 3.9 7.8 - - + +
72A GLU* 2.7 44.0 + - - +
106A ALA* 2.9 23.9 + - + +
107A GLU* 4.0 4.5 - - - +
109A TYR* 1.3 74.6 + - - +
111A ARG* 1.3 63.5 + - - +
112A VAL 3.2 0.6 + - - -
113A ARG* 3.1 34.0 + - - +
114A PRO* 3.6 8.3 - - + +
115A LYS* 3.5 29.5 - - - +
118A ARG* 4.0 2.0 - - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 3.1 35.9 + - - +
108A ARG* 3.5 21.8 - - - +
109A TYR 3.1 0.6 - - - -
110A ARG* 1.3 79.3 - - - +
112A VAL* 1.3 64.5 + - + +
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Residues in contact with VAL 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 ARG 3.9 9.4 - - - +
109A TYR* 3.0 20.4 - - - +
111A ARG* 1.3 87.7 - - + +
113A ARG* 1.3 58.2 + - - +
114A PRO* 4.6 1.3 - - - -
200A GLU* 4.1 27.1 - - + +
203A LEU* 3.9 22.7 - - + -
204A LEU* 3.4 38.9 - - + +
207A ALA* 3.2 20.4 - - - +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.1 33.7 + - - +
49A LEU 2.8 30.6 + - - -
50A ASP* 3.6 17.6 + - - +
109A TYR 3.0 11.6 + - - +
110A ARG* 3.1 21.6 + - - +
111A ARG 3.6 0.8 - - - -
112A VAL* 1.3 81.4 - - - +
114A PRO* 1.3 101.8 + - + +
116A ALA* 3.7 19.5 - - - +
203A LEU* 3.4 43.3 - - + +
206A TRP* 3.8 24.5 + - - +
207A ALA* 4.3 3.3 - - + +
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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