Contacts of the helix formed by residues 86 - 111 (chain A) in PDB entry 4RWN
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 SER 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 1.3 82.5 + - - +
87A PHE* 1.3 59.7 + - - +
88A GLU* 3.4 10.0 + - - +
89A ASP* 2.9 23.9 + - - +
90A GLN 3.0 22.0 + - - -
152A PHE* 3.4 26.9 - - - +
171A GLN* 4.1 8.1 - - - +
175A GLU* 4.0 9.2 - - - -
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Residues in contact with PHE 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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86A SER* 1.3 70.7 - - - +
88A GLU* 1.3 62.2 + - - +
90A GLN* 3.1 3.2 + - - +
91A LEU* 2.9 25.6 + - - +
152A PHE* 3.9 9.0 - + - -
154A ALA* 3.6 32.1 - - + -
168A ILE* 4.0 8.3 - - + -
171A GLN* 3.4 43.7 - - + -
172A LEU* 3.7 34.1 - - + -
175A GLU* 3.8 13.2 + - + +
185A PHE* 3.1 46.3 - + + -
188A CYS* 3.8 15.5 - - - -
189A PHE* 4.0 15.5 - + - -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 3.5 7.6 - - - +
87A PHE* 1.3 77.5 - - - +
89A ASP* 1.3 63.4 + - - +
91A LEU* 3.1 10.2 + - - +
92A ARG* 2.8 54.9 + - - +
175A GLU* 3.2 26.6 + - - +
179A ARG* 3.5 33.6 + - - +
185A PHE* 5.3 0.9 - - - -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS 2.9 15.1 - - - +
84A LEU* 3.2 9.6 - - + +
85A THR* 2.9 29.0 + - - +
86A SER* 2.9 28.1 + - - +
88A GLU* 1.3 78.4 - - - +
90A GLN* 1.3 58.2 + - - +
92A ARG* 4.0 5.1 - - - +
93A ARG* 3.0 56.5 + - - +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.7 11.6 - - + +
86A SER 3.0 12.9 + - - +
87A PHE* 3.1 9.4 + - - +
89A ASP* 1.3 74.8 - - - +
91A LEU* 1.3 65.8 + - - +
94A ARG* 3.1 43.4 + - + +
150A PRO 3.8 17.7 + - - +
151A ALA* 3.6 5.4 - - - +
152A PHE* 2.7 36.0 + - + +
184A GLU 5.2 1.0 + - - -
185A PHE* 4.1 14.4 - - + +
187A THR* 3.1 26.7 + - - -
188A CYS* 3.0 20.8 - - - -
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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
----------------------------------------------------------
87A PHE 2.9 12.2 + - - +
88A GLU* 3.5 9.0 - - - +
90A GLN* 1.3 78.3 - - - +
92A ARG* 1.3 63.0 + - + +
94A ARG* 3.8 31.1 - - - +
127A ASN* 2.7 33.8 + - - +
179A ARG* 4.1 41.3 - - + +
181A LYS* 4.4 20.4 - - + -
184A GLU* 4.0 16.8 - - + +
185A PHE* 3.9 12.5 - - + -
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 2.8 51.8 + - - +
89A ASP* 4.4 4.8 - - - +
91A LEU* 1.3 86.3 - - + +
93A ARG* 1.3 67.8 + - + +
94A ARG 3.6 0.7 - - - -
95A GLY* 4.8 2.9 + - - -
96A GLU* 4.6 5.9 + - - +
127A ASN* 5.0 2.4 + - - +
179A ARG* 4.6 11.3 - - - +
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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
----------------------------------------------------------
83A LYS* 3.6 29.3 + - - +
84A LEU* 4.2 2.0 - - + -
89A ASP* 3.0 38.9 + - - +
90A GLN 4.2 0.2 - - - -
92A ARG* 1.3 83.7 - - + +
94A ARG* 1.3 65.4 + - - +
95A GLY 3.2 2.7 - - - -
96A GLU* 3.1 42.8 + - - +
97A PHE* 3.1 54.6 + - + -
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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
----------------------------------------------------------
84A LEU* 5.4 2.2 - - + -
90A GLN* 3.1 33.9 + - + +
91A LEU* 3.8 20.8 - - - +
93A ARG* 1.3 77.8 - - - +
95A GLY* 1.3 61.0 + - - +
97A PHE* 3.4 4.5 + - - -
98A ILE* 2.9 34.8 + - + +
127A ASN* 3.0 43.0 + - - +
128A PRO 3.1 21.9 + - - +
129A ARG* 3.4 26.4 - - - +
150A PRO* 3.8 28.1 - - + +
184A GLU* 2.7 38.9 + - - +
185A PHE* 5.0 1.2 - - - -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG 4.8 2.5 + - - -
93A ARG* 3.2 1.4 - - - +
94A ARG* 1.3 84.9 - - - +
96A GLU* 1.3 60.5 + - - +
98A ILE* 3.4 10.2 + - - +
99A GLN* 3.0 31.1 + - - +
127A ASN* 4.1 12.3 + - - -
128A PRO* 5.1 4.0 - - - -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG 4.6 5.1 - - - +
93A ARG* 3.1 49.3 + - - +
95A GLY* 1.3 78.1 - - - +
97A PHE* 1.3 62.5 + - + +
99A GLN* 3.3 5.9 + - - +
100A GLU* 3.1 27.6 + - - +
103A ARG* 4.5 2.8 + - - -
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.1 14.3 - + + -
52A VAL* 4.4 23.1 - - + -
81A LEU* 3.5 32.3 - - + -
83A LYS* 4.4 12.8 - - + -
84A LEU* 3.9 21.8 - - + -
93A ARG* 3.1 65.9 + - - -
94A ARG* 4.0 4.7 - - - +
96A GLU* 1.3 81.9 - - + +
98A ILE* 1.3 60.4 + - - +
100A GLU* 3.8 6.1 - - + +
101A ILE* 2.9 39.6 + - + +
150A PRO* 4.3 7.6 - - + -
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Residues in contact with ILE 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* 2.9 27.4 + - + +
95A GLY* 3.6 8.5 - - - +
96A GLU 3.3 0.2 - - - -
97A PHE* 1.3 76.8 - - - +
99A GLN* 1.3 67.5 + - + +
101A ILE* 3.2 10.8 + - + +
102A ARG* 2.9 26.9 + - - +
128A PRO* 3.5 32.1 - - + +
129A ARG 3.9 12.1 - - - +
130A ALA 3.9 19.7 - - - +
131A LEU* 3.9 31.2 - - + +
150A PRO* 3.8 17.7 - - + -
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Residues in contact with GLN 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 GLY 3.0 21.4 + - - +
96A GLU* 3.7 5.8 - - - +
98A ILE* 1.3 82.7 - - + +
100A GLU* 1.3 57.9 + - - +
102A ARG* 3.2 25.8 + - - +
103A ARG* 2.8 49.9 + - - +
131A LEU* 5.7 0.2 - - - +
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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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44A CYS 4.8 1.6 - - - +
45A PHE* 4.7 18.6 - - + -
96A GLU 3.1 16.4 + - - +
97A PHE* 3.8 9.4 - - + +
98A ILE 3.2 0.2 - - - -
99A GLN* 1.3 73.4 - - - +
101A ILE* 1.3 65.4 + - - +
103A ARG* 2.7 46.3 + - - +
104A GLN* 3.0 55.6 + - + +
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Residues in contact with ILE 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 PHE* 4.0 10.4 - - + -
40A LEU* 4.4 9.6 - - + -
44A CYS* 4.0 10.8 - - - -
45A PHE* 3.8 27.1 - - + -
79A VAL* 4.4 13.2 - - + -
81A LEU* 5.8 0.4 - - + -
97A PHE* 2.9 29.0 + - + +
98A ILE* 3.5 7.6 - - + +
100A GLU* 1.3 76.4 - - - +
102A ARG* 1.3 58.0 + - - +
104A GLN* 3.3 2.4 + - - +
105A LEU* 2.9 38.8 + - + +
131A LEU* 3.7 18.6 - - + -
133A PHE* 5.7 0.7 - - + -
148A VAL* 4.4 23.3 - - + -
150A PRO* 5.0 7.0 - - + -
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 2.9 13.6 + - - +
99A GLN* 3.2 28.4 + - - +
101A ILE* 1.3 76.8 - - - +
103A ARG* 1.3 62.9 + - - +
105A LEU* 3.3 5.7 + - - +
106A GLU* 3.0 45.4 + - - +
118A PHE* 3.7 48.0 - - + +
121A GLN* 4.7 11.3 + - - -
131A LEU* 3.8 22.1 - - + +
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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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96A GLU 4.5 2.4 + - - -
99A GLN* 2.8 32.4 + - - +
100A GLU* 2.7 55.7 + - - +
102A ARG* 1.3 74.6 - - - +
104A GLN* 1.3 58.9 + - + +
106A GLU* 3.4 14.4 + - - +
107A ALA* 3.0 25.7 + - - +
110A ARG* 4.5 2.4 + - - -
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Residues in contact with GLN 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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39A PHE* 3.7 20.6 - - + -
43A ARG* 4.4 19.8 + - - +
44A CYS* 3.2 30.9 + - - +
47A GLY* 4.9 13.1 - - - -
100A GLU* 3.0 38.6 + - - +
101A ILE 3.9 1.1 - - - +
103A ARG* 1.3 74.4 - - - +
105A LEU* 1.3 65.1 + - - +
107A ALA* 3.3 12.0 + - - +
108A CYS* 3.0 27.5 + - - -
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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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36A VAL* 6.0 4.5 - - + -
39A PHE* 3.5 30.5 - - + -
101A ILE* 2.9 25.9 + - + +
102A ARG 3.3 4.5 + - - +
104A GLN* 1.3 76.5 - - - +
106A GLU* 1.3 57.0 - - - +
108A CYS* 3.1 5.2 + - - +
109A GLN* 2.9 27.0 + - - +
114A PHE* 3.9 25.8 - - + -
116A VAL* 4.3 11.7 - - + -
118A PHE* 3.9 23.1 - - + -
131A LEU* 4.0 10.1 - - + -
133A PHE* 3.9 34.5 - - + -
135A LEU* 5.8 0.7 - - + -
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Residues in contact with GLU 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 ARG* 3.0 49.2 + - - +
103A ARG* 3.7 14.4 - - - +
105A LEU* 1.3 75.8 - - - +
107A ALA* 1.3 61.7 + - - +
109A GLN* 3.3 19.9 + - - +
110A ARG* 3.2 46.5 + - - +
116A VAL* 4.8 0.2 - - - -
118A PHE* 4.1 18.3 - - + -
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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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43A ARG* 4.6 10.8 - - - +
103A ARG 3.0 14.5 + - - +
104A GLN* 3.3 20.9 - - - +
105A LEU 3.1 0.4 - - - -
106A GLU* 1.3 76.6 - - - +
108A CYS* 1.3 61.2 + - - +
110A ARG* 3.2 30.1 + - - +
111A GLU* 3.4 21.3 + - - +
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Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.8 24.7 - - - -
43A ARG* 4.0 31.0 - - - -
104A GLN 3.0 16.0 + - - -
105A LEU 3.1 4.2 + - - +
107A ALA* 1.3 73.0 - - - +
109A GLN* 1.3 66.3 + - - +
111A GLU* 3.1 19.2 + - - +
113A LYS* 3.2 29.7 + - + +
114A PHE* 3.6 27.4 - - + -
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Residues in contact with GLN 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 LEU 2.9 13.0 + - - +
106A GLU* 3.4 21.6 + - - +
107A ALA 3.2 0.2 - - - -
108A CYS* 1.3 77.1 - - - +
110A ARG* 1.3 58.0 + - + +
112A GLN* 3.0 26.7 + - - +
114A PHE* 3.3 24.9 - - + +
115A LYS* 3.3 15.5 - - + +
116A VAL* 3.0 46.9 + - + +
118A PHE* 5.6 0.2 - - - -
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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
----------------------------------------------------------
103A ARG 4.5 2.4 + - - -
106A GLU* 3.2 32.0 + - - +
107A ALA* 3.2 38.0 + - - +
109A GLN* 1.3 77.3 - - + +
111A GLU* 1.3 58.4 + - + +
112A GLN* 3.1 22.8 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 2.7 35.1 + - - -
107A ALA* 3.4 17.9 - - - +
108A CYS* 3.1 8.0 + - - +
109A GLN 3.1 1.4 - - - -
110A ARG* 1.3 76.4 - - + +
112A GLN* 1.3 71.1 + - - +
113A LYS* 2.4 48.4 + - + +
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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