Contacts of the helix formed by residues 97 - 123 (chain A) in PDB entry 5XVO
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 THR 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 3.9 9.6 - - - +
96A TRP* 1.3 73.4 - - - +
98A GLU* 1.3 67.4 + - - +
99A GLU* 3.8 6.5 + - - +
100A ARG* 3.0 28.5 + - - +
101A LYS* 3.0 22.7 + - - +
276A LEU 5.4 0.2 + - - -
278A GLN* 3.5 19.6 + - - +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP 3.9 1.2 + - - -
97A THR* 1.3 74.1 - - - +
99A GLU* 1.3 61.7 + - - +
101A LYS* 3.6 20.7 + - + +
102A GLY 3.1 16.5 + - - -
142A PHE* 3.6 29.8 - - + -
202A LEU 4.9 2.6 - - - +
203A LYS 5.3 3.8 - - - +
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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
----------------------------------------------------------
97A THR* 3.2 6.6 + - - +
98A GLU* 1.3 78.8 - - - +
100A ARG* 1.3 64.4 + - - +
102A GLY* 3.0 3.6 + - - -
103A GLN* 2.9 47.3 + - + +
141A LEU* 4.1 13.0 - - + +
142A PHE* 5.7 0.2 - - - -
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 3.0 25.0 + - - +
99A GLU* 1.3 76.7 - - - +
101A LYS* 1.3 63.9 + - - +
103A GLN* 3.3 22.9 + - - +
104A VAL* 3.0 31.9 + - - +
275A VAL* 3.1 37.4 + - - +
276A LEU* 3.7 28.9 - - + +
278A GLN* 3.4 32.6 + - - +
280A GLU 3.5 9.5 + - - -
281A GLU* 3.1 34.2 + - - +
282A GLY 5.2 0.2 - - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 4.0 33.9 + - + +
97A THR 3.0 23.9 + - - +
98A GLU* 3.8 21.7 + - - +
100A ARG* 1.3 76.3 - - - +
102A GLY* 1.3 53.9 + - - +
104A VAL* 3.4 0.9 + - - +
105A TRP* 2.7 37.8 + - - +
142A PHE* 3.9 2.9 - - + -
200A LEU* 6.4 0.2 - - - +
201A GLY 4.0 9.2 + - - -
202A LEU* 3.3 51.7 + - + +
205A ALA* 5.0 7.7 - - - +
276A LEU* 4.0 10.3 - - + -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU 3.1 7.7 + - - -
99A GLU 3.0 6.9 + - - -
101A LYS* 1.3 74.3 - - - +
103A GLN* 1.3 64.0 + - - +
106A THR* 2.6 33.4 + - - -
141A LEU* 4.0 10.1 - - - -
142A PHE* 3.2 33.1 - - - -
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 2.9 45.3 + - - +
100A ARG* 3.6 33.2 + - - +
102A GLY* 1.3 75.1 - - - +
104A VAL* 1.3 58.6 + - + +
106A THR* 3.9 2.5 - - - -
107A ALA* 2.9 31.9 + - - +
141A LEU* 4.0 17.2 - - + +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.0 22.3 + - - +
101A LYS 3.9 2.5 - - - +
103A GLN* 1.3 79.7 - - + +
105A TRP* 1.3 65.0 + - - +
107A ALA* 3.3 2.1 + - - +
108A ILE* 3.0 42.4 + - + +
202A LEU* 4.0 9.9 - - + -
272A VAL* 3.9 18.8 - - + -
275A VAL* 3.6 30.1 - - + -
276A LEU* 3.9 19.5 - - + -
283A VAL* 4.0 14.8 - - + -
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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
----------------------------------------------------------
101A LYS 2.7 23.0 + - - +
102A GLY 4.0 1.8 - - - +
104A VAL* 1.3 74.0 - - - +
106A THR* 1.3 69.6 + - + +
108A ILE* 3.2 9.1 + - + +
109A ILE* 2.9 45.6 + - + +
142A PHE* 3.6 33.0 - + + -
143A ASP* 3.7 20.6 - - + -
148A GLU* 4.0 22.2 - - - -
202A LEU* 4.0 23.7 - - + +
203A LYS* 3.6 39.1 - - + +
216A ASP* 3.5 38.2 + - + +
219A GLU* 5.9 4.2 - - + +
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 2.6 22.7 + - - -
103A GLN* 3.9 3.8 - - - -
105A TRP* 1.3 84.3 - - + +
107A ALA* 1.3 65.7 + - - +
109A ILE* 3.1 12.3 - - + +
110A ALA* 3.0 23.9 + - - +
139A LEU* 4.5 17.3 - - + -
140A ARG 3.9 22.4 - - - +
141A LEU* 3.6 7.4 - - + -
142A PHE 3.1 21.7 + - - +
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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
----------------------------------------------------------
103A GLN 2.9 19.1 + - - +
104A VAL 3.5 6.1 - - - +
106A THR* 1.3 75.4 - - - +
108A ILE* 1.3 62.8 + - - +
110A ALA* 3.3 8.6 - - - +
111A GLN* 3.2 27.2 + - - +
283A VAL* 4.2 24.5 - - + -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 3.0 36.8 + - + +
105A TRP* 3.4 9.9 - - + +
107A ALA* 1.3 74.9 - - - +
109A ILE* 1.3 66.9 + - - +
111A GLN* 2.9 20.6 + - - +
112A LYS* 3.1 8.7 + - - +
202A LEU* 4.7 6.1 - - + -
216A ASP* 3.5 22.4 - - + +
217A LEU* 4.1 26.2 - - + +
219A GLU* 4.1 4.9 - - + -
220A PRO* 3.7 22.6 - - + +
268A TYR* 3.9 13.7 - - - +
272A VAL* 4.3 7.9 - - + -
283A VAL* 4.5 9.9 - - + -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TRP* 2.9 31.7 + - + +
106A THR* 3.1 24.2 - - - +
108A ILE* 1.3 79.0 - - - +
110A ALA* 1.3 65.8 + - - +
112A LYS* 3.0 25.2 + - + +
113A ILE* 2.9 28.2 + - + +
139A LEU* 4.0 20.6 - - + -
143A ASP* 5.5 0.2 - - + -
148A GLU* 3.4 48.5 - - + +
219A GLU* 3.9 9.6 - - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 3.0 13.9 + - - +
107A ALA* 3.3 13.5 - - - +
109A ILE* 1.3 77.2 - - - +
111A GLN* 1.3 57.3 + - + +
113A ILE* 3.2 2.9 + - - -
114A THR* 2.8 33.1 + - - +
136A ARG* 3.6 21.0 - - + +
139A LEU* 3.9 21.1 - - + -
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Residues in contact with GLN 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* 3.2 13.5 + - - +
108A ILE* 2.9 9.4 + - - +
110A ALA* 1.3 76.6 - - + +
112A LYS* 1.3 61.6 + - - +
114A THR* 2.5 22.6 + - - +
115A ASN* 3.0 19.1 + - - -
220A PRO* 4.0 9.7 - - + +
268A TYR* 3.3 17.9 + - - -
283A VAL* 3.3 18.2 - - - +
284A PRO 2.8 22.6 + - - -
285A GLU* 3.5 21.3 - - + +
286A PHE 3.1 27.9 + - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE 3.1 6.1 + - - +
109A ILE* 3.0 22.9 + - + +
111A GLN* 1.3 74.9 - - - +
113A ILE* 1.3 53.6 + - - +
115A ASN* 3.0 5.8 + - - +
116A GLN* 2.7 70.3 + - + +
148A GLU* 3.4 25.6 + - - +
152A ALA* 4.7 8.9 - - - +
219A GLU* 3.0 53.9 + - + +
220A PRO* 3.9 10.0 - - - +
222A ARG* 4.3 14.2 - - + +
223A PRO* 4.3 4.4 - - + +
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 2.9 25.5 + - + +
110A ALA 3.7 6.3 - - - +
112A LYS* 1.3 77.4 - - + +
114A THR* 1.3 63.7 + - - +
116A GLN* 3.1 18.8 + - - +
117A SER* 2.9 21.8 + - - -
132A LEU* 3.6 34.9 - - + +
133A LEU* 5.4 0.2 - - - -
135A MET 5.2 0.2 - - - -
136A ARG* 4.0 14.1 - - + +
139A LEU* 4.2 24.7 - - + -
147A ARG* 4.5 2.2 - - + +
148A GLU* 4.1 25.1 - - - +
151A ALA* 4.3 15.9 - - + -
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Residues in contact with THR 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 ALA 2.8 11.2 + - - +
111A GLN* 2.5 31.1 + - - -
113A ILE* 1.3 73.0 - - - +
115A ASN* 1.3 62.2 + - - +
117A SER* 2.4 25.8 + - - -
118A LEU* 2.8 22.4 + - - +
133A LEU* 4.7 6.5 - - + -
136A ARG* 3.2 46.0 - - - +
286A PHE 5.4 0.3 + - - -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN 3.0 20.1 + - - +
112A LYS 3.0 4.0 + - - +
114A THR* 1.3 77.3 + - - +
116A GLN* 1.3 67.1 + - - +
118A LEU* 3.9 8.3 - - - +
119A HIS* 3.0 19.4 + - - +
220A PRO* 3.0 23.6 + - - +
223A PRO* 3.7 17.8 - - + +
286A PHE* 3.0 25.7 + - - +
287A GLY* 3.2 20.4 - - - -
288A ILE* 3.3 30.0 + - + +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 2.7 52.1 + - + +
113A ILE* 3.4 21.3 - - - +
115A ASN* 1.3 76.9 - - - +
117A SER* 1.3 62.2 + - - +
119A HIS 3.3 1.6 + - - -
120A LEU* 3.0 18.0 + - - +
132A LEU* 3.7 5.8 - - + -
148A GLU 4.8 0.2 - - - +
151A ALA* 4.3 13.3 - - - +
152A ALA* 4.2 13.0 + - - +
155A TYR* 3.2 62.8 - - + -
156A PHE* 4.9 4.0 - - - -
222A ARG* 6.3 1.4 - - - +
223A PRO* 3.9 9.1 - - + +
226A ASP* 4.9 2.4 + - - -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE 2.9 11.9 + - - -
114A THR* 2.4 27.5 + - - -
116A GLN* 1.3 75.6 - - - +
118A LEU* 1.3 57.7 + - - +
120A LEU* 2.8 26.6 + - - +
121A ALA* 2.8 13.1 + - - -
129A ALA* 3.4 19.1 - - - +
132A LEU* 3.8 14.1 - - - +
133A LEU* 2.9 37.1 - - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 2.8 25.4 + - - +
115A ASN* 3.8 23.8 - - - +
116A GLN 3.4 0.2 - - - -
117A SER* 1.3 73.4 + - - +
119A HIS* 1.3 58.2 + - - +
121A ALA* 3.4 11.1 + - + +
122A GLN* 2.9 28.2 + - - +
287A GLY* 5.1 2.9 - - - -
288A ILE* 4.1 25.6 - - + +
68N GLN* 5.7 0.5 - - - -
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN 3.0 18.3 + - - +
116A GLN 3.4 5.2 - - - +
117A SER 3.1 0.2 - - - -
118A LEU* 1.3 73.9 - - - +
120A LEU* 1.3 66.0 + - - +
122A GLN* 3.2 19.6 - - - +
123A ARG* 3.2 44.0 + - + +
155A TYR* 2.8 29.0 + - - +
159A LEU* 3.7 21.0 - - + +
223A PRO* 4.7 2.2 + - + -
226A ASP* 3.8 5.9 - - - +
227A GLN* 3.5 37.4 - - + -
230A TYR* 4.2 4.5 - - + +
288A ILE* 3.9 10.9 - - + +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN 3.0 11.9 + - - +
117A SER* 2.8 9.1 + - - +
119A HIS* 1.3 73.9 - - - +
121A ALA* 1.3 64.6 + - - +
123A ARG* 2.9 14.6 + - - +
124A ASP 3.4 0.2 + - - -
125A TYR* 3.1 36.7 + - + +
128A LYS* 4.1 15.3 - - + +
129A ALA* 4.1 8.7 - - + +
132A LEU* 3.7 39.0 - - + -
155A TYR* 3.8 12.3 - - + +
158A THR* 3.5 25.6 - - - +
159A LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 2.8 15.0 + - - +
118A LEU* 3.5 17.5 - - + +
120A LEU* 1.3 69.9 - - - +
122A GLN* 1.3 58.8 + - - +
124A ASP* 2.8 23.0 + - - -
125A TYR 4.5 6.3 - - - +
126A GLY* 4.8 4.8 + - - +
129A ALA* 3.9 15.3 - - + +
68N GLN* 3.3 23.7 - - + +
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU 2.9 14.6 + - - +
119A HIS* 3.2 15.1 - - - +
121A ALA* 1.3 75.8 - - - +
123A ARG* 1.3 96.4 + - - +
124A ASP* 3.3 5.8 + - - +
227A GLN* 3.0 28.7 + - - +
231A GLU* 4.5 2.6 - - - +
288A ILE* 5.1 6.7 + - - +
89M HIS* 4.5 7.5 + - + -
68N GLN* 3.7 30.6 + - - +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 3.2 38.8 + - - +
120A LEU 2.9 8.5 + - - +
122A GLN* 1.3 101.9 + - - +
124A ASP* 1.3 69.9 + - - +
125A TYR* 3.3 28.8 + - + -
159A LEU* 4.2 10.1 - - + -
227A GLN* 3.5 11.5 + - - +
230A TYR* 3.7 33.0 - - + +
231A GLU* 3.1 40.4 + - - +
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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