Contacts of the helix formed by residues 134 - 157 (chain I) in PDB entry 5XRZ
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 134 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I PHE* 3.7 1.8 - - - -
132I LEU* 3.6 1.5 - - - +
133I ALA* 1.3 77.6 - - - +
135I LYS* 1.3 65.0 + - - +
136I ALA 3.8 2.4 + - - -
137I LEU* 3.7 32.1 + - - +
138I SER* 3.1 24.9 + - - -
130J GLU* 3.0 35.0 + - - -
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Residues in contact with LYS 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I VAL* 4.1 20.9 - - + +
103I PHE* 3.3 46.7 - - + -
105I VAL* 5.7 1.1 - - + -
134I SER* 1.3 71.0 + - - +
136I ALA* 1.3 64.4 + - - +
138I SER* 3.3 4.1 + - - -
139I LEU* 2.9 36.2 + - + +
95J PHE* 3.5 38.0 - - + +
97J ASP* 3.3 32.8 + - - +
130J GLU* 5.4 0.4 + - - -
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Residues in contact with ALA 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I SER* 3.3 5.6 + - - +
135I LYS* 1.3 78.8 - - - +
137I LEU* 1.3 58.8 + - - +
139I LEU 3.4 0.3 + - - -
140I GLU* 2.9 31.1 + - - +
95J PHE* 3.3 24.1 - - + -
105J VAL 4.3 2.2 - - - +
106J GLY* 4.3 3.8 - - - -
126J TYR* 3.6 13.4 - - + -
128J VAL* 3.6 35.7 - - + -
130J GLU* 5.0 3.6 - - + +
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Residues in contact with LEU 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I LEU* 4.0 31.0 - - + +
134I SER* 3.4 30.6 + - - +
135I LYS 3.3 0.4 - - - -
136I ALA* 1.3 78.1 - - - +
138I SER* 1.3 64.0 + - - +
140I GLU* 3.3 13.6 + - - +
141I LYS* 3.0 24.8 + - - +
128J VAL* 4.4 15.9 - - + -
130J GLU* 3.8 13.5 - - - +
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Residues in contact with SER 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I PHE* 3.9 16.4 + - - +
105I VAL* 3.8 18.8 - - - -
129I SER* 3.1 35.7 + - - -
132I LEU* 3.4 16.1 - - - +
134I SER 3.1 18.1 + - - -
135I LYS 3.6 4.3 - - - -
137I LEU* 1.3 75.7 - - - +
139I LEU* 1.3 58.2 + - - +
142I ALA* 2.9 27.1 + - - +
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Residues in contact with LEU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I VAL* 4.4 15.5 - - + -
96I VAL* 3.9 16.4 - - + -
105I VAL* 3.6 26.5 - - + -
107I VAL* 4.7 3.8 - - + -
135I LYS* 2.9 21.6 + - + +
138I SER* 1.3 74.0 - - - +
140I GLU* 1.3 65.0 + - - +
142I ALA* 4.4 2.0 - - - +
143I ARG* 2.9 33.9 + - + +
94J ASP* 3.7 14.4 - - + +
95J PHE* 3.5 29.8 - - + -
126J TYR* 3.2 30.1 - - + +
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Residues in contact with GLU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ALA 2.9 15.2 + - - +
137I LEU* 3.6 16.4 - - - +
139I LEU* 1.3 76.1 - - - +
141I LYS* 1.3 64.4 + - - +
143I ARG* 4.0 0.6 - - - +
144I LYS* 2.9 66.4 + - + +
301I K 2.9 23.7 - - - -
126J TYR* 3.6 30.6 - - + +
128J VAL* 4.1 15.7 - - - +
36L T 5.4 1.4 - - - +
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Residues in contact with LYS 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I VAL 3.2 20.5 + - - +
129I SER* 3.7 22.9 + - - +
130I GLU 5.1 2.0 - - - +
132I LEU* 4.8 11.1 - - + +
137I LEU 3.0 16.5 + - - +
138I SER 3.7 2.9 - - - +
140I GLU* 1.3 77.5 - - - +
142I ALA* 1.3 65.5 + - - +
144I LYS* 4.0 3.0 - - - +
145I GLU* 2.9 34.2 + - - +
33L T 5.2 4.5 + - - -
34L T 3.2 48.0 + - - +
35L T 5.6 4.9 - - - +
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Residues in contact with ALA 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I VAL* 3.7 15.7 - - + +
107I VAL* 3.6 27.3 - - + +
127I GLY* 3.3 26.9 - - - +
128I VAL 4.1 3.4 - - - +
129I SER 4.6 2.0 - - - +
138I SER 2.9 17.5 + - - +
139I LEU 3.3 2.4 + - - +
141I LYS* 1.3 76.6 - - - +
143I ARG* 1.3 58.8 + - - +
146I ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I GLN* 2.4 54.9 + - - +
93I VAL* 3.8 24.3 - - - +
107I VAL* 3.9 20.4 - - + -
139I LEU* 2.9 25.5 + - + +
140I GLU* 4.1 2.5 - - - +
142I ALA* 1.3 76.7 - - - +
144I LYS* 1.3 62.7 + - + +
146I ALA* 3.2 2.6 + - - +
147I VAL* 3.0 21.9 + - - +
92J ASN* 4.7 6.1 - - - +
94J ASP* 2.9 26.6 + - - -
108J CYS* 2.7 40.5 - - - -
110J PHE* 4.2 6.2 - - - -
124J VAL* 4.5 11.4 - - + -
126J TYR* 4.1 15.0 - - + -
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Residues in contact with LYS 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I GLU* 2.9 55.1 + - + +
141I LYS* 4.1 2.9 - - - +
143I ARG* 1.3 76.1 - - + +
145I GLU* 1.3 62.2 + - - +
147I VAL* 3.3 3.5 + - - -
148I THR* 3.0 28.9 + - - -
123J ASP* 5.3 0.7 - - - -
124J VAL* 4.9 9.4 - - + +
125J GLY* 4.5 1.8 - - - -
126J TYR* 4.2 12.3 - - + +
149J ASP* 2.9 28.5 + - - -
153J ARG* 3.7 40.8 + - - +
34L T 6.1 0.2 - - + -
35L T 4.3 21.0 + - - +
36L T 3.4 14.5 + - - -
37L T 5.9 0.2 + - - -
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Residues in contact with GLU 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301H K 3.3 22.5 - - - -
126I TYR 3.7 8.5 - - - +
127I GLY* 3.8 4.0 - - - -
128I VAL* 3.3 38.0 + - - +
141I LYS* 2.9 23.2 + - - +
144I LYS* 1.3 76.4 - - - +
146I ALA* 1.3 58.2 + - - +
148I THR* 3.9 0.5 - - - -
149I ASP* 2.9 36.0 + - + +
33L T 5.4 10.0 + - - +
34L T 3.6 33.5 + - - +
35L T 4.2 9.4 + - - -
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Residues in contact with ALA 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I VAL* 3.6 16.4 - - + +
108I CYS 3.9 2.5 - - - -
109I ALA* 3.7 17.6 - - + +
125I GLY* 3.5 15.9 - - - +
126I TYR 3.4 13.0 - - - -
127I GLY* 3.5 11.8 - - - +
142I ALA 2.9 18.7 + - - +
143I ARG 3.2 4.2 + - - +
145I GLU* 1.3 76.1 - - - +
147I VAL* 1.3 57.8 + - - +
150I GLY 2.9 24.4 + - - -
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Residues in contact with VAL 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I HIS* 5.0 5.2 - - + +
88I ILE* 3.7 22.4 - - + -
91I GLN* 3.3 27.6 - - - +
109I ALA* 3.8 12.1 - - + -
111I VAL* 3.3 10.4 - - + +
143I ARG 3.0 10.7 + - - +
144I LYS 3.9 2.9 - - - +
146I ALA* 1.3 75.8 - - - +
148I THR* 1.3 60.2 + - - +
150I GLY 3.3 1.0 + - - -
151I LEU* 2.9 26.2 + - + +
122J GLU 4.8 2.2 - - - +
123J ASP* 3.6 34.1 - - - +
124J VAL* 3.5 16.8 - - + -
153J ARG* 4.6 0.7 - - - +
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Residues in contact with THR 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I GLY* 4.4 22.2 - - - -
72I ILE* 6.3 2.9 - - + -
144I LYS 3.0 12.7 + - - -
145I GLU* 4.0 2.2 - - - -
147I VAL* 1.3 78.0 - - - +
149I ASP* 1.3 58.2 + - - +
151I LEU* 3.1 11.5 + - + +
152I LYS* 2.9 33.9 + - + +
123J ASP* 4.9 0.7 + - - -
153J ARG* 3.1 15.9 + - - -
34L T 4.8 7.0 - - - +
35L T 2.8 37.1 + - - +
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Residues in contact with ASP 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H GLU* 5.2 1.4 - - - +
144H LYS* 2.8 34.7 + - - -
125I GLY* 3.7 3.1 - - - -
126I TYR 3.7 14.8 - - - +
145I GLU* 2.9 21.2 + - + +
146I ALA 3.9 1.8 - - - +
148I THR* 1.3 76.6 - - - +
150I GLY* 1.3 59.2 + - - +
152I LYS* 3.3 29.7 + - - +
153I ARG* 2.9 30.6 + - - +
32L T 3.7 7.0 + - - -
33L T 3.8 12.6 + - - -
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Residues in contact with GLY 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I VAL* 3.5 20.6 - - - +
123I ASP 4.1 2.6 - - - +
124I VAL 3.5 9.0 - - - -
125I GLY* 3.3 19.6 - - - -
146I ALA 2.9 12.7 + - - -
149I ASP* 1.3 76.1 - - - +
151I LEU* 1.3 57.8 + - - +
153I ARG* 3.8 1.2 - - - +
154I ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ILE* 4.3 22.7 - - + -
84I TRP* 3.8 17.5 - - + -
86I HIS* 3.6 46.9 - - + +
111I VAL* 3.4 9.9 - - + +
113I VAL* 3.7 10.5 - - + -
147I VAL* 2.9 15.1 + - + +
148I THR* 3.1 14.8 + - + +
150I GLY* 1.3 77.0 - - - +
152I LYS* 1.3 58.8 + - + +
154I ALA* 3.3 0.7 + - - -
155I LEU* 2.9 47.0 + - + +
123J ASP* 5.8 1.8 - - - +
157J SER* 5.0 1.6 - - - +
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Residues in contact with LYS 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ILE 3.6 18.6 + - - +
68I GLY* 4.4 17.5 - - - -
71I VAL* 4.3 22.1 - - + +
148I THR* 2.9 18.2 + - + +
149I ASP* 3.3 30.2 + - - +
151I LEU* 1.3 77.9 - - + +
153I ARG* 1.3 58.0 + - + +
155I LEU* 3.3 5.9 + - - +
156I ARG* 3.0 40.7 + - + +
162I LEU 4.8 1.2 - - - +
33L T 2.6 27.3 + - - -
34L T 2.4 34.8 + - - +
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Residues in contact with ARG 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H LYS* 3.6 38.9 + - - +
147H VAL* 4.4 1.8 - - - +
148H THR* 3.1 22.2 + - - -
123I ASP* 2.8 51.8 + - - +
124I VAL 3.2 23.7 + - - +
149I ASP* 2.9 17.1 + - - +
150I GLY 3.9 0.7 - - - +
152I LYS* 1.3 77.3 - - + +
154I ALA* 1.3 60.0 + - - +
156I ARG* 3.5 30.8 - - - +
157I SER* 3.8 6.2 + - - -
167I LEU* 5.6 0.4 - - - +
31L T 2.6 25.6 + - - -
32L T 3.2 30.7 + - - +
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Residues in contact with ALA 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 5.8 0.2 - - - -
111I VAL 3.7 19.3 - - - +
113I VAL* 3.6 23.7 - - + +
121I HIS* 3.7 29.3 + - - +
122I GLU 4.9 0.4 - - - -
123I ASP* 3.9 11.6 - - - +
150I GLY 2.9 17.8 + - - +
151I LEU 3.9 0.7 - - - +
153I ARG* 1.3 77.2 - - - +
155I LEU* 1.3 63.6 + - - +
156I ARG 3.2 0.6 + - - -
157I SER* 3.6 9.4 + - - -
158I PHE* 4.7 1.7 - - - -
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Residues in contact with LEU 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I VAL* 3.8 31.2 - - + +
72I ILE* 5.3 0.7 - - + +
75I ALA* 4.1 24.0 - - + -
79I PHE* 4.8 2.7 - - + -
84I TRP* 4.1 11.7 - - + -
113I VAL* 3.7 25.6 - - + -
151I LEU* 2.9 45.2 + - + +
152I LYS 3.9 2.7 - - - +
154I ALA* 1.3 74.7 - - - +
156I ARG* 1.3 65.9 + - - +
157I SER 3.2 0.4 + - - -
158I PHE* 3.4 28.4 + - + +
162I LEU* 3.4 24.8 - - + +
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Residues in contact with ARG 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ILE* 5.1 3.8 - - + -
65I TYR* 6.0 1.4 - - - +
66I ILE 6.1 0.2 - - - +
152I LYS* 3.0 28.7 + - + +
153I ARG* 3.5 26.0 - - - +
154I ALA 3.2 0.6 - - - -
155I LEU* 1.3 76.3 - - - +
157I SER* 1.3 54.0 + - - +
158I PHE 2.8 12.0 + - - -
159I GLY 3.3 18.4 + - - +
162I LEU 3.7 7.8 + - - +
163I GLY* 3.5 28.5 + - - +
164I ASN* 3.5 15.9 - - - +
166I ILE* 3.4 24.7 - - - +
167I LEU* 3.4 27.5 - - - +
32L T 2.7 51.0 + - - -
33L T 4.4 7.1 + - - -
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Residues in contact with SER 157 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ILE* 3.9 26.6 - - - +
76H ASN* 3.2 19.6 + - - +
84H TRP* 3.6 8.8 - - - -
86H HIS* 4.0 15.9 + - - -
151H LEU* 4.9 0.6 - - - +
121I HIS* 3.4 40.2 - - - -
123I ASP* 4.7 3.1 + - - -
153I ARG 3.8 11.6 + - - -
154I ALA 3.6 5.2 + - - -
155I LEU 3.2 1.8 - - - -
156I ARG* 1.3 72.8 - - - +
158I PHE* 1.3 57.5 + - - +
159I GLY 3.6 0.4 - - - -
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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