Contacts of the helix formed by residues 134 - 157 (chain R) in PDB entry 5XS0
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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R PHE* 3.9 0.7 - - - -
132R LEU* 3.4 3.2 - - - +
133R LYS* 1.3 76.6 - - - +
135R LYS* 1.3 63.2 + - - +
136R ALA 3.5 1.6 + - - -
137R LEU* 3.1 38.1 + - - +
138R SER* 2.8 28.5 + - - -
130S GLU* 3.5 24.6 + - - -
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Residues in contact with LYS 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R VAL* 4.1 16.4 - - + -
103R PHE* 3.5 50.8 - - + -
105R VAL* 6.0 0.4 - - + -
133R LYS 3.6 0.2 + - - -
134R SER* 1.3 72.3 + - - +
136R ALA* 1.3 57.2 + - - +
138R SER* 3.3 3.4 + - - -
139R LEU* 2.9 38.5 + - + +
95S PHE* 3.5 37.1 - - + +
97S ASP* 2.8 34.2 + - - -
130S GLU* 5.6 0.8 + - - -
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Residues in contact with ALA 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R SER* 3.3 6.1 + - - +
135R LYS* 1.3 80.7 - - - +
137R LEU* 1.3 57.3 + - - +
140R GLU* 2.9 26.2 + - - +
95S PHE* 3.5 25.5 - - + -
105S VAL 4.5 3.4 - - - +
126S TYR* 3.3 15.6 - - + -
128S VAL* 3.6 36.1 - - + -
130S GLU* 4.2 6.8 + - - +
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Residues in contact with LEU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R LEU* 4.5 15.3 - - + +
134R SER* 3.1 30.0 + - - +
136R ALA* 1.3 75.4 - - - +
138R SER* 1.3 62.0 + - - +
140R GLU* 3.7 17.7 - - - +
141R LYS* 2.9 32.1 + - - +
128S VAL* 4.7 11.7 - - + -
130S GLU* 4.2 11.2 - - - +
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Residues in contact with SER 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R PHE* 3.8 14.2 + - - +
105R VAL* 4.0 17.7 - - - -
129R SER* 3.2 29.7 + - - -
132R LEU* 3.2 23.6 - - - +
134R SER 2.8 22.0 + - - -
135R LYS 3.6 4.5 - - - -
137R LEU* 1.3 78.4 - - - +
139R LEU* 1.3 56.5 + - - +
141R LYS 3.3 0.2 + - - -
142R ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R VAL* 4.5 8.7 - - + -
96R VAL* 4.0 18.4 - - + -
105R VAL* 3.9 23.3 - - + -
107R VAL* 4.9 1.8 - - + -
135R LYS* 2.9 23.3 + - + +
138R SER* 1.3 76.4 - - - +
140R GLU* 1.3 58.4 + - - +
142R ALA* 3.3 2.8 + - - -
143R ARG* 2.9 47.2 + - + +
94S ASP* 3.5 21.1 - - + +
95S PHE* 3.6 24.0 - - + -
126S TYR* 3.3 28.5 - - + +
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Residues in contact with GLU 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R ALA 2.9 17.1 + - - +
137R LEU* 3.7 23.3 - - - +
139R LEU* 1.3 76.5 - - - +
141R LYS* 1.3 64.4 + - - +
143R ARG* 4.0 1.4 - - - +
144R LYS* 2.8 65.4 + - + +
126S TYR* 3.6 32.4 - - + +
128S VAL* 4.5 8.1 - - - +
149S ASP* 4.2 0.9 - - - +
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Residues in contact with LYS 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R VAL* 2.8 24.9 + - - +
129R SER* 3.6 16.5 - - - +
132R LEU* 4.7 11.2 - - + -
137R LEU 2.9 17.9 + - - +
138R SER 3.6 3.1 - - - +
140R GLU* 1.3 78.1 - - - +
142R ALA* 1.3 58.3 + - - +
144R LYS* 4.2 2.6 - - - +
145R GLU* 2.5 70.2 + - + +
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Residues in contact with ALA 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R VAL* 3.7 16.4 - - + +
107R VAL* 3.7 19.3 - - + -
127R GLY* 3.1 34.5 - - - +
128R VAL 4.0 6.3 - - - +
129R SER* 4.5 0.2 - - - -
138R SER 2.9 17.2 + - - +
139R LEU 3.9 1.8 - - - +
140R GLU 3.3 0.2 - - - -
141R LYS* 1.3 77.4 - - - +
143R ARG* 1.3 57.7 + - - +
146R ALA* 2.9 27.0 + - - +
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Residues in contact with ARG 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R GLN* 2.5 57.1 + - - +
93R VAL* 3.3 30.9 - - - +
107R VAL* 4.0 13.5 - - + -
139R LEU* 2.9 25.9 + - + +
140R GLU* 4.0 2.9 - - - +
142R ALA* 1.3 76.4 - - - +
144R LYS* 1.3 62.7 + - - +
146R ALA 3.2 1.6 + - - -
147R VAL* 3.0 21.0 + - - +
92S ASN* 4.9 5.5 - - - +
94S ASP* 2.8 33.1 + - - -
108S CYS* 3.5 37.3 - - - -
110S PHE* 4.4 4.9 - - - -
124S VAL* 4.1 11.4 - - + -
126S TYR* 4.0 9.2 - - + -
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Residues in contact with LYS 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140R GLU* 2.8 50.0 + - + +
141R LYS* 4.2 2.5 - - - +
143R ARG* 1.3 75.4 - - - +
145R GLU* 1.3 65.2 + - - +
147R VAL* 3.3 3.6 + - - -
148R THR* 3.0 28.6 + - - -
124S VAL* 4.1 15.5 - - + +
126S TYR* 4.1 7.0 - - + +
149S ASP* 2.6 36.3 + - - -
153S ARG* 3.4 46.2 + - - +
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Residues in contact with GLU 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R TYR 3.7 3.1 - - - +
127R GLY* 3.9 6.6 - - - -
128R VAL* 3.4 15.1 + - - +
141R LYS* 2.5 64.1 + - + +
142R ALA 3.9 2.5 - - - +
144R LYS* 1.3 77.0 - - + +
146R ALA* 1.3 56.4 + - - +
148R THR* 3.8 4.6 - - - +
149R ASP* 2.9 34.1 + - - +
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Residues in contact with ALA 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R VAL* 3.4 31.6 - - + +
109R ALA* 3.7 21.8 - - + +
125R GLY* 3.6 7.8 - - - -
126R TYR 3.3 14.3 + - - -
127R GLY 3.5 0.4 - - - +
142R ALA 2.9 19.1 + - - +
143R ARG 3.2 5.4 + - - +
145R GLU* 1.3 76.1 - - - +
147R VAL* 1.3 57.7 + - - +
149R ASP 3.5 0.2 + - - -
150R GLY 2.9 24.4 + - - -
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Residues in contact with VAL 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R HIS* 5.4 4.3 - - + +
88R ILE* 3.7 24.2 - - + -
91R GLN* 3.4 24.9 - - - +
109R ALA* 4.0 11.0 - - + -
111R VAL* 3.5 9.0 - - + +
143R ARG 3.0 12.0 + - - +
144R LYS 3.3 4.0 + - - +
146R ALA* 1.3 75.0 - - - +
148R THR* 1.3 64.7 + - - +
150R GLY 3.3 1.0 + - - -
151R LEU* 2.9 22.1 + - + +
122S GLU 4.8 2.5 - - - +
123S ASP* 3.4 33.0 - - - +
124S VAL* 3.7 20.4 - - + -
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Residues in contact with THR 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R GLY* 4.4 23.1 - - - +
144R LYS 3.0 17.2 + - - -
145R GLU* 4.0 4.9 - - - -
147R VAL* 1.3 78.2 - - - +
149R ASP* 1.3 57.9 + - - +
151R LEU* 3.2 12.0 + - + +
152R LYS* 2.9 39.6 + - + +
123S ASP* 5.0 3.7 + - - -
153S ARG* 3.7 14.0 + - - -
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Residues in contact with ASP 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q GLU* 4.3 0.7 - - - +
144Q LYS* 2.6 39.3 + - - -
125R GLY* 3.9 1.1 - - - -
126R TYR 3.2 21.5 + - - +
145R GLU 2.9 19.5 + - - +
146R ALA 3.8 2.0 - - - +
148R THR* 1.3 76.8 - - - +
150R GLY* 1.3 57.8 + - - +
152R LYS* 3.3 20.6 + - - +
153R ARG* 2.9 35.3 + - - +
156R ARG* 5.2 3.8 + - - -
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Residues in contact with GLY 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R VAL* 3.6 17.7 - - - +
123R ASP* 4.6 2.5 - - - +
124R VAL 4.0 4.0 - - - -
125R GLY* 3.4 23.3 - - - -
146R ALA 2.9 13.8 + - - -
147R VAL 3.7 3.1 - - - -
149R ASP* 1.3 75.2 - - - +
151R LEU* 1.3 57.2 + - - +
153R ARG* 3.8 1.1 - - - +
154R ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R VAL* 6.0 0.7 - - + -
72R ILE* 4.5 21.3 - - + -
84R TRP* 3.7 36.3 - - + -
86R HIS* 3.7 30.1 - - + +
111R VAL* 3.6 10.4 - - + +
113R VAL* 3.7 15.9 - - + -
147R VAL* 2.9 15.1 + - + +
148R THR* 3.2 14.1 + - + +
150R GLY* 1.3 77.2 - - - +
152R LYS* 1.3 64.3 + - + +
154R ALA* 3.3 0.9 + - - +
155R LEU* 3.0 30.7 + - + +
123S ASP* 5.4 4.5 - - - +
157S SER* 4.8 1.8 - - - +
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Residues in contact with LYS 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R TYR* 4.8 14.1 - - - +
66R ILE* 3.4 28.6 + - + +
67R GLU* 5.3 0.2 - - - +
68R GLY* 4.5 11.7 - - - +
71R VAL* 4.1 30.7 - - + -
148R THR* 2.9 29.0 + - + +
149R ASP* 3.7 24.4 + - - +
151R LEU* 1.3 77.3 - - + +
153R ARG* 1.3 58.6 + - + +
155R LEU* 3.3 2.8 + - - +
156R ARG* 2.9 41.3 + - - +
162R LEU 4.9 1.7 - - - +
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Residues in contact with ARG 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144Q LYS* 3.5 65.6 + - - +
147Q VAL* 4.7 0.4 - - - +
148Q THR* 3.8 12.7 + - - -
123R ASP* 2.9 43.1 + - + +
124R VAL 2.7 25.0 + - - +
149R ASP* 2.9 26.4 + - - +
150R GLY 4.0 1.6 - - - +
152R LYS* 1.3 76.7 - - + +
154R ALA* 1.3 61.7 + - - +
156R ARG* 3.5 51.4 - - - +
157R SER* 3.9 5.7 + - - -
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Residues in contact with ALA 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R VAL 3.7 15.0 - - - +
113R VAL* 3.6 18.2 - - + -
121R HIS* 3.5 40.7 - - - +
123R ASP* 3.8 10.5 - - - +
150R GLY 2.9 18.7 + - - +
151R LEU* 3.8 0.7 - - - +
153R ARG* 1.3 77.7 - - - +
155R LEU* 1.3 63.3 + - - +
157R SER* 3.4 10.4 + - - -
158R PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R VAL* 3.6 31.9 - - + +
72R ILE* 5.5 0.2 - - - -
75R ALA* 4.0 20.2 - - + -
79R PHE* 4.9 2.5 - - + -
84R TRP* 4.1 13.2 - - + -
113R VAL* 3.6 31.0 - - + -
151R LEU* 3.0 33.6 + - + +
152R LYS 3.8 3.6 - - - +
154R ALA* 1.3 74.3 - - - +
156R ARG* 1.3 66.7 + - - +
157R SER 3.1 1.1 + - - -
158R PHE* 3.2 26.1 + - + -
162R LEU* 3.5 33.3 - - + +
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Residues in contact with ARG 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q ILE* 4.8 5.6 - - + -
149R ASP* 5.2 4.4 + - - -
152R LYS* 2.9 27.8 + - + +
153R ARG* 3.5 48.7 - - - +
154R ALA 3.2 0.4 - - - -
155R LEU* 1.3 76.7 - - - +
157R SER* 1.3 56.1 + - - +
158R PHE 3.0 6.5 + - - -
159R GLY 3.4 16.3 + - - +
162R LEU 4.2 7.2 + - - +
163R GLY* 3.7 29.4 + - - +
164R ASN* 3.6 18.1 - - + +
166R ILE* 4.3 10.3 - - - +
167R LEU* 3.9 37.5 - - - +
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Residues in contact with SER 157 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q ILE* 3.5 28.5 - - - +
76Q ASN* 3.3 16.3 + - - +
84Q TRP* 3.8 5.4 - - - -
86Q HIS* 3.8 16.0 + - - -
151Q LEU* 4.8 2.3 - - - +
121R HIS* 3.5 41.9 + - - -
123R ASP* 4.6 4.2 + - - -
153R ARG 3.9 7.8 + - - -
154R ALA* 3.4 6.9 + - - -
155R LEU 3.1 2.4 + - - -
156R ARG* 1.3 75.6 - - - +
158R PHE* 1.3 56.2 - - - +
159R GLY 3.5 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