Contacts of the helix formed by residues 131 - 153 (chain B) in PDB entry 1BRR
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 TYR 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 4.1 24.2 - + - -
72B GLY* 4.1 22.7 - - - +
129B LYS 3.3 7.0 + - - -
130B VAL* 1.3 71.7 - - - +
132B SER* 1.3 70.9 + - - +
134B ARG* 3.2 30.7 + - - +
135B PHE* 3.5 28.3 - + - -
195B GLY* 3.1 30.1 + - - -
196B ALA* 3.7 13.3 - - - +
197B GLY 5.1 0.2 + - - -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.4 6.5 - - - +
131B TYR* 1.3 82.9 - - - +
133B TYR* 1.3 74.2 + - - +
135B PHE* 3.3 24.6 + - - +
136B VAL* 4.0 6.2 + - - +
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.7 66.6 - - + +
128B THR* 3.8 12.8 - - + -
130B VAL* 3.1 43.2 + - + +
132B SER* 1.3 79.0 - - - +
134B ARG* 1.3 56.2 + - - +
135B PHE 3.0 3.4 - - - -
136B VAL* 2.6 40.7 + - + +
137B TRP* 3.2 11.4 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 4.4 0.6 - - - +
71B PHE* 3.4 33.1 - - - -
78B ILE* 3.9 2.0 - - - +
125B GLY* 3.1 32.3 + - - +
126B ALA* 3.0 36.0 + - - +
127B LEU 4.1 1.0 - - - -
128B THR* 2.8 39.8 + - - +
130B VAL 3.8 4.5 - - - +
131B TYR* 3.2 36.0 + - - +
133B TYR* 1.3 75.8 - - - +
135B PHE* 1.3 61.3 + - + +
137B TRP* 3.3 6.7 + - - +
138B TRP* 3.0 24.6 + - - +
189B TRP* 3.8 14.4 - - + -
194B GLU* 3.0 40.8 + - - +
195B GLY* 4.8 0.8 - - - +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.5 48.9 - + - -
132B SER* 3.6 11.0 - - - +
133B TYR 3.0 0.8 - - - -
134B ARG* 1.3 78.0 - - + +
136B VAL* 1.3 63.4 + - + +
138B TRP* 3.7 12.9 - + + +
139B ALA* 3.2 22.2 + - - +
189B TRP* 4.6 7.0 - + - -
190B LEU* 3.5 33.9 - - + -
195B GLY* 3.6 35.7 - - - -
196B ALA* 4.0 3.6 - - + -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.2 26.2 - - + -
62A LEU* 4.5 11.4 - - + -
132B SER 4.2 4.5 - - - +
133B TYR* 2.6 36.6 + - + +
135B PHE* 1.3 74.2 - - - +
137B TRP* 1.3 61.3 + - + +
139B ALA* 3.6 5.3 + - - +
140B ILE* 3.0 33.4 + - + +
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Residues in contact with TRP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.5 38.1 - - + -
58A LEU* 3.4 31.9 - - + -
59A SER* 3.7 23.6 - - - -
62A LEU* 3.9 19.8 - - + +
64A TYR* 5.5 2.5 - - + +
121B THR* 3.0 34.1 - - + +
122B GLY* 5.6 0.9 - - - -
124B VAL* 3.3 29.5 - - + +
125B GLY* 3.6 17.9 - - - -
128B THR* 3.4 22.3 + - - +
133B TYR* 3.2 21.1 + - - +
134B ARG 3.6 6.1 - - - +
136B VAL* 1.3 76.4 - - - +
138B TRP* 1.3 54.7 + - - +
140B ILE* 3.1 12.0 + - + -
141B SER* 2.8 31.6 + - - -
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Residues in contact with TRP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLY* 6.3 0.7 - - - -
134B ARG 3.0 16.1 + - - +
135B PHE* 3.8 13.9 - + + +
136B VAL 3.3 0.2 - - - -
137B TRP* 1.3 76.9 - - - +
139B ALA* 1.3 78.9 + - + +
141B SER* 3.1 6.5 + - - -
142B THR* 2.7 61.2 + - + -
186B PRO* 2.9 41.9 + - + +
187B VAL* 5.6 0.9 - - + -
189B TRP* 3.2 37.9 - + + -
190B LEU* 3.8 31.6 - - + +
999B RET 3.8 16.4 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE 3.2 16.6 + - - +
136B VAL* 3.7 6.3 - - - +
137B TRP 3.3 0.2 - - - -
138B TRP* 1.3 93.8 - - + +
140B ILE* 1.3 58.0 + - + +
142B THR* 3.3 3.9 + - - -
143B ALA* 2.9 28.5 + - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 3.9 25.6 - - + -
55A THR* 4.8 7.2 - - - +
58A LEU* 3.4 32.8 - - + -
117B ILE* 5.1 4.2 - - + +
121B THR* 3.9 17.9 - - + +
136B VAL* 3.0 20.2 - - + +
137B TRP* 3.1 16.1 + - + +
139B ALA* 1.3 75.9 - - + +
141B SER* 1.3 63.3 + - - +
143B ALA* 3.4 6.9 + - - +
144B ALA* 3.2 21.0 + - - +
1000B ARC 4.8 13.9 - - + +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 6.5 0.2 - - - -
118B MET* 2.8 29.1 + - - +
121B THR* 3.6 10.7 - - - +
122B GLY* 4.3 1.8 - - - -
137B TRP 2.8 19.5 + - - -
138B TRP* 3.5 4.9 - - - -
140B ILE* 1.3 70.2 - - - +
142B THR* 1.3 66.8 + - - +
144B ALA* 3.1 9.1 + - - +
145B MET 3.0 17.3 + - - -
999B RET 3.0 42.5 - - - +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 2.7 57.7 + - + -
139B ALA* 3.6 6.7 - - - -
141B SER* 1.3 70.8 - - - +
143B ALA* 1.3 59.6 + - - +
145B MET* 3.1 15.1 + - + +
146B LEU* 2.8 52.6 + - + +
186B PRO* 4.1 8.6 - - + +
999B RET 3.5 12.2 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ALA 2.9 16.1 + - - +
140B ILE* 3.6 9.0 - - - +
141B SER 3.3 0.2 - - - -
142B THR* 1.3 75.7 - - - +
144B ALA* 1.3 57.1 + - - +
146B LEU* 3.4 13.3 + - - +
147B TYR* 3.1 28.9 + - - +
1000B ARC 3.6 18.3 - - + +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 4.1 9.2 - - + +
117B ILE* 4.7 6.5 - - + -
118B MET* 3.7 27.6 - - + +
140B ILE 3.2 12.9 + - - +
141B SER 3.1 10.5 + - - +
143B ALA* 1.3 75.0 - - - +
145B MET* 1.3 63.3 + - - +
147B TYR* 3.5 5.4 + - - +
148B ILE* 3.2 28.4 + - - +
1000B ARC 3.6 19.2 - - + +
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B MET* 3.5 26.8 - - - -
141B SER 3.0 5.1 + - - -
142B THR* 3.1 13.4 + - + +
144B ALA* 1.3 74.4 - - - +
146B LEU* 1.3 79.9 + - + +
148B ILE* 3.0 7.4 + - - +
149B LEU* 2.8 48.3 + - + +
182B TRP* 3.2 38.4 - - + +
183B SER* 3.8 14.1 - - - +
186B PRO* 3.7 25.8 - - + -
999B RET 3.8 15.5 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B THR* 2.8 38.3 + - + +
143B ALA* 3.7 10.1 - - - +
145B MET* 1.3 90.1 - - + +
147B TYR* 1.3 57.3 + - - +
149B LEU* 3.8 10.1 - - + +
150B TYR* 3.0 28.9 + - - +
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Residues in contact with TYR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.6 7.2 - - + -
110B ALA* 3.8 13.0 - - - +
111B LEU* 4.4 6.8 - - + +
114B ALA* 3.9 16.6 - - + -
143B ALA 3.1 13.2 + - - +
144B ALA 3.6 7.4 - - - +
145B MET 3.2 0.2 - - - -
146B LEU* 1.3 74.7 - - - +
148B ILE* 1.3 68.8 + - - +
150B TYR* 3.2 17.1 + + + +
151B VAL* 3.2 39.7 + - + +
1000B ARC 3.4 90.2 - - + +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.0 13.7 - - + -
111B LEU* 4.1 16.6 - - + +
114B ALA* 4.1 14.8 - - + +
115B ASP* 3.7 43.7 - - + +
118B MET* 4.4 10.3 - - - -
144B ALA 3.2 13.9 + - - +
145B MET* 3.0 7.5 + - - +
147B TYR* 1.3 82.1 - - + +
149B LEU* 1.3 62.1 + - - +
150B TYR 3.2 0.5 + - - -
151B VAL* 3.3 3.6 + - - +
152B LEU* 3.1 34.8 + - + +
182B TRP* 4.0 24.2 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B MET* 2.8 47.6 + - + +
146B LEU* 4.0 9.6 - - + +
148B ILE* 1.3 72.0 - - - +
150B TYR* 1.3 56.9 + - - +
152B LEU* 3.7 15.3 - - + +
153B PHE* 2.9 32.1 + - - +
178B THR 4.1 13.5 - - - +
179B VAL* 3.8 45.8 - - + +
182B TRP* 4.2 20.6 - - + -
183B SER* 4.3 9.2 - - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU 3.0 14.8 + - - +
147B TYR* 3.3 15.5 - + + +
148B ILE 3.2 0.4 - - - -
149B LEU* 1.3 77.0 - - - +
151B VAL* 1.3 65.9 + - + +
153B PHE* 3.2 0.4 + - - -
154B PHE* 2.8 77.1 + + + +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 5.8 3.4 - - - -
111B LEU* 3.2 39.9 - - + -
147B TYR* 3.2 42.1 + - + +
148B ILE 3.3 4.9 + - - +
150B TYR* 1.3 83.2 - - + +
152B LEU* 1.3 57.3 + - - +
155B GLY* 3.1 9.9 - - - +
156B PHE* 2.7 43.8 + - + -
1000B ARC 6.0 2.7 - - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.3 12.6 - - + -
97B LEU* 4.1 24.9 - - + -
111B LEU* 4.6 9.4 - - + -
148B ILE* 3.1 27.4 + - + +
149B LEU* 3.7 22.2 - - + +
150B TYR 3.2 0.2 - - - -
151B VAL* 1.3 83.2 - - + +
153B PHE* 1.3 61.0 + - - +
156B PHE* 3.2 36.3 - - + +
171B PHE* 3.1 28.5 - - + -
175B ARG* 3.7 10.1 - - + -
178B THR* 4.2 20.4 - - - +
179B VAL* 5.1 2.7 - - + -
182B TRP* 5.5 1.3 - - + -
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU 2.9 17.4 + - - +
150B TYR* 3.9 0.9 - - - +
152B LEU* 1.3 75.8 - - - +
154B PHE* 1.3 101.6 + + + +
155B GLY 2.9 9.5 + - - -
157B THR* 2.7 27.2 + - - -
175B ARG* 3.1 46.0 - - + +
176B ASN* 5.0 1.3 - - - -
179B VAL* 4.7 17.5 - - + +
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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) + - + + + + + -
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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