Contacts of the helix formed by residues 131 - 155 (chain B) in PDB entry 1U9O
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.1 1.2 - - - +
127B ALA 3.4 8.7 + - - -
128B ARG 3.5 5.2 + - - +
129B ALA 3.9 0.2 - - - -
130B THR* 1.3 82.1 - - - +
132B VAL* 1.3 68.1 + - - +
133B GLU* 2.9 25.2 + - - +
134B VAL* 3.0 28.7 + - - +
135B ALA* 2.9 20.4 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR 4.2 0.6 - - - -
131B SER* 1.3 71.2 - - - +
133B GLU* 1.3 87.2 + - + +
135B ALA* 3.1 8.3 + - - +
136B GLU* 2.7 43.3 + - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.4 31.8 - - + +
131B SER* 2.9 18.7 + - - +
132B VAL* 1.3 103.3 + - + +
134B VAL* 1.3 58.8 + - - +
136B GLU* 3.6 8.2 - - - +
137B LEU* 2.8 30.9 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 5.7 5.2 - - + -
73B LEU* 3.7 24.5 - - + -
76B LEU* 3.5 24.9 - - + +
124B GLY* 3.8 20.9 - - - +
127B ALA* 4.5 7.2 - - + +
128B ARG* 4.2 11.4 - - + -
131B SER* 3.0 26.5 + - - +
133B GLU* 1.3 74.3 - - - +
135B ALA* 1.3 67.6 + - - +
137B LEU* 3.1 7.5 + - - +
138B TRP* 2.9 25.9 + - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 4.0 35.0 + - + +
131B SER 2.9 12.3 + - - +
132B VAL* 3.5 12.1 - - - +
134B VAL* 1.3 76.3 - - - +
136B GLU* 1.3 53.1 + - + +
138B TRP* 3.6 3.1 - - - +
139B SER* 2.6 39.3 + - - -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 2.7 38.4 + - + +
133B GLU* 3.6 6.7 - - - +
135B ALA* 1.3 69.2 - - + +
137B LEU* 1.3 65.9 + - - +
138B TRP 2.6 5.9 + - - -
139B SER* 2.8 7.6 + - - -
140B THR* 2.6 32.7 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.1 11.7 - - + -
76B LEU* 3.8 24.7 - - + -
77B ASP* 3.3 56.3 - - + +
80B VAL* 4.8 7.2 - - + +
133B GLU 2.8 21.4 + - - +
134B VAL* 3.5 4.9 - - - +
136B GLU* 1.3 71.8 - - - +
138B TRP* 1.3 59.1 + - - +
140B THR* 3.9 4.4 - - - -
141B PHE* 3.3 40.0 + - + +
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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
----------------------------------------------------------
76B LEU* 4.7 11.2 - - + -
80B VAL* 3.4 34.5 - - + -
114B PHE* 4.0 18.2 - + - -
121B THR* 6.2 0.9 - - + -
128B ARG* 3.4 32.5 - - + +
134B VAL* 2.9 19.0 + - + +
135B ALA* 3.6 3.8 - - - +
136B GLU 2.6 4.4 + - - -
137B LEU* 1.3 72.8 - - - +
139B SER* 1.3 56.2 + - - +
140B THR 2.6 15.8 + - - -
141B PHE* 3.2 3.7 + - + +
142B MET* 3.0 52.5 + - + +
145B TRP* 3.9 16.4 - + - -
180B GLU* 2.5 27.7 + - + -
217B CNS 3.9 34.3 - - + -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLN* 2.4 39.5 + - - +
192A PRO* 4.2 2.2 - - - +
128B ARG* 5.6 3.6 - - - +
135B ALA 2.6 24.0 + - - -
136B GLU* 2.8 7.1 + - - -
138B TRP* 1.3 74.7 - - - +
140B THR* 1.3 62.7 + - - +
142B MET* 4.4 6.5 - - - -
143B GLN* 3.5 21.7 + - - +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 2.6 32.0 + - - +
137B LEU* 3.9 7.7 + - - -
138B TRP 2.6 4.9 + - - -
139B SER* 1.3 68.4 - - - +
141B PHE* 1.3 64.5 + - + +
142B MET 3.1 0.7 - - - -
143B GLN* 2.5 44.7 + - - +
144B LYS* 3.5 2.9 + - + -
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Residues in contact with PHE 141 (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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80B VAL* 3.5 28.9 - - + -
81B ASN* 3.8 24.2 - - - -
84B ASP* 3.7 39.5 - - + -
137B LEU* 3.3 33.2 - - + +
138B TRP* 3.2 3.4 + - - +
140B THR* 1.3 87.6 - - + +
142B MET* 1.3 55.3 + - - +
143B GLN 2.7 11.1 + - - -
144B LYS* 2.7 32.6 + - - +
145B TRP* 2.8 39.0 + + + -
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Residues in contact with MET 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PRO* 4.3 19.7 - - + -
138B TRP* 3.0 61.6 + - + +
139B SER* 4.4 1.8 - - - +
140B THR 2.9 0.4 + - - -
141B PHE* 1.3 74.8 - - - +
143B GLN* 1.3 57.5 + - - +
145B TRP* 4.0 17.2 - - + +
146B ILE* 2.8 32.4 + - + +
176B ASN* 4.4 23.7 - - + +
177B LEU* 3.9 24.7 - - + -
180B GLU* 3.6 16.4 - - + +
217B CNS 4.8 9.0 - - + -
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLN* 2.7 43.9 + - - +
192A PRO* 4.1 19.1 - - + -
139B SER 3.5 17.8 - - - +
140B THR* 2.5 21.4 + - - +
142B MET* 1.3 73.8 - - - +
144B LYS* 1.3 57.3 + - - +
145B TRP 3.3 0.2 - - - -
146B ILE* 3.1 9.9 - - + +
147B ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 2.8 41.4 + - - +
140B THR* 3.5 2.3 + - + -
141B PHE* 2.7 35.8 + - + +
143B GLN* 1.3 73.8 - - - +
145B TRP* 1.3 54.6 + - + +
147B ALA* 3.2 5.4 + - - +
148B TYR* 2.7 37.8 + - + +
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Residues in contact with TRP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.7 37.7 - - + -
83B ALA* 3.8 13.7 - - + -
84B ASP* 2.6 34.5 + - - +
87B LEU* 5.2 10.1 - - + +
110B PHE* 3.5 35.5 - + + -
114B PHE* 4.3 4.7 - + - -
138B TRP* 3.9 22.0 - + - -
141B PHE* 2.8 38.2 + + + +
142B MET* 4.0 21.3 - - - +
144B LYS* 1.3 77.0 - - + +
146B ILE* 1.3 66.6 + - - +
148B TYR* 3.7 8.0 - - + +
149B THR* 3.1 27.7 + - - -
176B ASN* 4.3 12.3 - - - +
217B CNS 4.5 11.2 - - + +
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Residues in contact with ILE 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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192A PRO* 3.9 21.5 - - + -
142B MET* 2.8 19.9 + - + +
143B GLN* 3.1 21.3 - - + +
144B LYS 3.3 0.2 - - - -
145B TRP* 1.3 76.6 - - - +
147B ALA* 1.3 64.1 + - - +
149B THR* 3.6 2.6 - - - -
150B ALA* 3.2 22.2 + - - +
169B HIS* 3.8 22.8 + - + +
172B ALA* 3.8 2.6 - - + +
173B THR* 3.1 51.8 - - + +
176B ASN* 3.5 27.8 - - + +
177B LEU* 5.2 2.5 - - + -
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLN 2.9 19.7 + - - +
144B LYS* 3.4 6.3 - - - +
145B TRP 3.1 0.2 - - - -
146B ILE* 1.3 76.2 - - + +
148B TYR* 1.3 68.4 + - - +
149B THR 2.9 1.9 + - - -
150B ALA* 3.0 7.7 + - - +
151B ALA* 2.8 23.9 + - - +
169B HIS* 5.0 8.3 - - + +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.7 35.8 + - + +
90B LEU* 4.7 4.5 + - - +
91B ALA* 4.1 30.4 + - + -
144B LYS* 2.7 21.8 + - + +
145B TRP* 3.7 9.4 - - + +
147B ALA* 1.3 70.1 - - - +
149B THR* 1.3 67.6 + - - +
151B ALA* 2.9 23.5 - - + +
152B VAL* 3.2 19.6 + - + +
217B CNS 3.2 55.3 - - + +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TRP* 4.4 4.3 - - + -
145B TRP 3.1 8.9 + - - -
146B ILE 3.6 1.6 - - - -
147B ALA 2.9 0.2 + - - -
148B TYR* 1.3 78.1 - - - +
150B ALA* 1.3 72.2 + - - +
151B ALA 2.9 0.9 - - - -
152B VAL* 2.7 20.5 + - - +
153B ILE* 2.9 19.9 + - + +
172B ALA* 3.4 22.2 - - + -
176B ASN* 3.2 26.2 + - - +
207B TRP* 3.7 16.8 - - + -
211B ILE* 5.6 0.4 - - + -
217B CNS 3.4 26.2 - - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE 3.2 10.2 + - - +
147B ALA* 3.0 12.1 + - - +
149B THR* 1.3 76.4 - - - +
151B ALA* 1.3 67.2 + - - +
153B ILE* 3.1 23.0 + - - +
154B ASP* 3.1 11.5 + - - +
168B ALA* 3.7 7.7 - - + +
169B HIS* 3.8 29.2 - - + +
172B ALA* 3.8 13.0 - - + -
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Residues in contact with ALA 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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147B ALA 2.8 12.2 + - - +
148B TYR* 2.9 22.0 - - + +
149B THR 2.7 3.4 + - - -
150B ALA* 1.3 71.4 - - - +
152B VAL* 1.3 57.2 + - + +
154B ASP* 2.8 26.0 + - - +
155B ALA* 2.8 15.2 + - - +
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Residues in contact with VAL 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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102B MET* 4.8 15.0 - - + -
103B TRP* 4.1 24.5 - - + -
148B TYR* 3.4 28.7 - - + +
149B THR 2.7 9.7 + - - +
151B ALA* 1.3 73.1 - - + +
153B ILE* 1.3 62.1 + - - +
155B ALA* 3.4 11.9 - - + -
156B GLU* 2.9 33.8 + - + +
217B CNS 4.1 27.6 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TRP* 3.3 11.4 - - + -
149B THR* 2.9 23.9 + - + +
150B ALA* 3.2 17.7 - - - +
152B VAL* 1.3 77.1 - - - +
154B ASP* 1.3 58.2 + - - +
156B GLU* 3.7 7.8 + - - +
157B ARG* 2.8 49.6 - - - +
162B ALA* 4.6 1.6 - - + +
168B ALA* 3.7 20.9 - - + -
171B LEU* 4.2 10.3 - - + -
172B ALA* 4.7 4.7 - - + -
211B ILE* 3.2 52.0 - - + +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ALA 3.1 11.4 + - - +
151B ALA* 2.8 11.9 + - - +
153B ILE* 1.3 74.9 - - - +
155B ALA* 1.3 53.2 + - - +
156B GLU 2.6 5.8 + - - -
157B ARG* 2.5 44.5 + - - +
158B ASP* 2.9 27.5 + - - +
164B ARG* 5.3 3.6 + - - -
168B ALA* 3.7 18.9 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA 2.8 13.4 + - - +
152B VAL* 3.0 16.8 + - + +
154B ASP* 1.3 74.0 - - - +
156B GLU* 1.3 65.2 - - - +
157B ARG 3.5 0.7 - - - -
158B ASP* 4.6 6.7 - - - +
159B ARG* 4.1 13.1 - - - +
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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