Contacts of the helix formed by residues 140 - 161 (chain A) in PDB entry 1O94
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 ASP 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LYS* 4.5 6.6 + - - +
138A GLU 3.5 2.2 + - - -
139A MET* 1.3 77.0 - - - +
141A LEU* 1.3 67.0 + - - +
142A SER* 2.8 25.3 + - - -
143A ASP* 3.0 24.6 + - - +
144A ILE* 3.2 18.7 + - - +
187A ARG* 4.6 5.4 - - - +
651B TRP* 5.3 3.6 + - - -
655B LYS* 3.8 26.2 - - - +
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Residues in contact with LEU 141 (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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140A ASP* 1.3 76.9 - - - +
142A SER* 1.3 56.9 + - - +
144A ILE* 3.2 11.1 + - + +
145A ALA* 3.0 26.0 + - - +
187A ARG* 4.8 1.1 - - - +
189A ASP* 4.1 17.9 - - - +
190A LYS* 4.8 12.8 - - + -
191A TYR* 3.8 29.4 - - + -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP* 2.8 23.5 + - - -
141A LEU* 1.3 74.7 - - - +
143A ASP* 1.3 62.5 + - - +
145A ALA* 3.2 8.6 + - - +
146A GLN* 2.8 37.6 + - - +
655B LYS* 5.4 4.2 + - - -
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 2.8 41.2 + - - +
137A LYS* 2.8 34.7 + - - +
139A MET* 3.6 17.5 - - + -
140A ASP* 3.0 34.2 + - - +
142A SER* 1.3 79.7 + - - +
144A ILE* 1.3 57.5 + - - +
146A GLN* 3.1 4.7 + - - +
147A VAL* 2.8 34.1 + - - +
701B GLN* 6.1 0.9 - - - +
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Residues in contact with ILE 144 (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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139A MET* 3.4 25.1 - - + -
140A ASP 3.2 10.2 + - - +
141A LEU* 3.4 11.4 - - + +
142A SER 3.2 0.2 - - - -
143A ASP* 1.3 79.1 - - - +
145A ALA* 1.3 57.0 + - - +
147A VAL* 3.4 1.4 + - - +
148A GLN* 2.9 47.6 + - - +
179A PHE* 3.9 20.9 - - + -
187A ARG* 4.0 18.2 - - - +
191A TYR* 3.8 44.6 - - + +
201A PHE* 3.7 18.6 - - + -
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Residues in contact with ALA 145 (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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141A LEU 3.0 12.9 + - - +
142A SER* 3.5 12.1 - - - +
144A ILE* 1.3 78.9 - - - +
146A GLN* 1.3 59.9 + - - +
148A GLN* 3.7 12.2 - - - +
149A GLN* 3.0 23.7 + - - +
208A LYS* 5.2 7.9 + - - +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.0 41.2 + - - +
142A SER* 2.8 21.7 + - - +
143A ASP* 3.1 11.9 + - - +
145A ALA* 1.3 72.9 - - - +
147A VAL* 1.3 59.7 + - - +
149A GLN* 3.2 7.9 + - - +
150A PHE* 3.0 44.0 + - + -
699B ASN* 4.4 13.4 + - - +
702B ILE* 3.9 17.1 - - - +
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Residues in contact with VAL 147 (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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63A ILE* 4.7 0.2 - - + -
66A GLU* 4.1 6.5 - - - +
106A TYR* 4.0 25.6 - - + +
121A ARG* 4.0 26.0 - - - +
139A MET* 4.0 17.3 - - + -
143A ASP 2.8 22.6 + - - +
144A ILE 4.1 2.2 - - - +
146A GLN* 1.3 71.9 - - - +
148A GLN* 1.3 67.5 + - - +
150A PHE* 3.1 11.2 + - + +
151A TYR* 3.1 28.5 + - + -
175A LEU* 3.8 27.1 - - + -
201A PHE* 4.3 2.5 - - + -
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Residues in contact with GLN 148 (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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144A ILE* 2.9 30.2 + - - +
145A ALA* 3.7 8.9 - - - +
146A GLN 3.3 0.2 - - - -
147A VAL* 1.3 77.2 - - - +
149A GLN* 1.3 60.0 + - - +
151A TYR* 3.1 12.7 + - - +
152A VAL* 3.1 25.8 + - - +
191A TYR* 4.9 0.2 + - - -
201A PHE* 3.6 30.5 + - + +
204A GLU* 3.0 42.4 + - - +
205A THR* 3.6 17.1 + - - +
208A LYS* 3.4 33.9 + - + +
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Residues in contact with GLN 149 (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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145A ALA 3.0 14.5 + - - +
146A GLN* 3.5 11.4 - - - +
147A VAL 3.2 0.2 - - - -
148A GLN* 1.3 73.8 - - - +
150A PHE* 1.4 55.9 + - + +
152A VAL* 3.1 24.7 + - - +
153A ASP* 2.7 70.6 + - - +
156A LYS* 5.2 3.8 - - - +
208A LYS* 5.7 0.4 - - - +
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Residues in contact with PHE 150 (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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63A ILE* 3.6 22.6 - - + +
64A ASN* 3.4 42.0 - - + -
66A GLU* 3.7 14.8 - - - -
106A TYR* 4.4 8.1 - + - -
121A ARG* 3.5 29.8 - - - -
146A GLN* 3.0 28.4 + - + -
147A VAL* 3.1 22.2 + - + +
149A GLN* 1.4 76.9 - - + +
151A TYR* 1.3 57.1 + - - +
153A ASP* 3.9 10.9 - - - +
154A ALA* 2.9 30.3 + - - +
157A ARG* 4.9 0.2 + - - -
702B ILE* 5.4 6.7 - - + -
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Residues in contact with TYR 151 (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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63A ILE* 3.6 23.5 - - + +
104A LEU* 3.8 42.6 - - + +
106A TYR* 3.5 19.2 + - + +
147A VAL* 3.1 38.6 + - + -
148A GLN* 3.1 9.4 + - - +
150A PHE* 1.3 75.3 - - - +
152A VAL* 1.3 58.2 + - - +
154A ALA* 3.2 5.7 + - - +
155A ALA* 2.9 30.7 + - - +
168A VAL* 4.4 15.5 - - + -
169A TYR 4.7 1.1 + - - -
175A LEU* 4.3 1.7 - - + +
176A PRO* 3.5 29.4 - - + +
201A PHE* 4.3 10.5 - + - -
205A THR* 3.7 24.9 - - + -
209A VAL* 4.0 13.9 - - + -
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Residues in contact with VAL 152 (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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148A GLN 3.1 14.3 + - - +
149A GLN* 3.1 28.2 + - - +
151A TYR* 1.3 78.7 - - - +
153A ASP* 1.4 62.1 + - - +
155A ALA* 3.1 8.2 + - - +
156A LYS* 3.0 40.7 + - + +
208A LYS* 3.6 42.0 - - + +
209A VAL* 4.5 3.6 - - + +
212A ALA* 3.9 13.9 - - + -
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Residues in contact with ASP 153 (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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149A GLN* 2.7 55.5 + - - +
150A PHE* 3.9 10.8 - - - +
152A VAL* 1.4 70.8 - - - +
154A ALA* 1.3 63.4 + - - +
156A LYS* 3.3 16.5 + - - +
157A ARG* 3.0 51.5 + - - +
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Residues in contact with ALA 154 (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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63A ILE* 3.6 30.3 - - + -
77A ILE* 3.7 19.5 - - + +
104A LEU* 3.8 5.6 - - + -
150A PHE 2.9 18.8 + - - +
151A TYR 3.7 3.1 - - - +
152A VAL 3.2 0.2 - - - -
153A ASP* 1.3 78.4 - - - +
155A ALA* 1.3 56.7 + - - +
157A ARG* 3.4 14.7 + - - +
158A SER* 2.7 32.3 + - - -
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Residues in contact with ALA 155 (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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104A LEU* 4.0 9.2 - - + +
151A TYR 2.9 17.5 + - - +
152A VAL* 3.1 6.3 + - - +
154A ALA* 1.3 77.1 - - - +
156A LYS* 1.3 62.4 + - - +
158A SER* 3.1 10.2 + - - -
159A ARG 3.0 18.7 + - - -
166A VAL* 4.2 2.8 - - + +
209A VAL* 3.9 29.4 - - + -
212A ALA* 5.3 0.7 - - + -
213A VAL* 3.4 24.4 - - + +
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Residues in contact with LYS 156 (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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149A GLN* 5.2 2.6 - - - +
152A VAL* 3.0 32.9 + - + +
153A ASP* 3.7 18.1 + - - +
155A ALA* 1.3 75.1 - - - +
157A ARG* 1.4 61.4 + - - +
159A ARG* 3.3 22.5 + - - +
160A ASP* 3.1 27.6 + - - +
212A ALA* 4.1 17.9 - - + +
213A VAL* 4.0 9.2 - - + -
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Residues in contact with ARG 157 (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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63A ILE 4.0 10.3 + - - -
77A ILE* 2.9 44.3 + - + -
78A TRP* 3.4 18.0 + - - +
79A ASP* 3.7 27.8 - - - +
80A GLU* 6.3 0.9 - - + -
83A VAL* 3.8 11.5 - - + +
150A PHE 4.9 0.2 + - - -
153A ASP* 3.0 36.7 + - - +
154A ALA* 3.7 24.7 - - - +
156A LYS* 1.4 75.0 - - - +
158A SER* 1.3 57.5 + - - +
160A ASP* 3.1 15.5 + - - +
161A ALA* 2.8 28.8 + - - +
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Residues in contact with SER 158 (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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77A ILE* 4.4 6.6 - - - +
102A VAL* 3.3 35.6 - - - +
104A LEU* 3.7 10.6 - - - +
154A ALA 2.7 24.5 + - - -
155A ALA* 3.1 10.3 + - - -
157A ARG* 1.3 70.8 - - - +
159A ARG* 1.3 67.3 + - - +
161A ALA* 3.0 13.5 + - - +
162A GLY 3.2 0.2 + - - -
163A PHE* 3.1 27.0 + - - -
166A VAL* 3.9 11.2 - - - -
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Residues in contact with ARG 159 (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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155A ALA 3.0 12.6 + - - +
156A LYS* 3.7 28.5 + - - +
158A SER* 1.3 75.1 - - - +
160A ASP* 1.4 63.4 + - - +
162A GLY* 2.9 20.8 + - - -
163A PHE 4.5 9.8 - - - +
212A ALA 3.0 27.6 + - - -
213A VAL* 3.7 10.5 - - + +
216A ASP* 2.8 49.2 + - + -
217A CYS* 4.2 17.2 - - - -
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Residues in contact with ASP 160 (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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83A VAL* 3.9 19.4 - - + +
87A LYS* 4.1 12.1 - - - +
156A LYS* 3.1 20.2 + - - +
157A ARG* 3.1 16.2 + - - +
159A ARG* 1.4 81.8 + - - +
161A ALA* 1.3 60.8 + - - +
162A GLY* 3.1 1.5 + - - -
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Residues in contact with ALA 161 (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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77A ILE* 4.9 2.7 - - + -
83A VAL* 3.8 30.5 - - + +
86A LEU* 4.6 2.0 - - + -
87A LYS* 3.5 17.7 - - - +
90A THR* 2.6 30.8 + - - +
157A ARG 2.8 15.5 + - - +
158A SER* 3.0 8.4 + - - +
160A ASP* 1.3 76.4 - - - +
162A GLY* 1.3 51.1 + - - +
163A PHE* 3.5 20.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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