Contacts of the helix formed by residues 173 - 190 (chain A) in PDB entry 1O9D
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 HIS 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP* 2.9 23.0 + - - -
169A LEU* 3.7 29.7 - - + +
170A ALA* 3.0 25.8 + - + +
171A PRO 4.5 0.2 - - - +
172A THR* 1.3 77.2 + - - +
174A PRO* 1.3 73.4 - - + +
175A ILE* 3.2 43.0 + - + +
176A ARG* 3.1 7.9 + - + +
177A LEU* 2.8 27.9 + - - +
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Residues in contact with PRO 174 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A THR 3.3 8.7 - - - +
173A HIS* 1.3 93.4 - - + +
175A ILE* 1.3 54.8 - - + +
177A LEU* 4.1 4.7 - - + -
178A GLY* 2.7 30.5 + - - -
222A ASP* 3.6 27.8 - - + +
223A SER* 4.6 11.0 - - - +
226A ILE* 3.4 21.3 - - + +
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Residues in contact with ILE 175 (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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48A ARG* 4.2 11.0 - - - +
122A ASP* 3.8 22.0 - - + +
125A VAL* 3.6 26.7 - - + +
126A PHE* 3.9 37.5 - - + +
129A LYS* 4.4 10.5 - - + +
169A LEU* 4.7 1.8 - - + -
173A HIS* 3.2 28.7 + - + +
174A PRO* 1.3 74.6 - - + +
176A ARG* 1.3 66.3 + - - +
178A GLY* 3.4 1.0 + - - -
179A LEU* 3.0 23.4 + - - +
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Residues in contact with ARG 176 (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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125A VAL* 4.9 0.4 - - - -
165A ALA* 3.6 32.1 + - + -
166A THR* 3.4 31.5 + - - +
169A LEU* 2.6 35.4 + - + +
170A ALA 3.5 10.4 + - - +
171A PRO* 3.6 35.3 - - - +
173A HIS* 3.1 14.9 + - + +
175A ILE* 1.3 81.1 - - - +
177A LEU* 1.3 62.7 + - - +
179A LEU* 3.2 7.6 + - + +
180A ALA* 3.0 24.5 + - - +
204A ALA* 6.0 6.3 - - - -
207A GLU* 3.3 26.1 + - - -
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Residues in contact with LEU 177 (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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171A PRO 3.5 21.7 + - - +
172A THR* 3.5 27.8 - - - +
173A HIS 2.8 13.6 + - - +
174A PRO* 3.7 5.2 - - + +
176A ARG* 1.3 75.3 - - - +
178A GLY* 1.3 57.8 + - - +
180A ALA* 3.3 5.2 + - - +
181A LEU* 2.9 28.1 + - - +
204A ALA* 4.0 23.8 - - + +
208A ALA* 4.0 6.1 - - + -
223A SER* 4.0 19.3 - - - +
226A ILE* 3.8 16.8 - - + +
227A MET* 4.0 21.5 - - + -
230A LEU* 4.0 19.3 - - + +
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Residues in contact with GLY 178 (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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129A LYS* 3.7 10.1 - - - -
174A PRO 2.7 21.8 + - - -
175A ILE 3.8 1.1 - - - -
176A ARG 3.3 0.2 - - - -
177A LEU* 1.3 70.7 - - - +
179A LEU* 1.3 59.7 + - - +
181A LEU* 3.4 1.6 + - - +
182A ASN* 2.9 35.9 + - - +
226A ILE* 4.0 4.7 - - - +
5P VAL* 3.7 24.5 - - - -
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Residues in contact with LEU 179 (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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125A VAL* 4.2 3.6 - - + -
129A LYS* 3.9 19.5 - - + +
158A TYR* 3.7 35.0 - - + +
161A ALA* 3.6 23.3 - - + +
162A GLN* 3.5 37.7 - - + +
165A ALA* 4.1 13.2 - - + -
175A ILE 3.0 18.2 + - - +
176A ARG* 3.4 5.6 - - + +
178A GLY* 1.3 72.8 - - - +
180A ALA* 1.3 63.7 + - - +
182A ASN* 3.2 1.2 + - - -
183A PHE* 2.8 39.3 + - + +
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Residues in contact with ALA 180 (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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176A ARG* 3.0 14.6 + - + +
177A LEU* 3.6 9.0 - - - +
179A LEU* 1.3 78.4 - - - +
181A LEU* 1.3 63.1 + - - +
183A PHE* 4.4 2.0 - - - -
184A SER* 3.0 27.4 + - - -
200A LEU* 3.6 18.4 - - + +
204A ALA* 3.5 31.9 - - + -
230A LEU* 4.3 6.4 - - + +
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Residues in contact with LEU 181 (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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177A LEU 2.9 16.8 + - - +
178A GLY* 3.6 4.5 - - - +
179A LEU 3.2 0.2 - - - -
180A ALA* 1.3 77.2 - - - +
182A ASN* 1.3 60.7 + - - +
184A SER* 3.1 6.0 + - - +
185A VAL* 3.1 26.2 + - - +
226A ILE* 4.4 6.7 - - + +
229A LEU* 3.8 37.2 - - + +
230A LEU* 3.6 26.6 - - + +
233A ASN* 3.3 26.9 - - - +
3P TYR 3.5 9.0 - - - +
4P TPO 3.6 31.2 - - - -
5P VAL* 3.8 13.2 - - + +
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Residues in contact with ASN 182 (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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129A LYS* 3.4 10.3 - - - +
133A ASP* 2.9 28.8 + - - +
136A ARG* 3.5 14.2 + - - +
158A TYR* 3.7 10.9 - - + +
178A GLY 2.9 16.9 + - - +
179A LEU 4.0 1.6 - - - +
181A LEU* 1.3 75.0 - - - +
183A PHE* 1.3 60.7 + - - +
185A VAL* 3.2 8.3 + - - +
186A PHE* 3.0 27.4 + - - +
4P TPO 3.2 15.8 + - - +
5P VAL 2.8 43.7 + - - +
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Residues in contact with PHE 183 (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 LEU* 4.0 11.4 - - + -
158A TYR* 3.7 54.0 - + + -
159A LYS* 3.9 18.8 - - + -
162A GLN* 3.8 33.4 - - + -
179A LEU* 2.8 26.9 + - + +
180A ALA* 4.0 4.3 - - - +
182A ASN* 1.3 70.7 - - - +
184A SER* 1.3 63.7 + - - +
186A PHE* 3.1 23.8 + + - +
187A TYR* 3.2 43.7 + + - -
200A LEU* 3.8 14.1 - - + -
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Residues in contact with SER 184 (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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180A ALA 3.0 16.2 + - - -
181A LEU* 3.1 14.0 + - - -
183A PHE* 1.3 74.6 - - - +
185A VAL* 1.3 63.4 + - - +
187A TYR* 3.3 10.2 + - - -
188A TYR* 3.1 18.7 + - - +
197A ALA* 3.3 35.0 - - - +
200A LEU* 4.1 5.7 - - - +
201A ALA* 3.8 18.3 - - - +
230A LEU* 4.7 0.9 - - - +
233A ASN* 5.3 1.0 + - - -
237A TRP* 3.5 13.9 - - - -
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Residues in contact with VAL 185 (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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136A ARG* 4.3 11.4 - - - +
181A LEU 3.1 16.0 + - - +
182A ASN 3.2 7.8 + - - +
184A SER* 1.3 77.1 - - - +
186A PHE* 1.3 59.0 + - - +
188A TYR* 3.2 0.7 + - - +
189A GLU* 2.7 53.0 + - + +
233A ASN* 3.6 14.1 - - - +
237A TRP* 4.0 9.0 - - + -
2P SER* 3.7 13.2 - - - +
3P TYR 3.4 22.4 - - - +
4P TPO 3.7 20.0 - - + +
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Residues in contact with PHE 186 (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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136A ARG* 4.0 12.3 - - + +
151A ALA* 3.5 22.9 - - - -
154A THR* 3.3 33.9 - - + -
155A LEU* 3.8 22.2 - - + -
158A TYR* 3.9 9.2 - - + -
182A ASN 3.0 12.3 + - - +
183A PHE* 3.1 25.1 - + - +
185A VAL* 1.3 77.7 - - - +
187A TYR* 1.3 67.2 + + - +
190A ILE* 3.0 53.8 + - + -
191A LEU* 3.3 36.2 + - + -
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Residues in contact with TYR 187 (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 LEU* 3.8 6.2 - - + +
159A LYS* 3.3 26.0 + - - -
183A PHE* 3.2 43.5 + + - -
184A SER* 3.3 7.8 + - - +
185A VAL 3.3 0.2 - - - -
186A PHE* 1.3 79.5 - + - +
188A TYR* 1.3 58.4 + - - +
191A LEU* 3.3 27.5 - - + +
192A ASN 3.1 11.4 + - - -
193A SER* 2.9 26.6 + - - +
196A ARG* 3.5 55.8 + - + -
197A ALA 3.8 15.5 - - - +
200A LEU* 3.6 22.7 - - + -
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Residues in contact with TYR 188 (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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184A SER 3.1 14.5 + - - +
185A VAL* 3.6 3.6 - - - +
187A TYR* 1.3 80.1 - - - +
189A GLU* 1.3 83.6 + - + +
192A ASN* 3.4 22.7 - - - +
193A SER 4.2 3.5 + - - +
194A PRO* 3.7 33.2 - - + +
197A ALA* 3.7 7.8 - - + +
236A LEU 5.4 0.3 + - - -
237A TRP* 3.5 65.5 + + + -
239A SER 5.4 2.4 + - - -
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Residues in contact with GLU 189 (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 GLU* 5.7 0.7 - - - +
147A ARG* 4.4 4.7 + - - -
185A VAL* 2.7 34.4 + - + +
188A TYR* 1.3 94.4 - - + +
190A ILE* 1.3 71.3 + - + +
192A ASN* 4.2 11.2 + - - +
1P GLN* 3.1 35.3 + - - +
2P SER* 2.9 29.6 + - - -
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Residues in contact with ILE 190 (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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136A ARG* 4.1 13.5 - - + +
139A ALA* 3.9 21.8 - - + +
140A GLU* 4.2 38.4 - - + +
147A ARG* 3.2 43.7 + - - +
151A ALA* 4.3 6.5 - - + -
186A PHE* 3.0 43.5 + - + +
189A GLU* 1.3 86.8 - - + +
191A LEU* 1.3 65.9 + - + +
192A ASN* 3.3 10.7 + - - -
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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