Contacts of the helix formed by residues 180 - 195 (chain A) in PDB entry 4OA5
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A SER* 5.0 1.6 - - - -
178A LYS 4.2 0.4 + - - -
179A VAL* 1.3 74.3 - - - +
181A SER* 1.3 58.0 + - - +
182A ASN* 3.3 12.8 + - - +
183A ALA* 3.0 28.8 + - - +
184A HIS* 2.9 27.7 + - - +
302A IOD 3.8 13.6 - - - +
310A IOD 4.7 6.5 - - - -
319A IOD 4.4 8.1 - - - -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.8 23.5 - - - +
176A THR 5.2 0.9 + - - -
179A VAL 3.3 4.9 + - - -
180A SER* 1.3 69.5 + - - +
182A ASN* 1.3 59.9 + - - +
184A HIS* 3.7 6.8 + - - +
185A ALA* 2.9 31.5 + - - +
319A IOD 3.8 15.0 - - - +
118D LEU* 3.9 29.1 + - - +
122D ASN* 5.1 8.1 + - - -
144D ALA* 4.1 5.5 - - - +
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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
----------------------------------------------------------
140A SER* 3.8 18.1 - - - +
180A SER* 3.3 8.6 + - - +
181A SER* 1.3 78.2 - - - +
183A ALA* 1.3 61.4 + - - +
185A ALA* 3.5 2.0 + - - +
186A SER* 3.1 25.1 + - - -
118D LEU* 3.4 20.3 - - + +
138D ASN* 5.4 0.8 - - - +
140D SER 4.3 4.1 - - - +
141D SER* 2.7 37.3 + - - -
144D ALA* 3.6 10.0 - - - +
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Residues in contact with ALA 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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139A LYS* 3.7 26.5 - - + +
140A SER* 3.9 12.5 - - - +
166A LEU* 3.7 6.1 - - + -
180A SER* 3.0 28.0 + - - +
182A ASN* 1.3 75.8 - - - +
184A HIS* 1.3 58.3 + - - +
186A SER* 3.3 2.1 + - - -
187A MET* 2.9 31.7 + - - +
302A IOD 4.1 13.0 - - + -
310A IOD 4.1 5.6 - - + -
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Residues in contact with HIS 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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166A LEU* 3.4 13.4 - - + +
169A SER* 3.0 34.0 + - - -
170A VAL* 4.2 4.5 - - - -
172A ASP 2.9 27.8 + - - -
173A GLU 3.3 18.6 - - - -
175A PRO* 3.6 38.6 - - + +
179A VAL* 4.1 2.0 - - + -
180A SER 2.9 16.7 + - - +
181A SER 3.7 4.5 + - - +
182A ASN 3.3 0.2 - - - -
183A ALA* 1.3 76.8 - - - +
185A ALA* 1.3 59.1 + - - +
187A MET* 3.3 1.4 + - - +
188A ARG* 2.9 52.1 + - + +
147D ASN* 5.1 3.9 + - - -
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Residues in contact with ALA 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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181A SER 2.9 17.4 + - - +
182A ASN 3.9 3.6 - - - +
184A HIS* 1.3 77.4 + - - +
186A SER* 1.3 62.4 + - - +
188A ARG* 3.8 3.6 - - - +
189A ALA* 3.2 16.8 + - - +
321A EDO 5.0 0.5 + - - -
143D LEU* 3.6 21.7 - - + +
144D ALA* 4.0 23.8 - - + +
147D ASN* 3.4 29.2 + - - +
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Residues in contact with SER 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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139A LYS 3.2 17.6 + - - -
140A SER 3.4 16.3 + - - -
142A TYR* 3.4 3.3 + - - +
143A LEU* 3.3 25.5 + - - +
182A ASN 3.1 18.3 + - - -
183A ALA 3.6 3.6 - - - -
185A ALA* 1.3 79.0 - - - +
187A MET* 1.3 57.3 + - - +
189A ALA* 3.4 2.8 + - - +
190A PHE* 2.9 28.5 + - - +
316D IOD 4.2 15.0 - - - -
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Residues in contact with MET 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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139A LYS* 4.1 24.6 + - + +
142A TYR* 3.4 46.2 - - + -
163A ASN 3.5 17.0 - - - +
164A THR* 3.6 38.6 - - - +
166A LEU* 4.3 14.6 - - + -
170A VAL* 4.0 10.8 - - + -
183A ALA 2.9 15.6 + - - +
184A HIS 4.0 2.5 - - - +
186A SER* 1.3 73.5 - - - +
188A ARG* 1.3 67.9 + - - +
190A PHE* 4.1 5.8 - - - -
191A ASN* 2.9 26.4 + - - +
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Residues in contact with ARG 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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170A VAL* 2.9 37.8 + - + +
171A PHE 3.7 12.9 + - - -
172A ASP 3.8 4.0 + - - -
173A GLU* 3.5 43.6 + - - +
184A HIS* 2.9 49.7 + - + +
185A ALA* 3.8 6.7 - - - +
187A MET* 1.3 76.7 - - - +
189A ALA* 1.3 57.0 + - - +
191A ASN* 4.0 2.1 - - - +
192A ASP* 3.0 28.8 + - - +
314A IOD 3.7 22.3 - - - +
321A EDO 3.8 22.8 + - - -
147D ASN* 5.4 4.7 - - - +
12F TYR* 3.6 20.0 + - - -
16F LEU* 5.6 0.3 - - - +
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Residues in contact with ALA 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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143A LEU* 4.0 27.8 - - + +
185A ALA 3.2 15.7 + - - +
186A SER 3.9 3.1 - - - +
187A MET 3.2 0.4 - - - -
188A ARG* 1.3 77.2 - - - +
190A PHE* 1.3 59.9 + - - +
192A ASP* 3.7 1.4 - - - +
193A GLU* 2.9 32.6 + - - +
321A EDO 4.0 18.6 - - - +
143D LEU* 4.0 11.7 - - + -
189D ALA* 5.0 3.8 - - + -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.0 15.3 - - + -
142A TYR* 3.5 44.6 - + + -
143A LEU* 4.0 10.6 - - - +
146A LEU* 3.7 24.0 - - + +
159A ILE* 4.6 3.8 - - + -
161A ALA* 3.7 21.8 - - + -
164A THR* 3.8 20.6 - - + -
186A SER 2.9 18.6 + - - +
187A MET* 3.3 9.6 + - - +
189A ALA* 1.3 77.9 - - - +
191A ASN* 1.3 75.4 + - - +
193A GLU* 3.4 2.3 + - - +
194A LEU* 3.1 50.8 + - + +
212A MET* 4.2 2.9 - - + -
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Residues in contact with ASN 191 (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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164A THR* 2.9 33.9 + - - -
170A VAL* 3.7 9.1 - - - +
187A MET* 2.9 14.8 + - - +
188A ARG 4.0 0.7 - - - +
190A PHE* 1.3 91.1 - - - +
192A ASP* 1.3 57.4 + - - +
194A LEU 3.2 1.2 + - - -
195A ALA* 3.0 24.4 + - - +
204A ILE* 3.9 14.2 - - - +
212A MET* 3.5 15.0 - - - +
12F TYR* 3.0 32.7 + - - +
16F LEU* 4.3 1.1 - - + -
17F PHE* 3.5 17.4 - - + -
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Residues in contact with ASP 192 (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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188A ARG 3.0 19.7 + - - +
189A ALA* 3.7 4.0 - - - +
191A ASN* 1.3 74.3 - - - +
193A GLU* 1.3 67.7 + - - +
195A ALA* 3.2 19.5 + - - +
196A ASN* 3.8 4.0 + - - +
321A EDO 3.7 28.4 + - - +
16F LEU* 4.5 15.1 - - + +
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Residues in contact with GLU 193 (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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146A LEU* 3.5 24.5 - - + -
150A LYS* 3.4 12.4 + - - +
189A ALA 2.9 18.6 + - - +
190A PHE 3.8 3.4 - - - +
192A ASP* 1.3 76.7 + - - +
194A LEU* 1.3 57.2 + - - +
195A ALA 3.1 0.2 - - - -
196A ASN* 3.1 27.3 + - - +
199A LYS* 3.6 12.1 + - - +
200A TYR* 2.8 43.5 + - + +
318A IOD 3.8 24.3 - - + +
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Residues in contact with LEU 194 (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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146A LEU* 3.8 19.3 - - + -
159A ILE* 4.2 10.1 - - + -
190A PHE* 3.1 53.2 + - + +
191A ASN 3.2 4.2 + - - +
193A GLU* 1.3 75.0 - - - +
195A ALA* 1.3 58.6 + - - +
196A ASN 3.2 2.3 + - - +
200A TYR* 3.6 43.8 - - + +
202A SER* 2.7 30.3 + - - +
212A MET* 3.7 26.7 - - + -
214A SER* 3.7 11.9 - - - +
17F PHE* 3.9 2.5 - - - -
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Residues in contact with ALA 195 (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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191A ASN 3.0 11.8 + - - +
192A ASP* 3.5 14.4 - - - +
193A GLU 3.1 0.8 - - - -
194A LEU* 1.3 77.1 - - - +
196A ASN* 1.3 57.5 + - - +
197A LYS* 3.1 16.9 + - - +
200A TYR 5.4 0.4 - - - -
16F LEU* 3.3 45.2 - - + +
17F PHE* 3.7 8.3 - - + -
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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