Contacts of the helix formed by residues 180 - 195 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140F SER* 5.0 1.7 - - - -
178F LYS 4.2 0.4 + - - -
179F VAL* 1.3 75.0 - - - +
181F SER* 1.3 57.4 + - - +
182F ASN* 3.3 11.8 + - - +
183F ALA* 3.0 30.4 + - - +
184F HIS* 2.9 27.5 + - - +
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Residues in contact with SER 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F PRO* 3.8 24.0 - - - +
176F THR 5.2 1.0 + - - -
179F VAL 3.3 4.9 + - - -
180F SER* 1.3 70.2 + - - +
182F ASN* 1.3 62.3 + - - +
184F HIS* 3.7 7.1 + - - +
185F ALA* 2.9 31.5 + - - +
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Residues in contact with ASN 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F SER* 3.9 18.1 - - - +
180F SER* 3.2 8.8 + - - +
181F SER* 1.3 78.1 - - - +
183F ALA* 1.3 64.7 + - - +
185F ALA* 3.5 5.2 + - - +
186F SER* 3.1 24.9 + - - -
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Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LYS* 3.7 27.7 - - + +
140F SER* 3.8 15.6 - - - +
166F LEU* 3.7 13.2 - - + +
180F SER* 3.0 29.1 + - - +
182F ASN* 1.3 75.5 - - - +
184F HIS* 1.3 58.4 + - - +
186F SER* 3.3 2.4 + - - -
187F MET* 2.9 31.5 + - - +
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Residues in contact with HIS 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F LEU* 3.4 13.7 - - + +
169F SER* 3.0 34.6 + - - -
170F VAL* 4.2 4.7 - - - -
172F ASP 2.9 28.8 + - - -
173F GLU 3.3 19.5 + - - -
175F PRO* 3.7 36.3 - - + +
179F VAL* 4.2 1.8 - - + -
180F SER 2.9 16.3 + - - +
181F SER 3.7 4.0 + - - +
182F ASN 3.3 0.2 - - - -
183F ALA* 1.3 76.5 - - - +
185F ALA* 1.3 60.0 + - - +
187F MET* 3.3 0.9 + - - +
188F ARG* 2.9 53.0 + - + +
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Residues in contact with ALA 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F SER 2.9 17.3 + - - +
182F ASN* 3.9 5.8 - - - +
184F HIS* 1.3 80.4 + - - +
186F SER* 1.3 62.8 + - - +
188F ARG* 3.7 5.7 + - - +
189F ALA* 3.3 23.4 + - - +
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Residues in contact with SER 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F LYS 3.2 16.7 + - - -
140F SER 3.4 16.2 + - - -
142F TYR* 3.4 3.3 + - - +
143F LEU* 3.3 31.2 + - - +
182F ASN 3.1 17.8 + - - -
183F ALA 3.6 4.3 - - - -
185F ALA* 1.3 75.7 - - - +
187F MET* 1.3 59.0 + - - +
189F ALA* 3.4 3.9 + - - +
190F PHE* 2.9 28.3 + - - +
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Residues in contact with MET 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LYS* 4.1 24.0 + - + +
142F TYR* 3.4 46.9 - - + -
163F ASN 3.5 17.3 - - - +
164F THR* 3.6 38.1 - - - +
166F LEU* 4.3 14.1 - - + -
170F VAL* 4.1 9.6 - - + -
183F ALA 2.9 16.0 + - - +
184F HIS 4.0 2.2 - - - +
186F SER* 1.3 73.5 + - - +
188F ARG* 1.3 67.9 + - - +
190F PHE* 3.6 7.8 - - - +
191F ASN* 2.9 26.0 + - - +
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Residues in contact with ARG 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.7 18.4 + - - -
16A LEU* 5.7 0.2 - - - +
170F VAL* 2.9 37.7 + - + +
171F PHE 3.6 15.6 + - - -
172F ASP 3.8 4.0 + - - -
173F GLU* 3.7 32.9 + - - +
184F HIS* 2.9 49.9 + - + +
185F ALA* 3.9 6.1 - - - +
187F MET* 1.3 77.8 - - - +
189F ALA* 1.3 57.2 + - - +
191F ASN* 4.0 1.7 - - - +
192F ASP* 3.0 29.7 + - - +
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Residues in contact with ALA 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 3.9 27.2 - - + +
185F ALA 3.3 14.7 + - - +
186F SER 3.9 3.1 - - - +
187F MET 3.2 0.4 - - - -
188F ARG* 1.3 76.8 - - - +
190F PHE* 1.3 60.0 + - - +
192F ASP* 3.7 5.6 - - - +
193F GLU* 2.9 32.2 + - - +
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Residues in contact with PHE 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ILE* 4.0 15.7 - - + -
142F TYR* 3.4 37.9 - + + -
143F LEU* 4.0 5.7 - - - +
146F LEU* 3.7 29.7 - - + +
159F ILE* 4.6 4.5 - - + -
161F ALA* 3.7 21.8 - - + -
164F THR* 3.8 21.1 - - + -
186F SER 2.9 18.7 + - - +
187F MET* 3.6 14.6 - - - +
189F ALA* 1.3 75.5 - - - +
191F ASN* 1.3 76.3 + - - +
193F GLU* 3.4 1.9 + - - +
194F LEU* 3.1 51.0 + - + +
212F MET* 4.2 3.4 - - + -
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Residues in contact with ASN 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.1 30.0 + - - +
16A LEU* 4.3 1.8 - - + -
17A PHE* 3.4 18.2 - - + -
164F THR* 2.9 33.9 + - - -
170F VAL* 3.7 10.7 - - - +
187F MET* 2.9 14.6 + - - +
188F ARG 4.0 0.4 - - - +
190F PHE* 1.3 93.0 - - - +
192F ASP* 1.3 57.4 + - - +
194F LEU 3.2 1.2 + - - -
195F ALA* 3.0 24.4 + - - +
204F ILE* 3.9 15.7 - - - +
212F MET* 3.5 14.5 - - - +
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Residues in contact with ASP 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.3 24.9 - - + +
188F ARG 3.0 19.1 + - - +
189F ALA* 3.7 7.0 - - - +
190F PHE 3.3 0.2 - - - -
191F ASN* 1.3 73.7 - - - +
193F GLU* 1.3 66.8 + - - +
195F ALA* 3.2 15.5 + - - +
196F ASN* 3.7 3.8 + - - +
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LEU* 5.1 4.7 - - + -
146F LEU* 3.5 24.2 - - + -
147F ASN* 5.9 0.2 - - - +
150F LYS* 3.4 17.2 + - - +
189F ALA 2.9 17.8 + - - +
190F PHE 3.8 3.6 - - - +
192F ASP* 1.3 77.5 + - - +
194F LEU* 1.3 55.2 + - - +
196F ASN* 3.1 25.3 + - - +
199F LYS* 3.2 27.5 + - - -
200F TYR* 2.8 42.1 + - + +
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.8 2.2 - - - -
146F LEU* 3.8 18.2 - - + -
159F ILE* 4.2 9.2 - - + -
190F PHE* 3.1 52.7 + - + +
191F ASN 3.2 4.5 + - - +
193F GLU* 1.3 74.6 - - - +
195F ALA* 1.3 58.0 + - - +
196F ASN 3.2 2.0 + - - +
200F TYR* 3.6 44.0 - - + +
202F SER* 2.7 31.0 + - - +
212F MET* 3.7 28.5 - - + -
214F SER* 3.7 11.9 - - - +
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.3 46.9 - - + +
17A PHE* 3.6 12.1 - - + -
191F ASN 3.0 11.6 + - - +
192F ASP* 3.5 11.4 - - - +
193F GLU 3.1 0.6 - - - -
194F LEU* 1.3 75.5 - - - +
196F ASN* 1.3 59.2 + - - +
197F LYS* 3.1 17.0 + - - +
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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