Contacts of the helix formed by residues 180 - 195 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER* 5.0 1.7 - - - -
178B LYS 4.3 0.4 + - - -
179B VAL* 1.3 74.2 - - - +
181B SER* 1.3 57.6 + - - +
182B ASN* 3.3 12.0 + - - +
183B ALA* 3.0 28.0 + - - +
184B HIS* 2.9 27.0 + - - +
310B IOD 3.8 13.1 - - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO* 3.8 23.2 - - - +
176B THR 5.3 1.0 + - - -
179B VAL 3.4 4.9 + - - -
180B SER* 1.3 69.2 + - - +
182B ASN* 1.3 62.8 + - - +
184B HIS* 3.7 7.2 + - - +
185B ALA* 2.9 31.4 + - - +
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.9 17.6 - - - +
180B SER* 3.3 7.9 + - - +
181B SER* 1.3 81.1 - - - +
183B ALA* 1.3 61.9 + - - +
185B ALA* 3.9 4.9 - - - +
186B SER* 3.0 26.0 + - - -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 4.1 19.6 - - + +
140B SER* 3.9 15.2 - - - +
166B LEU* 3.7 7.3 - - + +
180B SER* 3.0 26.6 + - - +
182B ASN* 1.3 75.9 - - - +
184B HIS* 1.3 58.6 + - - +
186B SER* 3.3 2.1 + - - -
187B MET* 2.9 31.5 + - - +
310B IOD 4.0 18.2 - - + -
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Residues in contact with HIS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.4 13.0 - - + +
169B SER* 3.0 34.7 + - - -
170B VAL* 4.1 4.4 - - - +
172B ASP 2.9 29.3 + - - -
173B GLU 3.4 18.4 - - - -
174B HIS 4.1 0.2 - - - -
175B PRO* 3.6 38.2 - - + +
179B VAL* 4.1 2.2 - - + -
180B SER 2.9 16.3 + - - +
181B SER 3.7 3.8 + - - +
183B ALA* 1.3 77.0 - - - +
185B ALA* 1.3 60.5 + - - +
187B MET* 3.3 0.7 + - - +
188B ARG* 2.9 52.1 + - + +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER 2.9 17.8 + - - +
182B ASN* 3.9 5.8 - - - +
184B HIS* 1.3 81.0 + - - +
186B SER* 1.3 61.5 + - - +
188B ARG* 3.8 5.8 - - - +
189B ALA* 3.2 24.1 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS 3.2 20.7 + - - -
140B SER 3.4 16.2 + - - -
142B TYR* 3.3 3.4 + - - +
143B LEU* 3.3 30.5 + - - +
182B ASN 3.0 18.3 + - - -
183B ALA 3.6 0.7 - - - -
184B HIS 3.2 0.2 - - - -
185B ALA* 1.3 78.6 - - - +
187B MET* 1.3 58.1 + - - +
189B ALA* 3.4 3.4 + - - +
190B PHE* 2.9 28.3 + - - +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 3.8 28.4 + - + +
142B TYR* 3.4 41.1 - - + -
163B ASN 3.5 17.5 - - - +
164B THR* 3.6 40.2 - - - +
166B LEU* 4.3 14.1 - - + -
170B VAL* 4.0 10.1 - - + -
183B ALA 2.9 14.9 + - - +
184B HIS 4.0 2.5 - - - +
186B SER* 1.3 73.3 - - - +
188B ARG* 1.3 66.5 + - - +
190B PHE* 3.5 5.6 - - - +
191B ASN* 2.9 25.8 + - - +
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 2.9 38.1 + - + +
171B PHE 3.7 13.1 + - - -
172B ASP 3.8 12.2 + - - -
173B GLU* 3.6 30.2 + - - +
184B HIS* 2.9 38.0 + - + +
185B ALA* 3.8 6.7 - - - +
187B MET* 1.3 77.6 - - - +
189B ALA* 1.3 57.2 + - - +
191B ASN* 3.6 2.1 + - - +
192B ASP* 3.0 29.2 + - - +
302B IOD 3.9 26.4 - - + +
318B EDO 5.1 0.2 - - - -
12C TYR* 3.5 21.8 + - - -
16C LEU* 5.7 0.2 - - - +
302C IOD 3.9 21.8 - - - +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.9 28.2 - - + +
185B ALA 3.2 16.0 + - - +
186B SER 3.9 2.7 - - - +
187B MET 3.2 0.6 - - - -
188B ARG* 1.3 75.8 - - - +
190B PHE* 1.3 60.9 + - - +
192B ASP* 3.7 5.5 - - - +
193B GLU* 2.9 32.4 + - - +
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Residues in contact with PHE 190 (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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135B ILE* 4.0 14.6 - - + -
142B TYR* 3.5 39.0 - + + -
143B LEU* 4.0 5.5 - - - +
146B LEU* 3.8 29.1 - - + +
159B ILE* 4.6 4.3 - - + -
161B ALA* 3.7 22.7 - - + -
164B THR* 3.8 20.6 - - + -
186B SER 2.9 18.2 + - - +
187B MET* 3.5 14.4 - - - +
189B ALA* 1.3 76.8 - - - +
191B ASN* 1.3 77.4 + - - +
193B GLU* 3.4 2.3 + - - +
194B LEU* 3.1 49.2 + - + +
212B MET* 4.1 3.1 - - + -
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Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR* 2.9 33.5 + - - -
170B VAL* 3.7 9.5 - - - +
187B MET* 2.9 17.3 + - - +
188B ARG 4.0 0.7 - - - +
190B PHE* 1.3 89.0 - - - +
192B ASP* 1.3 56.5 + - - +
194B LEU 3.2 1.4 + - - -
195B ALA* 3.0 24.6 + - - +
204B ILE* 3.9 16.0 - - - +
212B MET* 3.5 14.3 - - - +
12C TYR* 3.0 31.0 + - - +
16C LEU* 4.5 1.3 - - - -
17C PHE* 3.4 17.7 - - + -
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG 3.0 19.5 + - - +
189B ALA* 3.7 7.4 - - - +
190B PHE 3.3 0.2 - - - -
191B ASN* 1.3 72.7 - - - +
193B GLU* 1.3 67.3 + - - +
195B ALA* 3.2 19.9 + - - +
196B ASN* 3.8 4.5 + - - +
302B IOD 4.1 20.4 - - + +
15C LYS* 5.3 6.1 + - - -
16C LEU* 4.6 14.2 - - + +
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Residues in contact with GLU 193 (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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143B LEU* 5.1 4.5 - - + -
146B LEU* 3.5 25.6 - - + -
150B LYS* 3.4 23.7 + - - +
189B ALA 2.9 18.1 + - - +
190B PHE 3.8 4.3 - - - +
192B ASP* 1.3 77.8 + - - +
194B LEU* 1.3 56.7 + - - +
196B ASN* 3.1 26.8 + - - +
199B LYS* 3.6 15.7 + - - +
200B TYR* 2.8 42.6 + - + +
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Residues in contact with LEU 194 (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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146B LEU* 3.8 17.0 - - + -
159B ILE* 4.2 10.8 - - + -
190B PHE* 3.1 51.0 + - + +
191B ASN 3.2 4.5 + - - +
193B GLU* 1.3 74.6 - - - +
195B ALA* 1.3 57.6 + - - +
196B ASN 3.2 2.1 + - - +
200B TYR* 3.6 44.9 - - + +
202B SER* 2.7 30.7 + - - +
212B MET* 3.7 28.9 - - + -
214B SER* 3.7 11.4 - - - +
17C PHE* 3.9 2.2 - - - -
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Residues in contact with ALA 195 (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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191B ASN 3.0 11.5 + - - +
192B ASP* 3.5 13.0 - - - +
193B GLU 3.1 1.0 - - - -
194B LEU* 1.3 74.8 - - - +
196B ASN* 1.3 60.1 + - - +
197B LYS* 3.1 17.0 + - - +
200B TYR 5.5 0.2 - - - -
16C LEU* 3.3 42.8 - - + +
17C PHE* 3.6 12.6 - - + -
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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