Contacts of the helix formed by residues 180 - 195 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 5.0 1.4 - - - -
178D LYS 4.2 0.2 + - - -
179D VAL* 1.3 74.2 - - - +
181D SER* 1.3 58.3 + - - +
182D ASN* 3.6 2.6 - - - +
183D ALA* 3.0 28.4 + - - +
184D HIS* 2.9 27.5 + - - +
303D IOD 3.8 13.3 - - - +
323D GOL 2.6 41.6 + - - -
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.1 24.1 - - - +
144A ALA* 4.2 7.6 - - - +
175D PRO* 3.9 23.1 - - - +
176D THR 5.2 1.2 + - - -
179D VAL 3.3 3.2 + - - -
180D SER* 1.3 69.8 - - - +
182D ASN* 1.3 60.7 + - - +
184D HIS* 3.7 6.6 + - - +
185D ALA* 2.9 32.2 + - - +
323D GOL 3.1 18.9 + - - -
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Residues in contact with ASN 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.5 10.2 - - - +
138A ASN* 5.5 0.6 - - - +
140A SER 4.4 3.6 - - - +
141A SER* 2.7 36.6 + - - -
144A ALA* 3.6 14.2 - - - +
140D SER* 3.9 19.2 - - - +
180D SER* 3.6 2.2 - - - +
181D SER* 1.3 77.2 - - - +
183D ALA* 1.3 61.8 + - - +
185D ALA* 3.5 2.4 + - - +
186D SER* 3.1 24.9 + - - -
323D GOL 2.8 26.0 + - - +
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 4.1 23.4 - - + +
140D SER* 3.9 12.5 - - - +
166D LEU* 3.7 11.4 - - + +
180D SER* 3.0 27.7 + - - +
182D ASN* 1.3 75.8 - - - +
184D HIS* 1.3 58.6 + - - +
186D SER* 3.3 2.3 + - - -
187D MET* 2.9 31.9 + - - +
303D IOD 4.1 9.2 - - + -
320D IOD 4.1 6.7 - - + -
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Residues in contact with HIS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 5.2 3.4 + - - -
166D LEU* 3.4 13.0 - - + +
169D SER* 3.0 34.4 + - - -
170D VAL* 4.2 4.9 - - - -
172D ASP 2.9 29.1 + - - -
173D GLU 3.4 18.2 - - - -
175D PRO* 3.6 39.2 - - + +
179D VAL* 4.1 2.0 - - + -
180D SER 2.9 17.2 + - - +
181D SER 3.7 4.2 + - - +
183D ALA* 1.3 77.2 - - - +
185D ALA* 1.3 59.5 + - - +
187D MET* 3.3 1.0 + - - +
188D ARG* 2.9 52.6 + - + +
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.6 14.7 - - + +
144A ALA* 4.0 23.3 - - + +
147A ASN* 3.6 25.0 - - + +
181D SER 2.9 18.1 + - - +
182D ASN* 3.9 4.3 - - - +
184D HIS* 1.3 77.7 + - - +
186D SER* 1.3 62.3 + - - +
188D ARG* 3.6 3.9 + - - +
189D ALA* 3.2 23.9 + - - +
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Residues in contact with SER 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS 3.2 17.7 + - - -
140D SER 3.4 16.2 + - - -
142D TYR* 3.4 3.6 + - - +
143D LEU* 3.3 24.9 + - - +
182D ASN 3.1 18.1 + - - -
183D ALA 3.6 3.8 - - - -
185D ALA* 1.3 78.4 - - - +
187D MET* 1.3 57.4 + - - +
189D ALA* 3.4 3.2 + - - +
190D PHE* 2.9 28.3 + - - +
316D IOD 3.9 15.7 - - - +
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Residues in contact with MET 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 3.8 28.0 - - + +
142D TYR* 3.4 41.3 - - + -
163D ASN 3.5 17.0 - - - +
164D THR* 3.6 39.5 - - - +
166D LEU* 4.3 15.0 - - + -
170D VAL* 4.0 10.8 - - + -
183D ALA 2.9 15.7 + - - +
184D HIS 4.0 2.0 - - - +
186D SER* 1.3 73.5 - - - +
188D ARG* 1.3 66.7 + - - +
190D PHE* 3.5 6.2 - - - +
191D ASN* 2.9 26.1 + - - +
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Residues in contact with ARG 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 5.5 2.9 - - - +
170D VAL* 2.9 37.6 + - + +
171D PHE* 3.7 14.8 + - - +
172D ASP 3.8 3.6 + - - -
173D GLU* 3.7 34.4 + - - +
184D HIS* 2.9 49.5 + - + +
185D ALA* 3.8 6.3 - - - +
187D MET* 1.3 77.3 - - - +
189D ALA* 1.3 56.8 + - - +
191D ASN* 4.0 2.4 - - - +
192D ASP* 3.0 30.2 + - - +
317D IOD 3.7 30.7 - - - +
322D IOD 4.2 10.1 - - + +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.1 10.5 - - + -
189A ALA* 5.0 4.7 - - + -
321A EDO 5.2 2.5 - - - +
143D LEU* 3.9 27.9 - - + +
185D ALA 3.2 14.7 + - - +
186D SER 3.9 3.1 - - - +
187D MET 3.2 0.4 - - - -
188D ARG* 1.3 76.2 - - - +
190D PHE* 1.3 61.4 + - - +
192D ASP* 3.7 5.7 - - - +
193D GLU* 2.9 31.9 + - - +
322D IOD 4.4 4.2 - - - +
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Residues in contact with PHE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ILE* 4.0 16.6 - - + -
142D TYR* 3.4 41.3 - + + -
143D LEU* 4.0 10.0 - - - +
146D LEU* 3.8 21.9 - - + +
159D ILE* 4.6 4.3 - - + -
161D ALA* 3.7 20.9 - - + -
164D THR* 3.9 19.7 - - + -
186D SER 2.9 18.6 + - - +
187D MET* 3.5 13.9 - - - +
189D ALA* 1.3 77.0 - - - +
191D ASN* 1.3 75.5 + - - +
193D GLU* 3.4 2.3 + - - +
194D LEU* 3.1 51.4 + - + +
212D MET* 4.1 4.9 - - + -
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Residues in contact with ASN 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D THR* 2.9 33.5 + - - -
170D VAL* 3.7 20.8 - - + +
187D MET* 2.9 13.9 + - - +
188D ARG* 4.0 3.8 - - - +
190D PHE* 1.3 92.6 - - - +
192D ASP* 1.3 57.1 + - - +
194D LEU* 3.2 3.1 + - - +
195D ALA* 3.0 28.7 + - - +
204D ILE* 3.9 17.9 - - + +
212D MET* 3.5 18.5 - - + +
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Residues in contact with ASP 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ARG 3.0 20.5 + - - +
189D ALA* 3.7 4.0 - - - +
190D PHE 3.2 0.2 - - - -
191D ASN* 1.3 73.5 - - - +
193D GLU* 1.3 67.8 + - - +
195D ALA* 3.2 21.3 + - - +
196D ASN* 3.8 4.0 + - - +
322D IOD 4.1 18.8 - - + -
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Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A EDO 4.9 14.3 - - - +
143D LEU* 5.1 4.5 - - + -
146D LEU* 3.5 25.1 - - + -
150D LYS* 3.4 22.8 + - - +
189D ALA 2.9 17.8 + - - +
190D PHE 3.8 3.4 - - - +
192D ASP* 1.3 77.0 + - - +
194D LEU* 1.3 56.8 + - - +
195D ALA 3.1 0.2 - - - -
196D ASN* 3.1 26.8 + - - +
199D LYS* 3.6 17.5 + - - +
200D TYR* 2.8 42.5 + - + +
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.8 18.4 - - + -
159D ILE* 4.2 9.6 - - + -
190D PHE* 3.1 52.5 + - + +
191D ASN 3.2 4.4 + - - +
193D GLU* 1.3 74.4 - - - +
195D ALA* 1.3 56.0 + - - +
196D ASN 3.2 2.6 + - - +
200D TYR* 3.6 44.8 - - + +
202D SER* 2.7 31.4 + - - +
212D MET* 3.7 27.6 - - + -
214D SER* 3.7 11.7 - - - +
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ASN 3.0 12.4 + - - +
192D ASP* 3.5 17.3 - - - +
193D GLU 3.1 0.8 - - - -
194D LEU* 1.3 74.6 - - - +
196D ASN* 1.3 59.2 + - - +
197D LYS* 3.1 22.1 + - - +
200D TYR 5.4 0.2 - - - -
202D SER* 5.3 1.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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