Contacts of the helix formed by residues 166 - 183 (chain D) in PDB entry 5OMA
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 ASN 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D GLU* 4.7 4.4 + - - -
162D MET* 3.8 20.3 - - + +
163D PRO* 3.1 34.1 + - + +
165D THR* 1.3 77.8 + - - +
167D PRO* 1.4 68.2 - - - +
168D ILE* 2.8 49.0 + - - +
169D ARG* 3.2 12.2 + - + +
170D LEU* 3.0 25.2 + - - +
208D LEU* 6.0 0.2 - - - -
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Residues in contact with PRO 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D THR 3.7 2.7 - - - +
166D ASN* 1.4 92.2 - - - +
168D ILE* 1.4 53.3 + - + +
170D LEU* 4.3 2.5 - - + -
171D GLY* 2.8 29.1 + - - -
212D SER* 4.6 16.6 - - - +
215D ASP* 4.3 19.7 - - + +
216D SER* 3.3 18.4 - - - +
219D ILE* 3.5 26.6 - - + +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLU* 4.1 20.0 - - + +
118D VAL* 3.9 27.1 - - + -
119D PHE* 5.6 2.5 - - - +
122D LYS* 6.4 2.2 - - + -
162D MET* 3.9 17.3 - - + -
166D ASN* 2.8 33.7 + - - +
167D PRO* 1.4 72.7 - - + +
169D ARG* 1.4 54.5 + - - +
171D GLY* 3.3 1.3 + - - -
172D LEU* 2.8 36.9 + - + +
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Residues in contact with ARG 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D MET* 5.2 0.6 - - - +
158D SER* 3.4 39.0 - - - +
159D LYS* 3.3 45.4 + - + +
162D MET* 3.3 21.1 + - + -
163D PRO 3.3 15.7 - - - -
164D PRO* 3.5 33.3 + - - +
166D ASN* 3.2 19.9 + - + +
168D ILE* 1.4 74.5 - - - +
170D LEU* 1.3 65.0 + - + +
172D LEU* 3.4 6.2 + - - +
173D ALA* 3.0 26.3 + - + +
197D THR* 5.5 7.2 - - + +
200D GLU* 3.4 25.7 + - - +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PRO 3.5 19.1 - - - +
165D THR* 3.5 26.0 - - - +
166D ASN 3.0 14.6 + - - +
167D PRO* 3.8 4.5 - - + +
169D ARG* 1.3 74.6 - - + +
171D GLY* 1.3 52.4 + - - +
173D ALA* 3.2 6.4 + - - +
174D LEU* 2.9 35.3 + - - +
197D THR* 3.8 21.4 - - + +
201D ALA* 3.7 17.3 - - + -
216D SER* 3.7 32.5 - - - +
219D ILE* 3.6 17.6 - - + +
220D MET* 4.5 10.5 - - + -
223D LEU* 5.6 2.9 - - + -
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Residues in contact with GLY 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LYS* 5.6 3.1 - - - -
167D PRO 2.8 21.5 + - - -
168D ILE* 3.7 1.8 - - - -
170D LEU* 1.3 70.5 - - - +
172D LEU* 1.3 56.0 + - - +
174D LEU* 3.5 4.5 + - - +
175D ASN* 3.1 38.5 + - - +
219D ILE* 4.0 14.1 - - - +
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Residues in contact with LEU 172 (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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118D VAL* 4.0 16.2 - - + -
122D LYS* 5.3 17.9 - - + +
151D TYR* 4.0 30.5 - - + +
154D ALA* 3.6 26.5 - - + +
155D MET* 3.8 15.9 - - + -
158D SER* 3.4 31.9 - - - +
168D ILE* 2.8 17.1 + - + +
169D ARG* 3.6 4.0 - - - +
171D GLY* 1.3 73.4 - - - +
173D ALA* 1.4 55.8 + - - +
175D ASN* 3.5 5.5 + - - +
176D PHE* 2.9 38.3 + - + +
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D MET* 3.9 21.1 - - + -
169D ARG* 3.0 19.0 + - + +
170D LEU 3.5 4.3 - - - +
172D LEU* 1.4 72.7 - - - +
174D LEU* 1.3 59.9 + - - +
176D PHE* 3.3 1.2 + - - -
177D SER* 2.9 31.2 + - - -
193D LEU* 3.6 8.7 - - + +
194D ALA* 6.5 0.9 - - - -
197D THR* 3.6 33.9 - - + +
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU 2.9 16.8 + - - +
171D GLY* 3.6 5.8 - - - +
173D ALA* 1.3 75.5 - - - +
175D ASN* 1.3 68.7 + - - +
177D SER* 2.9 22.2 + - - +
178D VAL* 3.1 17.1 + - + +
197D THR* 5.5 0.6 - - - +
219D ILE* 3.9 17.5 - - + +
222D LEU* 3.8 36.8 - - + +
223D LEU* 3.8 29.8 - - + -
226D ASN* 3.4 29.2 - - - +
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Residues in contact with ASN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LYS* 3.5 31.9 - - - +
126D ASP* 5.5 0.4 + - - -
129D ARG* 6.1 1.2 - - - +
151D TYR* 6.1 7.2 - - + -
171D GLY* 3.1 17.8 + - - +
172D LEU* 3.9 4.9 - - - +
174D LEU* 1.3 82.7 - - - +
176D PHE* 1.3 60.6 + - - +
178D VAL* 3.2 10.2 + - - +
179D PHE* 2.9 28.3 + - - +
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Residues in contact with PHE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 3.2 32.8 - - + -
151D TYR* 3.5 30.0 - + + -
152D GLN* 3.2 38.8 - - + -
155D MET* 3.4 24.5 - - + -
172D LEU* 2.9 20.9 + - + +
173D ALA 3.3 3.8 + - - +
175D ASN* 1.3 75.0 - - - +
177D SER* 1.4 56.2 + - - +
179D PHE* 3.4 34.2 - + - +
180D HIS* 3.0 46.9 + + - -
193D LEU* 4.0 7.0 - - + -
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ALA 2.9 14.9 + - - -
174D LEU* 2.9 21.0 + - - +
176D PHE* 1.4 75.0 - - - +
178D VAL* 1.4 57.6 + - - +
180D HIS* 3.2 5.2 + - - -
181D TYR* 3.0 24.8 + - - +
190D ALA* 3.2 33.1 - - - +
193D LEU* 3.6 15.8 - - - +
194D ALA* 4.3 9.3 - - - +
223D LEU* 5.0 0.3 - - - +
230D TRP* 3.6 15.8 - - - -
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D LEU* 3.1 19.2 + - + +
175D ASN* 3.2 11.4 + - - +
177D SER* 1.4 76.0 + - - +
179D PHE* 1.3 59.4 + - - +
181D TYR* 3.3 0.9 + - - +
182D GLU* 2.9 57.6 + - + +
183D ILE* 6.4 0.4 - - + -
226D ASN* 4.0 23.3 - - - +
230D TRP* 4.0 13.9 - - + -
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Residues in contact with PHE 179 (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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129D ARG* 4.2 14.8 - - + +
144D ILE* 3.3 33.4 - - + -
147D ALA* 4.1 9.6 - - + -
148D ARG* 3.6 32.8 - - + -
151D TYR* 3.8 22.2 - + + -
175D ASN 2.9 13.4 + - - +
176D PHE* 3.4 31.9 - + + +
178D VAL* 1.3 74.8 - - - +
180D HIS* 1.3 68.0 + + - +
183D ILE* 3.0 52.2 + - + +
184D ALA* 3.1 18.2 + - + -
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Residues in contact with HIS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 4.5 13.8 + - + +
152D GLN* 5.1 3.1 + - - -
176D PHE* 3.0 57.9 + + - -
177D SER* 3.2 10.7 + - - +
179D PHE* 1.3 83.4 - + - +
181D TYR* 1.3 57.0 + - - +
184D ALA* 3.7 8.8 - - + +
185D ASN 3.0 13.0 + - - -
186D SER* 2.9 40.2 + - - +
189D GLU* 3.7 42.1 + - + +
190D ALA* 3.8 6.7 - - + +
193D LEU* 4.1 10.5 - - + +
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Residues in contact with TYR 181 (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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177D SER 3.0 7.9 + - - +
178D VAL 3.9 1.3 - - - +
180D HIS* 1.3 78.6 - - - +
182D GLU* 1.3 74.8 + - + +
185D ASN* 3.5 24.3 + - - +
186D SER 4.4 2.5 - - - -
187D PRO* 3.6 37.5 - - + -
190D ALA* 3.6 12.9 - - + +
191D ILE* 5.3 1.1 - - + -
229D LEU 5.6 0.2 + - - -
230D TRP* 3.4 68.8 + + + -
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Residues in contact with GLU 182 (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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178D VAL* 2.9 42.8 + - + +
181D TYR* 1.3 92.3 - - + +
183D ILE* 1.3 74.6 + - + +
185D ASN* 3.8 10.5 - - - +
229D LEU* 6.0 0.9 - - - +
230D TRP* 4.3 11.3 + - - -
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Residues in contact with ILE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ARG* 4.6 20.2 - - + +
132D ALA* 5.8 3.1 - - + -
144D ILE* 3.9 34.6 - - + +
178D VAL* 6.4 0.4 - - + -
179D PHE* 3.0 42.6 + - + +
182D GLU* 1.3 87.3 - - + +
184D ALA* 1.3 65.1 + - - +
185D ASN* 3.2 4.1 + - - +
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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