Contacts of the helix formed by residues 182 - 193 (chain D) in PDB entry 1BQ4
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 GLY 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ARG* 4.0 34.5 - - - +
8D HIS* 5.4 0.8 + - - -
86D GLU* 3.9 5.6 + - - -
181D HIS* 1.3 75.0 - - - +
183D ASN* 1.3 57.6 + - - +
186D ARG* 2.9 44.3 + - - +
205D ILE* 3.7 3.9 - - - +
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Residues in contact with ASN 183 (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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86D GLU* 3.0 27.6 + - - +
87D ARG* 3.1 53.3 + - + +
89D TYR* 4.7 6.3 - - - -
151D LEU* 3.4 20.7 - - + +
154D VAL* 4.2 3.6 - - + -
182D GLY* 1.3 71.5 - - - +
184D SER* 1.3 58.1 + - - +
186D ARG* 2.9 28.3 + - - +
187D GLY* 2.5 36.2 + - - -
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Residues in contact with SER 184 (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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84D LEU* 2.9 21.8 + - - -
85D ASN 2.9 22.4 + - - -
86D GLU* 4.8 0.2 + - - -
154D VAL* 3.7 15.0 - - - +
158D LEU* 3.7 24.0 - - - +
180D ALA* 3.5 2.6 - - - +
181D HIS* 3.4 18.7 + - - +
183D ASN* 1.3 75.9 - - - +
185D LEU* 1.3 59.2 + - - +
187D GLY 3.5 0.9 + - - -
188D LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 185 (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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5D LEU* 3.5 50.0 - - + -
6D VAL 3.7 27.1 - - - +
7D ARG* 4.2 4.5 - - + +
84D LEU* 5.3 1.6 - - + -
178D ILE* 4.2 12.6 - - + +
180D ALA* 4.1 21.3 - - + +
181D HIS 3.2 23.6 + - - +
184D SER* 1.3 75.5 - - - +
186D ARG* 1.3 61.1 + - - +
188D LEU* 3.3 11.5 + - + +
189D VAL* 2.8 34.3 + - - +
205D ILE* 3.6 17.7 - - + -
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Residues in contact with ARG 186 (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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7D ARG* 5.5 3.6 - - - +
87D ARG* 5.7 1.0 - - - +
113D ARG 5.8 2.2 + - - -
114D ARG* 6.1 1.3 - - - +
151D LEU* 4.1 15.0 - - + +
182D GLY* 2.9 27.7 + - - +
183D ASN* 2.9 28.8 + - - +
185D LEU* 1.3 73.9 - - - +
187D GLY* 1.3 61.3 - - - +
189D VAL* 3.8 5.1 - - - -
190D LYS* 2.9 31.4 + - - +
200D ILE* 3.3 35.7 + - + +
201D ALA* 4.3 8.3 + - - +
203D LEU* 3.3 32.3 + - + -
204D ASN* 5.0 0.7 - - - +
205D ILE* 3.2 26.9 - - + +
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Residues in contact with GLY 187 (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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151D LEU* 4.0 8.7 - - - +
154D VAL* 5.1 1.8 - - - -
155D ILE* 3.7 37.0 - - - +
158D LEU* 5.2 2.5 - - - -
183D ASN 2.5 22.3 + - - -
184D SER* 3.7 2.9 - - - -
186D ARG* 1.3 75.1 - - - +
188D LEU* 1.3 61.1 + - - +
190D LYS* 3.6 4.1 - - - +
191D HIS* 3.6 14.9 + - - +
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Residues in contact with LEU 188 (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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5D LEU* 4.3 12.8 - - + -
84D LEU* 5.6 1.1 - - + -
158D LEU* 4.0 25.3 - - + +
159D LEU* 5.3 1.6 - - + -
162D TRP* 3.8 38.1 - - + -
166D ILE* 5.3 0.9 - - + -
178D ILE* 3.4 31.9 - - + -
184D SER 2.9 17.0 + - - +
185D LEU* 3.7 12.3 - - + +
186D ARG 3.2 0.2 - - - -
187D GLY* 1.3 77.0 - - - +
189D VAL* 1.3 52.3 + - + +
191D HIS* 3.0 17.0 + - + +
192D LEU* 2.9 50.0 + - + +
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Residues in contact with VAL 189 (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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5D LEU* 3.9 22.9 - - + -
185D LEU 2.8 28.5 + - - +
186D ARG* 3.8 4.5 - - - +
188D LEU* 1.3 73.2 - - - +
190D LYS* 1.3 63.5 + - - +
192D LEU* 3.9 7.4 - - - +
193D GLU* 3.0 40.0 + - - +
195D ILE* 3.8 6.3 - - + +
203D LEU* 3.7 27.6 - - + -
205D ILE* 5.0 4.3 - - + -
211D LEU* 4.4 12.3 - - + -
213D PHE* 4.0 17.3 - - + -
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Residues in contact with LYS 190 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.7 23.4 - - + -
151D LEU* 5.1 0.7 - - + -
155D ILE* 3.4 25.6 - - + -
186D ARG 2.9 18.3 + - - +
187D GLY 3.6 6.3 - - - +
189D VAL* 1.3 74.5 - - - +
191D HIS* 1.4 55.3 + - - +
194D GLY* 2.9 30.3 + - - -
195D ILE* 2.8 51.3 + - + +
196D SER* 4.2 0.4 - - - +
197D ASP* 3.5 33.5 + - - +
200D ILE* 3.9 22.9 - - + -
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Residues in contact with HIS 191 (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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141B ASP* 4.1 12.9 + - - -
143B ASN* 5.1 10.3 + - + -
155D ILE* 5.1 4.7 - - + -
159D LEU* 4.0 31.1 - - + +
162D TRP* 3.9 28.2 + + - -
163D GLN* 5.5 2.7 - - - -
187D GLY 3.6 7.8 + - - +
188D LEU* 3.0 13.0 + - + +
190D LYS* 1.4 79.9 - - - +
192D LEU* 1.3 80.5 + - + +
193D GLU 3.4 0.2 + - - -
194D GLY* 3.8 4.7 + - - -
219D LEU 5.3 2.6 + - - -
220D LYS* 4.0 24.1 + - - -
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Residues in contact with LEU 192 (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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3D LEU* 4.0 22.0 - - + -
5D LEU* 4.8 1.6 - - + -
162D TRP* 3.7 30.7 - - + -
188D LEU* 2.9 37.8 + - + +
189D VAL* 3.9 5.2 - - - +
191D HIS* 1.3 82.6 - - + +
193D GLU* 1.3 58.5 + - - +
213D PHE* 4.0 35.7 - - + -
215D LEU* 4.4 10.3 - - + -
219D LEU 3.9 15.3 - - - +
220D LYS* 4.3 12.0 + - - +
221D PRO* 3.3 24.0 - - + +
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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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189D VAL* 3.0 29.3 + - - +
192D LEU* 1.3 78.7 - - - +
194D GLY* 1.3 61.4 + - - +
195D ILE* 3.5 15.6 + - + +
203D LEU* 5.4 2.1 - - - +
213D PHE* 3.4 17.3 - - + -
221D PRO* 4.1 15.9 - - + +
224D PRO* 5.2 2.1 - - - +
225D SER* 3.1 30.1 + - - -
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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
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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