Contacts of the helix formed by residues 166 - 176 (chain D) in PDB entry 2BM9
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 PHE 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D ASN* 3.1 1.2 - - - +
165D THR* 1.3 81.9 - - - +
167D ASN* 1.3 55.0 + - - +
168D ILE 3.2 1.3 - - - -
169D MET* 3.2 33.1 - - + +
170D LYS* 2.8 32.4 + - - +
185D ILE* 5.5 3.4 - - + -
192D TRP* 4.2 21.1 - + - -
200D PHE* 3.9 27.1 - + - -
203D TYR* 3.9 31.0 - + + -
204D LEU* 4.1 11.9 - - + -
207D PHE* 4.1 12.1 - + - -
9F PHE* 3.6 31.1 - + + -
10F GLN 5.0 4.5 - - - +
12F LEU* 3.5 26.5 - - + -
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Residues in contact with ASN 167 (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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142D LEU* 3.6 17.7 - - + +
164D ASN* 3.1 38.0 + - - +
166D PHE* 1.3 75.9 - - - +
168D ILE* 1.3 59.5 + - - +
170D LYS* 3.7 17.3 + - - +
171D TRP* 3.1 23.9 + - - +
7F GLN 5.6 0.5 - - - +
8F ASN* 4.3 13.6 + - - +
9F PHE* 3.5 37.8 + - - +
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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
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88D LEU* 3.9 13.0 - - + -
139D CYS* 3.4 28.0 - - + +
142D LEU* 4.1 10.3 - - + -
145D PHE* 3.5 35.7 - - + -
157D PHE* 3.9 33.7 - - + -
163D ALA 3.7 17.7 - - - +
164D ASN 3.2 7.5 + - - +
165D THR* 4.5 6.5 - - + -
166D PHE 3.2 0.6 - - - -
167D ASN* 1.3 73.7 - - - +
169D MET* 1.3 61.2 + - - +
170D LYS 3.3 0.2 - - - -
171D TRP* 3.5 9.2 + - + +
172D ALA* 3.0 27.5 + - - +
183D PHE* 4.5 3.6 - - + -
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Residues in contact with MET 169 (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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165D THR 3.7 13.4 + - - +
166D PHE* 3.2 27.7 + - + +
168D ILE* 1.3 78.5 - - - +
170D LYS* 1.3 61.4 - - - +
172D ALA* 3.3 1.9 + - - +
173D VAL* 3.1 30.8 + - + +
183D PHE* 3.3 42.3 - - + -
185D ILE* 4.1 12.8 - - + -
204D LEU* 3.9 28.3 - - + -
207D PHE* 3.6 31.6 - - + -
211D LEU* 4.4 7.2 - - + -
229D LEU* 3.9 13.5 - - + -
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Residues in contact with LYS 170 (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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166D PHE 2.8 19.9 + - - +
167D ASN* 3.7 18.0 + - - +
168D ILE 3.3 0.2 - - - -
169D MET* 1.3 72.0 - - - +
171D TRP* 1.3 62.3 + - - +
173D VAL* 3.8 1.8 + - - +
174D ASP* 3.5 30.0 + - - +
207D PHE* 4.1 12.5 - - + -
4F TYR* 3.7 30.2 + - + +
5F SER* 3.9 23.8 + - - +
6F ARG 4.9 0.4 - - - -
7F GLN 3.0 22.4 + - - +
9F PHE* 3.7 16.8 - - + -
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Residues in contact with TRP 171 (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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142D LEU* 3.9 25.3 + - + -
145D PHE* 3.2 62.1 - + + -
146D GLU* 4.2 15.5 - - + +
148D LEU* 4.6 11.9 - - + -
157D PHE* 5.0 3.6 - + - -
167D ASN 3.1 17.1 + - - +
168D ILE* 3.9 10.8 - - + +
169D MET 3.2 0.2 - - - -
170D LYS* 1.3 76.7 - - - +
172D ALA* 1.3 74.0 + - + +
174D ASP* 3.5 1.9 + - - -
175D HIS* 3.0 74.7 + + + +
176D LEU* 4.2 30.3 - - + -
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Residues in contact with ALA 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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157D PHE* 5.3 3.1 - - + -
168D ILE 3.0 18.0 + - - +
169D MET 3.3 4.5 + - - +
171D TRP* 1.3 89.1 - - + +
173D VAL* 1.3 58.0 + - - +
176D LEU* 2.9 34.7 + - + -
177D LEU* 3.0 30.1 + - + -
183D PHE* 3.9 20.6 - - + -
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Residues in contact with VAL 173 (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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169D MET* 3.1 18.8 + - + +
170D LYS 4.2 3.4 - - - +
172D ALA* 1.3 77.6 - - - +
174D ASP* 1.3 60.5 - - - +
175D HIS 3.5 0.2 + - - -
176D LEU 4.4 0.7 + - - -
177D LEU* 4.1 20.1 - - + +
207D PHE* 3.9 12.1 - - + -
210D VAL* 3.6 33.9 - - + -
211D LEU* 3.9 28.9 - - + -
231D ARG* 3.0 37.0 + - - +
4F TYR* 4.1 14.1 - - + +
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Residues in contact with ASP 174 (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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170D LYS* 3.5 20.3 + - - +
171D TRP* 5.2 0.2 - - - -
172D ALA 3.4 0.2 - - - -
173D VAL* 1.3 79.0 - - - +
175D HIS* 1.3 75.0 + - + +
231D ARG* 5.7 0.3 + - - -
4F TYR* 2.6 44.4 + - - -
5F SER* 3.9 13.4 + - - -
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Residues in contact with HIS 175 (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 GLU* 5.7 4.8 - - + +
150D GLU* 4.4 12.6 - - - +
171D TRP* 3.0 55.9 + + + +
174D ASP* 1.3 96.6 - - + +
176D LEU* 1.3 57.0 + - - +
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Residues in contact with LEU 176 (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 VAL* 6.5 0.4 - - + -
148D LEU* 5.2 11.7 - - + +
149D ARG 4.7 13.7 - - - +
150D GLU* 4.3 15.7 - - - +
151D MET* 5.6 0.9 - - + +
153D HIS* 3.1 22.3 - - - +
155D LEU* 3.8 29.2 - - + -
157D PHE* 4.2 21.8 - - + -
171D TRP* 4.2 25.4 - - + -
172D ALA* 2.9 17.0 + - + +
173D VAL 4.4 0.8 + - - -
174D ASP 3.9 0.2 - - - -
175D HIS* 1.3 81.5 - - + +
177D LEU* 1.3 83.7 + - + +
178D GLU* 3.3 4.7 + - - +
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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