Contacts of the helix formed by residues 164 - 176 (chain J) in PDB entry 2BM8
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 164 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J CYS 3.0 28.8 + - - +
140J SER* 3.8 20.5 - - - +
142J LEU* 4.5 7.1 - - - +
162J HIS 4.1 0.6 + - - -
163J ALA* 1.3 72.1 - - - +
165J THR* 1.3 63.4 + - - +
166J PHE 3.4 3.3 + - - -
167J ASN* 2.5 41.1 + - - +
168J ILE* 3.2 19.6 + - - +
9L PHE 5.2 2.3 - - - +
11L ASP* 3.7 17.6 + - - +
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Residues in contact with THR 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J ASP* 3.3 23.0 + - - +
162J HIS* 3.2 32.5 + - - -
163J ALA 3.7 2.6 + - - -
164J ASN* 1.3 77.7 - - - +
166J PHE* 1.3 61.7 + - + +
168J ILE* 3.2 10.4 + - + +
169J MET* 3.0 27.6 + - - +
183J PHE* 4.4 9.6 - - + -
185J ILE* 4.0 24.2 - - + -
192J TRP* 3.8 19.4 - - + -
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Residues in contact with PHE 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J ASN 3.4 1.0 - - - -
165J THR* 1.3 76.7 - - + +
167J ASN* 1.3 63.0 + - - +
169J MET* 3.5 27.6 + - - +
170J LYS* 3.2 17.8 + - - +
185J ILE* 5.7 2.7 - - + -
192J TRP* 4.3 19.7 - + - -
200J PHE* 3.7 28.5 - + - -
203J TYR* 3.8 32.1 - + + -
204J LEU* 4.2 17.3 - - + -
207J PHE* 3.8 18.6 - + - -
9L PHE* 3.6 31.9 - + + -
10L GLN 5.3 3.4 - - - -
12L LEU* 3.6 26.9 - - + -
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Residues in contact with ASN 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 4.2 15.7 - - + +
164J ASN* 2.5 40.0 + - - +
165J THR 3.4 0.2 - - - -
166J PHE* 1.3 74.8 - - - +
168J ILE* 1.3 59.5 - - - +
170J LYS* 3.1 16.9 + - + +
171J TRP* 2.9 28.1 + - - +
7L GLN 5.2 0.9 - - - +
8L ASN* 5.7 2.5 + - - +
9L PHE* 3.5 31.5 + - - +
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Residues in contact with ILE 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J LEU* 4.1 14.1 - - + -
139J CYS* 3.9 11.7 - - + +
142J LEU* 4.1 14.4 - - + -
145J PHE* 3.8 36.3 - - + -
157J PHE* 3.9 34.5 - - + -
163J ALA 3.4 17.5 - - - +
164J ASN 3.3 16.8 - - - +
165J THR* 3.2 11.3 + - + +
167J ASN* 1.3 77.7 - - - +
169J MET* 1.3 50.6 + - - +
171J TRP* 3.3 4.6 + - + +
172J ALA* 2.8 33.7 + - + +
183J PHE* 4.0 6.1 - - + -
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Residues in contact with MET 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J THR* 3.0 11.3 + - - +
166J PHE* 3.5 32.1 - - - +
167J ASN 3.2 0.2 - - - -
168J ILE* 1.3 75.8 - - - +
170J LYS* 1.3 53.5 + - - +
172J ALA* 3.2 1.4 + - - +
173J VAL* 2.8 39.3 + - - +
183J PHE* 3.4 35.2 - - + -
185J ILE* 4.3 18.6 - - - -
204J LEU* 4.3 7.0 - - + -
207J PHE* 3.8 24.9 - - + -
211J LEU* 3.3 32.1 - - + -
229J LEU* 3.6 20.9 - - + -
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Residues in contact with LYS 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 6.2 3.1 - - + +
166J PHE 3.2 10.0 + - - +
167J ASN* 3.1 20.6 + - - +
169J MET* 1.3 75.7 - - - +
171J TRP* 1.3 66.8 + - - +
173J VAL* 3.3 1.3 + - - +
174J ASP* 3.1 40.3 + - - +
207J PHE* 4.0 10.0 - - + -
4L TYR* 3.7 31.0 - - + +
5L SER* 3.3 25.8 + - - +
7L GLN 5.6 2.7 + - - +
9L PHE* 5.0 3.1 - - + -
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Residues in contact with TRP 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LEU* 4.0 36.0 + - + +
145J PHE* 3.1 57.4 - + + -
146J GLU* 3.8 23.2 + - - -
148J LEU* 3.7 15.3 - - + -
149J ARG* 4.3 11.1 - - + +
157J PHE* 4.9 2.5 - + - -
167J ASN 2.9 12.4 + - - +
168J ILE* 3.6 9.9 - - + +
170J LYS* 1.3 78.6 - - - +
172J ALA* 1.3 65.0 + - + +
174J ASP* 5.2 0.4 - - - -
175J HIS* 3.0 66.6 + + + +
176J LEU* 3.7 29.2 - - + -
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Residues in contact with ALA 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J PHE* 5.2 2.2 - - + -
168J ILE* 2.8 21.6 + - + +
169J MET 3.6 4.3 - - - +
170J LYS 3.2 0.2 - - - -
171J TRP* 1.3 84.1 - - + +
173J VAL* 1.3 61.8 + - - +
176J LEU* 3.0 14.0 + - + -
177J LEU* 2.7 47.6 + - + -
183J PHE* 3.7 23.1 - - + -
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Residues in contact with VAL 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J MET 2.8 21.5 + - - +
170J LYS 3.3 3.3 + - - +
172J ALA* 1.3 79.1 - - - +
174J ASP* 1.3 63.2 + - - +
176J LEU 4.3 0.2 + - - -
177J LEU* 3.9 23.1 + - + +
207J PHE* 4.3 3.8 - - + -
210J VAL* 3.9 20.2 - - + -
211J LEU* 3.9 29.6 - - + -
231J ARG* 3.3 33.8 + - - +
4L TYR* 3.6 28.5 - - + +
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Residues in contact with ASP 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J LYS* 3.1 30.2 + - - +
171J TRP* 5.2 0.4 - - - -
173J VAL* 1.3 77.1 - - - +
175J HIS* 1.3 80.5 + - + +
231J ARG* 5.3 0.7 - - - +
4L TYR* 2.8 39.9 + - - -
5L SER* 4.5 4.8 + - - -
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Residues in contact with HIS 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J ARG* 3.0 51.6 + - - +
171J TRP* 3.0 47.1 + + - +
174J ASP* 1.3 96.2 - - + +
176J LEU* 1.3 58.8 + - - +
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J LEU* 3.2 54.3 - - + +
149J ARG* 4.0 11.0 - - + +
153J HIS* 2.9 31.3 + - + +
155J LEU* 4.3 23.8 - - + -
157J PHE* 4.2 18.2 - - + -
171J TRP* 3.7 16.2 - - + -
172J ALA* 3.0 18.6 + - + +
173J VAL 4.3 0.2 + - - -
174J ASP 3.8 1.4 - - - -
175J HIS* 1.3 79.3 - - - +
177J LEU* 1.3 67.9 + - + +
178J GLU* 4.3 2.1 - - - +
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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