Contacts of the helix formed by residues 162 - 179 (chain A) in PDB entry 4BT9
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 ASP 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 6.1 1.0 - - - +
122A ASP* 5.5 0.9 - - - +
157A ALA* 3.0 20.0 + - + +
158A TYR 4.6 0.2 + - - -
160A GLU* 3.1 8.7 - - + +
161A ALA* 1.3 74.1 - - - +
163A TYR* 1.3 57.0 + - - +
164A TYR* 3.4 10.0 + - - +
165A HIS* 2.7 47.6 + - - +
166A THR* 2.9 29.3 + - - -
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.7 33.1 + + - -
161A ALA* 3.4 37.9 + - + +
162A ASP* 1.3 70.4 - - - +
164A TYR* 1.3 60.1 + - - +
166A THR* 3.6 9.7 - - - -
167A GLU* 2.9 31.0 + - - +
196A TYR* 3.9 18.8 + + - -
197A ALA* 3.7 24.5 - - + +
200A GLN* 3.5 34.7 + - + -
201A GLN* 3.5 18.6 + - - +
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.2 7.2 - - - +
163A TYR* 1.3 79.9 - - - +
165A HIS* 1.3 87.6 + + - +
167A GLU* 3.5 5.0 + - - +
168A LEU* 3.2 52.8 + - + +
201A GLN* 3.6 29.1 + - - +
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Residues in contact with HIS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.8 10.8 + - + +
121A GLN* 3.7 39.8 + - - +
122A ASP* 3.9 35.3 + - + -
157A ALA* 3.9 13.0 - - + -
162A ASP* 2.7 39.6 + - - +
164A TYR* 1.3 101.5 - + - +
166A THR* 1.3 65.4 - - - +
168A LEU* 4.0 6.0 - - + +
169A TRP* 2.9 36.4 + - + +
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY* 3.9 17.5 - - - +
157A ALA* 3.7 1.2 - - - +
158A TYR* 3.0 37.0 + - + -
162A ASP 2.9 16.8 + - - -
163A TYR* 3.6 11.9 - - - -
165A HIS* 1.3 76.2 - - - +
167A GLU* 1.3 62.6 + - - +
169A TRP* 3.9 0.5 - - - +
170A MET* 3.0 44.7 + - + +
193A TYR* 4.3 8.7 - - + +
197A ALA* 3.6 20.2 - - + -
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR 2.9 20.1 + - - +
164A TYR* 3.7 6.0 - - - +
166A THR* 1.3 72.8 - - - +
168A LEU* 1.3 68.6 + - + +
170A MET 3.4 0.2 + - - -
171A GLU* 2.9 38.4 + - - +
194A LEU* 3.7 22.7 - - + +
197A ALA* 3.9 8.5 - - + +
198A VAL* 3.6 14.4 - - - +
201A GLN* 3.7 24.9 + - - +
206A LYS* 3.1 26.9 + - - +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 4.5 8.3 - - - +
126A LEU 5.9 0.4 - - - +
127A ASP* 6.5 0.4 - - - -
128A THR* 3.8 20.7 + - + +
164A TYR* 3.2 51.6 + - + +
165A HIS* 3.8 17.0 - - + +
166A THR 3.3 0.4 - - - -
167A GLU* 1.3 83.6 - - + +
169A TRP* 1.3 58.1 + - + +
171A GLU* 3.4 15.5 + - - +
172A GLN* 3.1 26.0 + - - +
175A ARG* 5.3 0.5 + - - -
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Residues in contact with TRP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.1 4.3 - - + -
118A LEU* 3.5 18.9 - - + +
121A GLN* 2.7 30.9 + - - +
128A THR* 3.6 37.2 - - + -
131A ILE* 4.0 24.2 - - + -
145A LEU* 3.7 32.5 - - + -
150A CYS* 3.5 47.5 - - + +
153A LEU* 3.8 21.1 - - + -
154A GLY* 3.6 11.0 - - - +
165A HIS* 2.9 30.9 + - + +
168A LEU* 1.3 73.4 - - + +
170A MET* 1.3 60.6 + - - +
172A GLN* 3.3 3.3 + - + +
173A ALA* 3.0 27.9 + - - +
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Residues in contact with MET 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.4 59.5 - - + +
154A GLY 3.7 5.8 - - - -
155A LYS* 3.6 17.0 - - + +
166A THR* 3.0 23.7 + - + +
167A GLU 4.0 1.1 - - - +
169A TRP* 1.3 75.9 - - - +
171A GLU* 1.3 59.5 + - - +
173A ALA* 3.4 1.6 + - - -
174A LEU* 3.0 24.5 + - - +
190A VAL* 3.2 21.5 - - + +
193A TYR* 3.7 37.9 - - + -
194A LEU* 3.8 25.8 - - + +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 2.9 33.2 + - - +
168A LEU* 3.7 15.0 - - - +
170A MET* 1.3 78.3 - - - +
172A GLN* 1.3 56.5 + - - +
174A LEU* 3.3 7.7 + - + +
175A ARG* 2.9 50.0 + - - +
194A LEU* 3.8 20.0 - - + +
206A LYS* 2.5 37.6 + - - -
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 2.9 33.3 + - - +
129A ASP* 3.1 34.5 + - - +
132A SER* 3.9 6.6 - - - -
133A LYS* 4.3 2.2 - - - +
150A CYS* 3.6 21.1 - - - -
168A LEU 3.1 9.1 + - - +
169A TRP* 3.6 10.1 - - + +
170A MET 3.2 0.2 - - - -
171A GLU* 1.3 74.3 - - - +
173A ALA* 1.3 65.4 + - - +
175A ARG* 2.5 41.1 + - - +
176A GLN* 3.0 48.0 + - - +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 3.6 27.7 - - - +
150A CYS* 3.8 10.2 - - + +
151A PHE* 4.1 6.5 - - - +
169A TRP 3.0 13.7 + - - +
170A MET* 3.6 9.6 - - - +
172A GLN* 1.3 74.3 - - - +
174A LEU* 1.3 64.7 + - - +
176A GLN* 3.2 3.7 + - - +
177A LEU* 3.0 28.4 + - - +
185A ILE* 4.2 9.9 - - + -
190A VAL* 4.2 12.1 - - + -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET 3.0 15.7 + - - +
171A GLU* 3.6 6.3 - - + +
172A GLN 3.2 0.2 - - - -
173A ALA* 1.3 75.8 - - - +
175A ARG* 1.3 63.5 + - - +
177A LEU* 3.3 6.4 + - + +
178A ASP* 3.0 39.8 + - - +
187A LYS* 4.2 36.8 - - + -
190A VAL* 4.2 12.5 - - + +
191A LEU* 3.8 30.7 - - + -
194A LEU* 3.9 20.4 - - + -
210A LEU* 5.2 2.9 - - + -
213A LYS* 6.0 2.9 - - + +
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR* 3.9 6.5 + - - -
129A ASP* 4.5 12.4 - - - +
168A LEU 5.3 0.2 + - - -
171A GLU* 2.9 38.4 + - - +
172A GLN* 2.5 56.4 + - - +
174A LEU* 1.3 77.1 - - - +
176A GLN* 1.3 57.2 + - + +
178A ASP* 3.2 10.0 + - - +
179A GLU* 3.1 45.9 + - + +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 2.5 26.0 + - - -
133A LYS* 4.0 17.4 + - - +
145A LEU 3.2 19.4 + - - -
146A THR 3.5 1.0 - - - -
147A ALA* 3.4 13.9 - - + +
150A CYS* 3.6 12.4 - - - -
172A GLN* 3.0 36.1 + - - +
173A ALA 3.9 3.4 - - - +
175A ARG* 1.3 74.8 - - + +
177A LEU* 1.3 64.3 - - - +
179A GLU* 3.3 18.7 + - - +
180A GLY 3.4 0.5 + - - -
181A GLU* 2.8 57.8 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ALA* 4.0 9.4 - - + -
173A ALA 3.0 18.8 + - - +
174A LEU* 3.6 10.8 - - - +
176A GLN* 1.3 78.2 - - - +
178A ASP* 1.3 61.1 + - - +
180A GLY* 3.2 13.5 + - - -
181A GLU 3.9 14.0 + - - +
183A SER* 3.7 29.4 - - - -
185A ILE* 3.9 20.6 - - + +
187A LYS* 3.8 48.3 + - + +
190A VAL* 4.2 15.5 - - + -
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.0 28.1 + - - +
175A ARG* 3.2 11.0 + - - +
177A LEU* 1.3 72.9 - - - +
179A GLU* 1.3 61.2 + - + +
180A GLY* 3.0 7.1 + - - -
187A LYS* 2.9 31.6 + - - +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 5.4 0.5 - - - +
133A LYS* 3.7 25.7 + - - -
175A ARG* 3.1 30.0 + - + +
176A GLN* 3.6 15.2 - - - +
177A LEU 3.3 0.4 - - - -
178A ASP* 1.3 76.4 - - - +
180A GLY* 1.3 58.2 + - - +
181A GLU* 3.7 0.7 - - + +
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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
------------------------------------------------------------
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