Contacts of the helix formed by residues 163 - 182 (chain A) in PDB entry 4OE4
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 ILE 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 3.6 25.1 - - + +
136A SER* 4.0 16.8 - - - +
140A ARG* 3.8 50.3 - - + +
143A MET* 4.4 1.8 - - + -
144A LEU* 3.8 20.0 - - + -
159A GLU* 3.2 19.5 + - + +
162A CYS* 1.3 95.6 - - - +
164A THR* 1.3 63.6 + - - +
167A SER* 3.0 36.8 + - - +
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Residues in contact with THR 164 (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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140A ARG* 5.8 0.5 + - - -
159A GLU* 3.0 15.7 + - - +
160A ILE* 3.7 20.2 - - + +
163A ILE* 1.3 78.9 - - - +
165A GLU* 1.3 68.9 + - + +
167A SER* 3.9 2.2 - - - -
168A ASP* 3.0 43.5 + - - +
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 3.0 39.6 + - + +
161A ASP* 3.6 9.0 - - - +
164A THR* 1.3 73.3 - - + +
166A LEU* 1.3 66.0 + - - +
168A ASP* 3.2 7.8 + - - +
169A PHE* 2.9 35.0 + - + -
213A PHE* 3.9 23.1 - - - +
215A ALA* 3.8 10.8 - - + +
216A ILE* 5.7 1.6 - - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 4.7 2.0 - - - -
135A ILE* 3.7 35.9 - - + -
143A MET* 4.8 1.3 - - + -
161A ASP 3.1 12.2 + - - +
162A CYS 3.6 25.6 - - - +
164A THR 3.3 0.4 - - - -
165A GLU* 1.3 75.5 - - - +
167A SER* 1.3 70.1 + - - +
169A PHE* 3.1 16.2 + - - +
170A PHE* 3.4 29.2 + - + -
214A THR* 4.0 25.6 - - + -
215A ALA* 3.5 12.8 - - + +
218A ALA* 3.7 24.2 - - + -
246A LEU* 4.4 5.2 - - + -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.4 21.2 + - - +
135A ILE* 5.2 0.5 - - - +
136A SER* 2.9 24.3 + - - -
163A ILE* 3.0 20.9 + - - -
164A THR* 3.9 3.8 - - - -
166A LEU* 1.3 77.3 - - - +
168A ASP* 1.3 59.5 + - - +
170A PHE* 3.4 2.6 + - - +
171A ARG* 2.9 58.9 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.0 35.4 + - - +
165A GLU* 3.2 7.8 + - - +
167A SER* 1.3 77.0 - - - +
169A PHE* 1.3 65.3 + - - +
171A ARG* 4.5 8.5 + - - +
172A TYR* 2.9 51.6 + - + +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 2.9 30.3 + - + -
166A LEU* 3.4 7.6 - - - +
168A ASP* 1.3 75.7 - - - +
170A PHE* 1.3 64.9 + - + +
172A TYR* 4.0 1.5 - - - +
173A TYR* 2.9 56.3 + + + -
215A ALA* 3.4 39.7 - - + -
216A ILE* 4.5 9.6 - - + -
218A ALA* 5.5 0.2 - - + -
219A ASN* 3.7 38.1 - - + +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.2 63.9 - + + +
129A LEU* 4.6 1.1 - - - -
131A ALA* 4.4 12.6 - - + -
132A ALA* 4.2 14.1 - - + -
166A LEU* 3.4 21.0 + - + -
167A SER 3.4 7.2 + - - +
169A PHE* 1.3 82.6 - - + +
171A ARG* 1.3 58.3 + - + +
173A TYR* 3.9 7.8 - + - +
174A VAL* 3.0 35.9 + - - +
218A ALA* 3.3 46.0 - - + -
219A ASN* 5.1 0.4 - - - -
221A ILE* 5.3 0.9 - - + -
222A GLY* 4.1 7.4 - - - -
226A LEU* 5.1 0.2 - - - +
246A LEU* 4.5 9.6 - - + -
250A LEU* 4.4 6.1 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.0 25.7 + - + +
132A ALA* 4.0 7.6 - - + +
133A ASP* 4.0 35.8 + - - +
136A SER* 4.0 14.3 + - - -
167A SER* 2.9 45.5 + - - +
168A ASP* 4.2 9.9 + - - +
170A PHE* 1.3 75.2 - - - +
172A TYR* 1.3 68.1 + - + +
174A VAL* 3.6 2.6 + - - +
175A LYS* 3.2 21.8 + - - +
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 2.9 50.7 + - + +
169A PHE* 4.2 2.0 - - - +
171A ARG* 1.3 78.6 - - + +
173A TYR* 1.3 64.7 + - + +
175A LYS* 3.3 14.5 + - + +
176A TYR* 2.9 30.1 + - - +
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 2.9 47.4 + + + +
170A PHE* 3.9 7.9 - + + +
172A TYR* 1.3 77.4 - - + +
174A VAL* 1.3 61.8 + - - +
176A TYR* 3.3 2.0 + - + -
177A ALA* 2.8 34.0 + - - +
219A ASN* 2.4 36.3 + - - -
222A GLY 4.9 2.0 - - - -
223A ALA* 3.8 24.7 - - + -
226A LEU* 3.6 16.8 - - + -
547A ASN 6.0 2.0 - - - -
548A ILE* 3.6 30.1 - - + +
549A LEU* 3.5 22.0 - - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.5 6.7 - - + -
125A SER* 3.7 45.1 - - - +
128A PHE* 4.8 4.5 - - + -
129A LEU* 3.9 29.2 - - + -
170A PHE 3.0 22.1 + - - +
171A ARG 3.9 4.3 - - - +
173A TYR* 1.3 76.0 - - - +
175A LYS* 1.3 58.2 + - - +
178A SER* 2.9 30.1 + - - -
226A LEU* 3.9 15.0 - - + -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG 3.2 17.6 + - - +
172A TYR* 3.7 16.4 - - + +
173A TYR 3.2 0.2 - - - -
174A VAL* 1.3 75.8 - - - +
176A TYR* 1.3 65.9 + - - +
178A SER* 3.3 8.4 + - - +
179A ASP* 3.2 31.3 + - - +
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR 2.9 20.5 + - - +
173A TYR* 4.6 2.5 - - + -
175A LYS* 1.3 73.1 - - - +
177A ALA* 1.3 62.6 + - - +
179A ASP* 3.1 22.5 + - - +
180A LEU* 3.1 15.3 + - + +
547A ASN 5.4 8.3 - - - +
549A LEU* 3.8 17.5 - - + -
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Residues in contact with ALA 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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121A PHE* 3.5 23.3 - - + -
173A TYR 2.8 21.7 + - - +
176A TYR* 1.3 73.5 - - - +
178A SER* 1.3 58.3 + - - +
180A LEU* 3.0 9.7 + - - +
181A TYR* 2.8 36.5 + - + -
226A LEU* 4.0 4.0 - - + -
227A MET* 3.7 26.2 - - - -
549A LEU* 3.7 7.1 - - + +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.4 23.5 - - - -
174A VAL* 2.9 19.7 + - - -
175A LYS* 3.6 9.2 + - - +
176A TYR 3.2 0.2 - - - -
177A ALA* 1.3 77.9 - - - +
179A ASP* 1.3 67.7 + - - +
181A TYR* 3.5 3.0 + - - +
182A ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 3.2 25.9 + - - +
176A TYR* 3.1 14.2 + - - +
178A SER* 1.3 81.4 + - - +
180A LEU* 1.3 67.2 + - + +
182A ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.1 11.3 + - + +
177A ALA* 3.0 9.8 + - - +
179A ASP* 1.3 80.8 - - + +
181A TYR* 1.3 61.2 + - + +
182A ALA 3.2 4.7 + - - -
183A GLN* 4.3 4.5 + - - +
198A TYR* 3.5 54.6 - - + +
227A MET* 3.9 26.2 - - + -
547A ASN* 6.3 0.7 - - - +
549A LEU* 4.2 18.4 - - + -
550A SER* 4.6 17.7 - - - +
553A VAL* 5.2 0.9 - - + -
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Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.5 46.7 - + + -
124A ARG* 3.1 22.7 + - - -
177A ALA* 2.8 27.0 + - + +
178A SER* 3.8 5.8 - - - +
180A LEU* 1.3 71.7 - - - +
182A ALA* 1.3 56.6 + - - +
183A GLN* 2.8 17.7 + - - +
198A TYR* 4.1 34.5 + + + -
227A MET* 3.3 47.1 + - + +
553A VAL* 4.4 2.4 - - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 3.1 12.6 + - - +
179A ASP* 3.0 20.3 + - - +
180A LEU 3.1 1.1 - - - -
181A TYR* 1.3 73.1 - - - +
183A GLN* 1.3 59.6 + - - +
184A GLN* 4.1 2.0 + - - +
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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