Contacts of the helix formed by residues 161 - 181 (chain A) in PDB entry 4AUP
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 THR 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS 5.7 0.9 - - - +
159A ARG* 2.8 16.5 + - - +
160A PHE* 1.3 76.8 - - - +
162A GLU* 1.3 61.7 + - - +
163A ALA* 3.8 6.2 + - - +
164A ASN* 3.1 28.9 + - - +
165A ARG* 2.9 27.8 + - - +
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Residues in contact with GLU 162 (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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160A PHE* 5.4 2.6 - - - +
161A THR* 1.3 74.3 - - - +
163A ALA* 1.3 62.5 + - - +
165A ARG* 2.8 46.3 + - - +
166A LYS* 3.1 22.2 + - - +
206A ARG* 4.9 4.9 + - - -
210A TRP* 3.7 17.5 - - - +
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Residues in contact with ALA 163 (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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161A THR* 3.4 6.0 + - - +
162A GLU* 1.3 76.0 - - - +
164A ASN* 1.3 63.4 + - - +
166A LYS* 3.5 7.2 + - - +
167A ARG* 3.3 27.7 + - - +
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 4.7 0.2 + - - -
154A TYR* 3.6 23.2 + - + -
159A ARG* 2.7 45.2 + - - +
160A PHE* 5.0 0.7 - - - -
161A THR* 3.1 20.8 + - - +
163A ALA* 1.3 73.8 - - - +
165A ARG* 1.3 66.1 + - - +
167A ARG* 3.1 27.8 + - - +
168A ILE* 3.1 29.5 + - - +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.3 18.4 + - + +
160A PHE* 3.6 33.3 - - + -
161A THR 2.9 18.3 + - - +
162A GLU* 2.8 47.5 + - - +
164A ASN* 1.3 74.2 - - - +
166A LYS* 1.3 57.1 + - - +
168A ILE* 3.4 11.7 + - - +
169A ASP* 2.8 34.6 + - - +
205A VAL 2.6 28.2 + - - -
206A ARG* 2.7 43.6 + - - +
209A GLY 3.2 14.1 - - - +
210A TRP* 3.1 24.1 - - - +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU 3.1 11.1 + - - +
163A ALA* 3.8 9.6 - - - +
164A ASN 3.2 0.4 - - - -
165A ARG* 1.3 74.3 - - - +
167A ARG* 1.3 57.4 + - - +
169A ASP* 3.7 1.2 - - - +
170A ASP* 2.8 66.5 + - - +
202A TYR* 4.1 9.7 + - - -
206A ARG* 3.6 41.0 - - - +
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Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.6 34.4 - - + +
154A TYR* 5.2 1.8 - - - -
163A ALA* 3.3 16.4 + - - +
164A ASN* 3.1 35.3 + - - +
166A LYS* 1.3 77.3 - - - +
168A ILE* 1.3 58.2 + - - +
170A ASP* 3.6 8.1 - - - +
171A ASN* 3.0 28.2 + - - +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.4 10.1 - - + -
102A TYR* 3.5 18.2 - - - +
147A HIS* 3.5 33.3 - - + +
150A GLY* 3.7 19.1 - - - +
151A TYR* 3.7 17.5 - - + +
154A TYR* 3.6 38.1 - - + -
160A PHE* 4.5 2.5 - - + -
164A ASN 3.1 18.7 + - - +
165A ARG* 3.6 9.9 - - - +
167A ARG* 1.3 74.1 - - - +
169A ASP* 1.3 59.2 + - - +
171A ASN* 3.4 7.4 + - - +
172A PHE* 3.1 21.7 + - - +
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A HIS* 2.6 32.9 + - - -
151A TYR* 2.6 19.9 + - - -
165A ARG* 2.8 18.9 + - - +
166A LYS 3.3 4.7 + - - +
168A ILE* 1.3 73.7 - - - +
170A ASP* 1.3 63.3 + - - +
172A PHE* 3.1 5.7 + - - +
173A LYS 3.1 17.5 + - - -
202A TYR* 3.4 10.9 - - + -
205A VAL* 3.7 21.5 - - + +
206A ARG* 2.9 44.7 + - - -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LYS* 2.8 46.2 + - - +
167A ARG* 3.6 7.7 - - - +
169A ASP* 1.3 73.1 - - - +
171A ASN* 1.3 57.6 + - - +
173A LYS* 3.2 5.9 + - - +
174A LYS* 3.0 26.6 + - - +
202A TYR* 2.7 33.5 + - - -
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.0 40.3 + - - +
102A TYR* 3.8 29.0 + - + +
146A ARG* 4.0 3.4 - - - +
167A ARG 3.0 17.3 + - - +
168A ILE* 3.6 6.4 - - - +
169A ASP 3.3 0.2 - - - -
170A ASP* 1.3 75.6 - - - +
172A PHE* 1.3 57.0 + - - +
174A LYS* 3.4 23.8 + - - +
175A ASP* 2.9 43.6 + - - +
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Residues in contact with PHE 172 (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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143A SER* 3.5 15.5 - - - -
144A CYS* 3.7 39.9 - - - -
147A HIS* 3.5 38.6 - + + +
168A ILE 3.1 4.4 + - - +
169A ASP 3.2 9.6 - - - +
171A ASN* 1.3 74.7 - - - +
173A LYS* 1.3 59.2 + - - +
175A ASP* 3.2 7.0 + - - +
176A LEU* 2.8 54.7 + - + +
201A TYR* 3.9 23.1 - + + -
202A TYR* 4.6 3.4 - - - -
205A VAL* 3.7 40.2 - - + -
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Residues in contact with LYS 173 (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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169A ASP 3.1 7.5 + - - -
170A ASP* 3.2 7.4 + - - +
172A PHE* 1.3 75.0 - - - +
174A LYS* 1.4 52.9 + - - +
176A LEU* 3.7 9.1 - - - -
177A TYR* 2.8 59.1 + - + +
198A ALA 5.1 2.0 - - - +
199A ASN* 3.0 32.0 + - - +
202A TYR* 3.7 52.2 - - + -
203A ASP* 5.6 0.8 + - - -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR 4.4 15.4 + - - -
170A ASP 3.0 13.8 + - - +
171A ASN* 3.5 23.8 - - - +
172A PHE 3.2 0.2 - - - -
173A LYS* 1.4 75.7 - - - +
175A ASP* 1.3 57.3 + - - +
177A TYR* 3.3 7.0 + - - +
178A ASN* 2.9 44.7 + - - +
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Residues in contact with ASP 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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106A MET* 3.5 14.1 - - + +
143A SER* 3.2 24.6 + - - +
146A ARG* 2.8 55.8 + - - +
171A ASN* 2.9 25.6 + - - +
172A PHE* 3.5 6.0 - - - +
174A LYS* 1.3 74.0 - - - +
176A LEU* 1.3 66.3 + - - +
178A ASN* 3.2 16.8 + - - +
179A GLU* 3.1 18.5 + - - +
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Residues in contact with LEU 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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139A ASN 5.3 0.7 - - - +
140A PHE* 3.4 39.3 - - + -
143A SER* 3.5 24.0 - - - +
172A PHE* 2.8 50.3 + - + +
173A LYS* 3.7 7.6 - - - +
175A ASP* 1.3 76.7 - - - +
177A TYR* 1.3 61.9 + - - +
179A GLU* 3.1 7.1 + - - +
180A CYS* 3.0 27.4 + - - -
198A ALA* 3.8 39.7 - - + +
201A TYR* 4.1 5.8 - - + -
202A TYR 4.8 0.2 - - - +
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Residues in contact with TYR 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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173A LYS* 2.8 40.9 + - + +
174A LYS* 3.7 6.1 - - - +
176A LEU* 1.3 73.7 - - - +
178A ASN* 1.3 58.0 + - - +
180A CYS* 3.8 5.0 - - - +
181A ALA* 3.0 30.7 + - - +
195A ARG* 3.4 48.1 + - + +
198A ALA* 3.9 12.3 - - + -
199A ASN* 2.6 38.3 + - - -
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Residues in contact with ASN 178 (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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146A ARG* 5.6 1.6 - - - +
174A LYS* 2.9 36.5 + - - +
175A ASP* 3.2 20.7 + - - +
177A TYR* 1.3 77.6 - - - +
179A GLU* 1.3 64.1 + - - +
181A ALA* 3.5 13.7 + - - +
182A LYS* 3.7 15.6 - - - +
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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
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138A PHE* 5.6 0.2 - - + -
139A ASN* 3.2 53.6 + - - +
140A PHE* 5.4 2.2 - - + -
142A ASP* 4.9 3.5 - - - +
143A SER* 5.1 2.7 - - - +
175A ASP 3.1 10.8 + - - +
176A LEU* 3.1 12.0 + - - +
178A ASN* 1.3 77.0 - - - +
180A CYS* 1.3 63.2 + - - +
182A LYS* 2.8 60.0 + - - +
183A TYR* 4.1 14.7 + - + -
194A CYS* 5.1 7.0 - - - -
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Residues in contact with CYS 180 (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 PHE* 4.5 1.3 - - - -
176A LEU 3.0 21.7 + - - -
177A TYR 3.8 4.5 - - - +
178A ASN 3.4 0.2 - - - -
179A GLU* 1.3 75.3 - - - +
181A ALA* 1.3 57.0 + - - +
182A LYS 3.0 5.7 + - - -
183A TYR* 3.2 23.9 + - - +
191A GLY* 3.8 9.5 - - - +
194A CYS* 2.0 67.3 - - + -
195A ARG* 3.5 27.8 + - + -
198A ALA* 4.4 4.9 - - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR 3.0 17.9 + - - +
178A ASN* 3.7 10.5 - - - +
179A GLU 3.3 0.8 - - - -
180A CYS* 1.3 71.6 - - - +
182A LYS* 1.3 54.6 + - - +
183A TYR 3.1 14.4 + - - +
184A SER* 5.7 1.2 - - - -
195A ARG* 4.3 10.5 - - - +
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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
------------------------------------------------------------
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