Contacts of the helix formed by residues 169 - 185 (chain A) in PDB entry 3KQ4
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 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.0 17.3 - - + +
130A SER* 4.5 10.1 - - - +
167A PRO 3.4 3.1 + - - +
168A PHE* 1.3 78.0 - - - +
170A VAL* 1.3 59.3 + - - +
171A ASP* 3.0 28.3 + - - +
172A THR* 2.6 44.0 + - - +
173A GLY* 2.9 23.2 + - - -
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Residues in contact with VAL 170 (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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168A PHE* 3.7 23.5 + - + -
169A ASN* 1.3 72.3 - - - +
171A ASP* 1.3 71.6 + - - +
173A GLY* 2.8 1.7 + - - -
174A ALA* 2.7 23.1 + - + +
210A ILE* 4.6 10.1 - - + -
213A LYS* 3.9 22.2 - - + +
220A ILE* 4.4 6.7 - - + +
221A GLY* 3.9 21.1 - - - +
225A SER* 3.5 23.1 - - - +
229A ALA* 4.0 23.6 - - + -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 4.0 18.3 - - + -
169A ASN* 3.0 25.6 + - - +
170A VAL* 1.3 78.4 + - - +
172A THR* 1.3 61.3 + - - +
174A ALA* 3.3 5.7 + - - +
175A MET* 3.2 22.9 + - - +
222A ASP* 4.5 3.1 - - - +
224A TYR 4.2 3.6 - - - +
225A SER* 3.2 34.1 + - - -
228A LEU* 4.2 14.8 - - + +
270A GLN* 5.4 1.4 - - - +
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Residues in contact with THR 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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129A ALA* 3.6 15.5 - - - +
130A SER* 3.1 18.5 - - - -
132A PHE* 3.5 15.3 - - + +
133A TYR* 3.3 41.7 - - - +
136A SER* 4.8 1.8 - - - +
161A LEU* 5.1 4.0 - - + -
169A ASN* 2.6 33.4 + - - -
171A ASP* 1.3 69.1 - - - +
173A GLY* 1.3 67.8 + - - +
174A ALA 3.1 1.6 - - - -
175A MET* 3.9 0.6 - - - +
176A ALA* 2.9 25.1 + - + +
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Residues in contact with GLY 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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161A LEU* 6.5 0.4 - - - -
168A PHE* 3.7 29.1 - - - -
169A ASN 2.9 9.5 + - - -
170A VAL 2.8 9.2 + - - -
172A THR* 1.3 73.2 - - - +
174A ALA* 1.3 55.2 + - - +
176A ALA* 3.3 3.0 + - - +
177A THR* 2.5 36.4 + - - +
206A ILE* 4.1 10.7 - - - +
210A ILE* 4.3 2.9 - - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL 2.7 15.2 + - - +
171A ASP 3.4 9.2 - - - +
173A GLY* 1.3 72.2 - - - +
175A MET* 1.3 62.6 + - - +
177A THR* 3.0 16.4 + - - -
178A LEU* 3.3 14.2 + - - +
210A ILE* 4.1 4.5 - - + +
228A LEU* 3.7 15.3 - - + +
229A ALA* 3.7 33.4 - - + +
232A ALA* 3.7 13.5 - - + +
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Residues in contact with MET 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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94A LEU* 6.1 0.2 - - + -
133A TYR* 3.6 45.1 - - + +
136A SER* 3.7 21.3 - - - +
137A LEU* 3.2 28.5 - - + -
140A LEU* 5.5 2.1 - - - +
171A ASP 3.2 7.8 + - - +
172A THR* 3.3 3.1 + - - +
174A ALA* 1.3 75.2 - - - +
176A ALA* 1.3 68.2 + - - +
178A LEU* 3.1 28.6 + - + +
179A ALA* 3.1 10.4 + - - +
228A LEU* 3.7 23.3 - - + -
270A GLN* 4.5 2.2 - - - +
280A TYR* 3.4 31.9 - - + -
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Residues in contact with ALA 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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136A SER* 3.3 18.9 + - - +
157A PHE* 4.2 5.8 - - + -
161A LEU* 3.9 20.2 - - + -
172A THR* 2.9 18.2 + - + +
173A GLY 3.5 4.5 - - - +
175A MET* 1.3 77.4 - - - +
177A THR* 1.3 58.5 + - - +
179A ALA* 3.3 1.9 + - - +
180A LEU* 2.8 34.9 + - + +
206A ILE* 3.9 18.6 - - + -
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Residues in contact with THR 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 GLY 2.5 30.7 - - - +
174A ALA* 3.0 11.5 + - - +
176A ALA* 1.3 74.9 - - - +
178A LEU* 1.3 53.0 + - - +
181A THR* 2.5 41.8 + - - -
203A LEU* 3.7 11.2 - - - +
206A ILE* 3.2 25.4 - - + -
207A VAL* 5.3 0.9 - - + -
210A ILE* 4.7 2.2 - - + -
232A ALA* 3.3 25.6 + - + +
235A VAL* 4.9 0.9 - - - +
236A THR* 3.6 23.0 - - + +
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Residues in contact with LEU 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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140A LEU* 4.0 16.6 - - + +
174A ALA 3.3 13.0 + - - +
175A MET* 3.1 27.4 + - + +
177A THR* 1.3 75.8 + - - +
179A ALA* 1.3 65.9 + - - +
181A THR* 3.3 3.0 + - - -
182A CYS* 3.0 25.3 + - - +
228A LEU* 5.3 3.1 - - + +
231A GLN* 3.8 38.8 - - + +
232A ALA* 4.6 2.9 - - - +
235A VAL* 4.1 12.3 - - + -
279A THR* 4.4 7.2 - - - -
280A TYR* 4.4 15.3 - - + -
281A LEU* 4.0 26.8 - - + +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 3.5 31.2 - - - +
139A ILE* 4.2 13.1 - - + +
140A LEU* 4.0 20.7 - - + +
143A CYS* 5.0 1.0 - - - +
157A PHE* 4.9 6.3 - - + -
175A MET 3.1 7.5 + - - +
176A ALA* 3.6 8.1 - - - +
178A LEU* 1.3 79.7 - - - +
180A LEU* 1.3 63.8 + - - +
182A CYS* 3.5 3.5 + - - +
183A MET* 3.3 24.9 + - - +
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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
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139A ILE* 5.4 0.9 - - + -
154A ALA* 4.7 4.0 - - + +
157A PHE* 3.6 37.7 - - + -
158A ALA* 4.2 7.6 - - + -
161A LEU* 4.4 3.8 - - + -
176A ALA* 2.8 16.7 + - + +
179A ALA* 1.3 78.8 - - + +
181A THR* 1.3 64.2 + - - +
183A MET* 4.0 8.3 - - + -
184A TYR* 3.2 23.0 + - - +
199A PHE* 4.1 35.3 - - + +
202A VAL* 3.8 28.9 - - + -
203A LEU* 3.5 21.5 - - + +
206A ILE* 5.6 0.4 - - + -
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Residues in contact with THR 181 (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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177A THR 2.5 28.9 + - - -
178A LEU 3.3 2.7 + - - -
180A LEU* 1.3 71.6 - - - +
182A CYS* 1.3 69.1 + - - +
184A TYR* 3.3 3.4 + - - +
185A ASN* 3.0 43.4 + - - +
203A LEU* 3.8 15.7 - - - +
235A VAL* 3.4 42.4 - - + +
236A THR* 3.8 8.1 - - - -
237A PRO* 4.0 10.0 - - + +
281A LEU* 4.4 6.5 - - + -
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Residues in contact with CYS 182 (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 LEU* 4.1 10.3 - - + -
143A CYS* 2.1 49.8 - - - -
144A GLN* 4.4 8.5 - - - -
178A LEU 3.0 17.5 + - - +
179A ALA 3.8 3.6 - - - +
180A LEU 3.3 0.2 - - - -
181A THR* 1.3 77.7 - - - +
183A MET* 1.3 61.2 + - - +
185A ASN* 3.2 14.7 + - - +
186A LYS* 3.4 19.5 - - - +
281A LEU* 3.7 22.8 - - + +
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Residues in contact with MET 183 (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 ILE* 4.6 4.0 - - + -
143A CYS* 3.8 27.8 - - + -
147A SER* 3.8 14.4 - - - +
150A THR* 3.9 11.7 - - - -
151A LEU* 3.3 54.7 - - + +
154A ALA* 3.6 20.0 - - + -
179A ALA 3.3 14.6 + - - +
180A LEU* 4.1 7.2 - - + +
181A THR 3.2 0.4 - - - -
182A CYS* 1.3 74.1 - - - +
184A TYR* 1.3 67.5 + - - +
186A LYS* 2.9 19.6 + - - +
187A ILE* 3.5 12.9 - - + +
199A PHE* 3.9 14.1 - - + -
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Residues in contact with TYR 184 (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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180A LEU 3.2 18.2 + - - +
181A THR 3.4 4.7 - - - +
183A MET* 1.3 78.9 - - - +
185A ASN* 1.3 74.7 + - - +
186A LYS 3.4 0.7 + - - -
187A ILE* 3.8 14.3 - - - +
196A ARG* 3.1 79.3 + - + +
199A PHE* 4.0 12.6 - - + -
200A GLY* 3.9 21.5 - - - -
203A LEU* 4.1 8.7 - - + -
237A PRO* 3.6 34.5 - - + +
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Residues in contact with ASN 185 (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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181A THR* 3.0 39.0 + - - +
182A CYS* 3.2 7.2 + - - +
183A MET 3.1 1.0 - - - -
184A TYR* 1.3 93.4 - - - +
186A LYS* 1.3 70.7 + - + +
187A ILE 3.7 1.1 - - - -
196A ARG* 5.2 2.1 + - - +
237A PRO* 5.7 0.6 - - - +
281A LEU* 6.1 0.8 - - - +
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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