Contacts of the helix formed by residues 176 - 191 (chain A) in PDB entry 5LSW
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 GLU 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 1.3 74.6 - - - +
177A LEU* 1.3 60.0 + - - +
179A LYS* 3.5 11.6 + - - +
180A THR* 3.0 31.0 + - - -
225A SER* 2.3 41.2 + - - +
227A ARG* 2.6 40.3 + - - -
228A LEU* 3.9 8.2 - - + +
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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
----------------------------------------------------------
137A LEU* 3.9 22.7 - - + -
175A SER* 3.3 4.1 + - - +
176A GLU* 1.3 79.8 + - - +
178A SER* 1.3 66.9 + - - +
180A THR* 3.2 7.7 + - + -
181A VAL* 3.2 26.5 + - + +
227A ARG* 3.6 33.7 - - - +
802B GLU* 3.6 36.1 - - + +
805B LEU* 3.8 30.3 - - + -
806B VAL* 5.0 2.9 - - + +
809B VAL* 6.4 0.2 - - + -
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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
----------------------------------------------------------
133A GLU* 3.1 15.4 + - - -
136A ARG* 4.8 7.5 + - - -
137A LEU* 3.4 15.8 + - - +
140A LEU* 4.0 13.0 - - - +
170A ILE* 3.5 18.5 - - - +
174A GLY* 4.6 1.3 - - - -
175A SER* 3.1 29.2 + - - -
177A LEU* 1.3 76.9 - - - +
179A LYS* 1.3 64.6 + - - +
181A VAL* 3.3 1.0 + - - -
182A ALA* 3.0 26.3 + - - +
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Residues in contact with LYS 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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170A ILE* 3.6 16.5 - - - +
171A MET* 2.6 35.3 + - - +
172A GLU 3.0 25.1 + - - -
173A SER* 3.6 1.8 - - - +
174A GLY 3.1 17.9 - - - +
175A SER 2.8 25.0 + - - +
176A GLU* 3.6 7.6 - - + +
177A LEU 3.3 0.2 - - - -
178A SER* 1.3 76.0 - - - +
180A THR* 1.3 57.7 + - - +
182A ALA* 3.8 0.9 - - - +
183A THR* 2.8 36.2 + - - -
216A MET* 4.5 3.3 - - + +
219A GLN* 3.5 24.1 + - - +
228A LEU* 3.9 26.2 - - + -
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Residues in contact with THR 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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176A GLU* 3.0 25.9 + - - -
177A LEU* 3.2 16.3 + - + -
178A SER 3.2 1.0 - - - -
179A LYS* 1.3 79.2 - - - +
181A VAL* 1.3 57.5 + - + +
183A THR* 3.7 2.3 - - - -
184A PHE* 2.9 26.9 + - - +
227A ARG* 4.2 22.6 + - + +
228A LEU* 3.7 17.9 - - - +
231A HIS* 4.1 14.3 - - + -
809B VAL* 3.7 27.8 - - + -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 5.2 0.2 - - + -
140A LEU* 3.7 41.1 - - + +
141A GLY* 4.5 1.6 - - - +
144A GLY* 4.9 6.3 - - - -
177A LEU* 3.2 20.5 + - + +
178A SER* 3.3 2.9 + - - +
180A THR* 1.3 73.0 - - - +
182A ALA* 1.3 61.5 + - - +
184A PHE* 3.2 2.6 + - + +
185A ILE* 3.0 32.3 + - + +
805B LEU* 4.2 33.7 - - + -
808B ILE* 5.8 1.8 - - + -
809B VAL* 3.9 24.5 - - + -
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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
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140A LEU* 4.4 7.7 - - + +
167A CYS* 3.7 28.8 - - - +
170A ILE* 3.6 21.8 - - + -
171A MET* 3.8 8.1 - - + -
178A SER 3.0 17.5 + - - +
181A VAL* 1.3 77.6 - - - +
183A THR* 1.3 61.6 + - - +
185A ILE* 3.3 12.3 + - - +
186A LEU* 3.0 22.9 + - - +
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Residues in contact with THR 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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171A MET* 3.4 28.9 - - + +
179A LYS 2.8 23.0 + - - -
180A THR 3.7 4.3 - - - -
182A ALA* 1.3 75.9 - - - +
184A PHE* 1.3 52.9 + - - +
186A LEU* 3.3 2.3 + - - +
187A GLN* 2.7 33.1 + - - +
213A LEU* 5.2 0.2 - - + -
216A MET* 3.4 13.3 - - - +
228A LEU* 3.9 3.5 - - - +
231A HIS* 3.6 37.5 - - + +
232A VAL* 4.0 10.1 - - + +
235A CYS* 3.9 9.8 - - - -
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Residues in contact with PHE 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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144A GLY* 3.7 29.8 - - - -
147A VAL* 3.9 11.2 - - + -
148A LYS* 4.3 14.8 - - + -
180A THR 2.9 17.6 + - - +
181A VAL* 3.2 6.0 + - + +
183A THR* 1.3 77.6 - - - +
185A ILE* 1.3 59.1 + - - +
187A GLN* 3.2 14.5 + - - +
188A LYS* 2.9 54.2 + - + +
231A HIS* 3.7 16.8 - + - +
808B ILE* 3.6 20.6 - - + -
809B VAL* 3.5 43.7 - - + -
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Residues in contact with ILE 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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123A LEU* 6.2 0.2 - - + -
140A LEU* 3.8 33.2 - - + +
143A ILE* 3.7 37.5 - - + -
144A GLY* 4.2 15.5 - - - -
147A VAL* 4.4 14.5 - - + +
158A LEU* 5.0 0.4 - - + -
163A ILE* 4.3 5.4 - - + -
167A CYS* 3.6 21.3 - - - -
181A VAL* 3.0 20.9 + - + +
182A ALA* 3.7 7.9 - - - +
184A PHE* 1.3 76.2 - - + +
186A LEU* 1.3 63.0 + - - +
188A LYS* 3.3 4.0 + - - +
189A ILE* 3.1 34.1 + - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.5 24.0 - - + -
167A CYS* 4.7 5.8 - - + -
168A LEU* 4.2 14.1 - - + -
171A MET* 3.7 32.8 - - + -
182A ALA 3.0 13.5 + - - +
183A THR 3.6 6.3 - - - +
185A ILE* 1.3 75.4 - - - +
187A GLN* 1.3 58.2 + - - +
189A ILE* 3.2 9.1 + - + +
190A LEU* 2.9 40.3 + - + +
199A ILE* 3.9 26.0 - - + -
209A VAL* 4.3 17.5 - - + -
213A LEU* 4.8 2.5 - - + -
235A CYS* 4.3 7.6 - - - -
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Residues in contact with GLN 187 (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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183A THR 2.7 19.9 + - - +
184A PHE* 3.3 18.8 - - - +
186A LEU* 1.3 73.2 - - - +
188A LYS* 1.3 59.7 + - - +
190A LEU* 3.2 6.2 + - - +
191A LEU* 2.9 48.5 + - + +
231A HIS* 2.6 46.4 + - - +
234A ARG* 3.6 31.5 - - + +
235A CYS* 3.8 16.9 - - - +
238A ARG* 5.7 0.8 - - + +
275A TRP* 5.5 4.1 - - - -
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Residues in contact with LYS 188 (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 VAL* 3.5 46.7 - - + +
148A LYS* 4.5 7.5 + - - +
150A ASP* 3.0 39.8 + - - -
155A ILE* 4.0 6.9 - - + +
184A PHE* 2.9 44.1 + - + +
185A ILE 3.3 4.7 + - - +
187A GLN* 1.3 79.3 - - - +
189A ILE* 1.3 61.9 + - - +
191A LEU* 3.4 23.1 + - + +
192A ASP* 3.4 20.3 + - - +
150C ASP* 5.5 0.4 + - - -
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Residues in contact with ILE 189 (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 VAL* 5.4 0.2 - - + -
155A ILE* 4.0 24.2 - - + -
158A LEU* 4.4 10.3 - - + -
159A LEU* 4.5 7.6 - - + -
163A ILE* 3.9 27.8 - - + -
164A ILE* 4.2 19.1 - - + -
167A CYS* 5.5 1.3 - - - -
185A ILE* 3.1 29.5 + - + +
186A LEU* 3.2 10.7 + - + +
188A LYS* 1.3 78.4 - - + +
190A LEU* 1.3 62.2 + - - +
191A LEU 3.4 0.2 + - - -
192A ASP* 3.4 9.5 + - - +
195A GLY* 3.2 37.3 - - - -
199A ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 190 (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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186A LEU* 2.9 31.6 + - + +
187A GLN* 3.6 4.9 - - - +
189A ILE* 1.3 77.1 - - - +
191A LEU* 1.3 52.8 + - - +
192A ASP 3.2 6.8 - - - +
196A LEU* 3.5 20.8 - - + +
199A ILE* 3.5 30.3 - - + -
209A VAL* 5.2 2.2 - - + -
235A CYS* 3.8 41.3 - - + +
238A ARG* 2.6 40.7 + - + +
239A LEU* 3.8 29.8 - - + -
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Residues in contact with LEU 191 (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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150A ASP* 5.5 2.9 - - - +
187A GLN* 2.9 42.4 + - + +
188A LYS* 3.9 29.8 - - + +
189A ILE 3.2 0.6 - - - -
190A LEU* 1.3 74.2 - - - +
192A ASP* 1.3 64.0 + - - +
193A ASP* 3.6 1.7 + - - +
234A ARG* 3.3 37.0 - - + +
238A ARG* 3.2 32.4 + - + +
149C THR* 5.3 4.9 - - - +
150C ASP* 5.3 12.5 - - - +
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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
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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