Contacts of the helix formed by residues 171 - 183 (chain A) in PDB entry 5LUQ
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 LEU 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ILE* 4.3 9.2 - - + +
167A PRO 3.2 26.9 - - - +
168A ASP* 3.1 5.5 + - - +
170A VAL* 1.3 80.3 - - + +
172A GLU* 1.3 62.7 + - - +
173A LYS 3.1 0.4 - - - -
174A VAL* 3.2 26.1 + - + +
175A TYR* 3.0 54.8 - - + +
200A PHE* 5.2 4.7 - - + -
203A GLU* 5.5 2.0 - - - +
204A LEU* 5.2 3.6 - - + -
207A GLN* 6.2 0.2 - - - +
218A PRO 4.7 0.4 - - - -
219A VAL* 3.7 36.3 - - + -
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Residues in contact with GLU 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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132A ILE* 4.6 20.6 - - - +
135A LEU* 5.4 3.6 - - + +
136A GLN* 5.5 1.0 + - - -
139A ARG* 5.0 4.9 + - - -
168A ASP 4.6 0.6 + - - -
170A VAL* 2.7 17.5 + - - +
171A LEU* 1.3 74.9 - - - +
173A LYS* 1.3 66.9 + - + +
174A VAL 3.2 0.2 + - - -
175A TYR 3.4 0.2 + - - -
176A GLU* 2.8 47.4 + - - +
218A PRO* 3.5 23.9 + - + +
221A ALA* 4.0 11.5 - - + +
222A GLY* 3.3 22.4 - - - +
225A LYS* 4.2 4.3 + - - -
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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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115A TYR* 3.3 37.7 + - - +
131A LEU* 3.6 12.3 - - - +
135A LEU* 3.3 50.3 - - + +
157A TYR* 6.5 0.2 - - - -
160A LEU* 5.2 10.5 - - - -
166A ILE* 5.3 3.6 - - - -
170A VAL* 2.7 47.9 + - + +
172A GLU* 1.3 73.6 - - - +
174A VAL* 1.3 87.5 + - + +
176A GLU* 3.0 15.2 + - - +
177A LEU* 2.8 33.7 + - + +
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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
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160A LEU* 6.2 2.9 - - + -
161A ALA* 3.8 26.2 - - + -
166A ILE* 6.1 4.5 - - + -
170A VAL* 5.5 1.1 - - + -
171A LEU* 3.2 31.8 + - + +
172A GLU 3.2 0.4 + - - -
173A LYS* 1.3 92.9 - - + +
175A TYR* 1.3 65.5 + - + +
177A LEU* 3.3 9.7 + - - +
178A LEU* 2.9 47.6 + - + +
200A PHE* 4.3 17.3 - - + -
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Residues in contact with TYR 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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171A LEU* 3.0 52.3 - - + +
172A GLU 3.4 0.2 + - - -
174A VAL* 1.3 73.8 - - + +
176A GLU* 1.3 69.3 + - - +
178A LEU* 3.8 16.6 - - + -
179A GLY* 3.0 16.5 + - - -
197A PHE* 5.2 4.0 - + - -
200A PHE* 3.1 50.0 - + + -
201A LEU* 6.1 1.6 - - + -
203A GLU* 3.9 2.3 + - - -
204A LEU* 3.0 32.2 - - + +
219A VAL* 3.9 8.1 - - + -
222A GLY* 3.0 21.1 - - - +
223A CYS* 3.2 22.4 - - - -
225A LYS 4.3 0.2 - - - -
226A GLY* 3.3 22.1 + - - +
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Residues in contact with GLU 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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135A LEU* 4.8 3.8 - - - +
139A ARG* 3.8 33.9 + - - +
172A GLU* 2.8 57.2 + - - +
173A LYS* 3.0 21.7 + - - +
175A TYR* 1.3 80.6 - - - +
177A LEU* 1.3 65.2 + - + +
179A GLY* 3.4 1.0 + - - -
180A LEU* 3.0 29.1 + - + +
222A GLY* 4.3 1.0 - - - -
225A LYS* 3.3 40.5 + - + -
229A SER* 5.4 1.0 - - - -
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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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135A LEU* 4.5 17.3 - - + +
138A PHE* 3.3 36.6 - - + -
139A ARG* 4.6 8.7 - - + -
157A TYR* 3.5 33.7 - - + +
160A LEU* 5.1 6.5 - - + -
161A ALA* 6.5 0.9 - - + -
173A LYS* 2.8 33.8 + - + +
174A VAL* 3.6 7.9 - - - +
176A GLU* 1.3 72.4 - - + +
178A LEU* 1.3 56.8 + - + +
180A LEU* 2.3 38.9 + - + -
181A LEU* 2.9 21.1 + - + +
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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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157A TYR* 4.9 2.0 - - + +
158A GLY* 4.6 15.5 - - - +
161A ALA* 4.2 18.8 - - + -
162A LEU* 5.6 4.3 - - + -
174A VAL* 2.9 50.8 + - + +
175A TYR* 3.8 16.2 - - + +
177A LEU* 1.3 72.8 - - + +
179A GLY* 1.3 62.1 + - - +
181A LEU* 3.5 17.1 - - + +
182A GLY* 3.0 19.8 + - - -
189A MSE 5.6 3.4 - - + -
193A ALA* 5.5 2.0 - - + +
197A PHE* 3.2 44.0 - - + -
200A PHE* 4.3 12.3 - - + -
230A LEU* 5.0 0.2 - - - +
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Residues in contact with GLY 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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175A TYR 3.0 13.1 + - - -
176A GLU 3.9 1.8 - - - -
178A LEU* 1.3 74.5 - - - +
180A LEU* 1.3 65.6 + - - +
182A GLY* 3.1 0.7 + - - -
183A GLU* 2.9 19.2 + - - +
197A PHE* 4.5 0.2 - - - -
226A GLY* 4.4 5.0 - - - -
229A SER* 2.7 43.7 + - - +
230A LEU* 4.3 5.4 - - - -
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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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138A PHE* 4.3 12.6 - - + +
139A ARG* 3.7 52.5 - - + +
141A SER 5.4 1.3 - - - +
142A ARG* 4.4 26.2 - - + +
176A GLU* 3.0 24.3 + - + +
177A LEU* 2.3 32.0 + - - +
179A GLY* 1.3 68.4 - - - +
181A LEU* 1.3 61.7 + - - +
183A GLU* 3.4 28.1 + - - +
184A VAL* 3.7 9.6 - - - +
229A SER* 4.3 0.2 - - - -
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Residues in contact with LEU 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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138A PHE* 4.9 6.9 - - + -
153A PHE* 4.2 14.3 - - + -
154A SER* 3.1 47.1 - - - +
157A TYR* 4.5 10.3 - - + -
158A GLY 5.3 0.2 - - - +
177A LEU* 2.9 36.6 + - + +
178A LEU* 3.5 15.5 - - + +
180A LEU* 1.3 72.6 - - - +
182A GLY* 1.3 80.9 + - - +
184A VAL* 2.9 28.2 + - + +
185A HIS 4.2 1.7 + - - -
186A PRO* 5.0 4.5 - - - +
189A MSE 3.4 24.6 - - + +
193A ALA* 5.0 4.0 - - + -
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Residues in contact with GLY 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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178A LEU 3.0 19.1 + - - -
179A GLY* 3.1 5.3 + - - -
181A LEU* 1.3 82.1 - - - +
183A GLU* 1.3 53.1 + - - +
184A VAL 3.5 0.5 + - - +
189A MSE 6.2 0.7 - - - -
190A ILE* 3.2 27.3 - - - +
193A ALA* 5.9 3.4 - - - -
197A PHE* 6.3 0.2 - - - -
229A SER 4.8 1.3 - - - -
230A LEU* 5.3 7.4 - - - -
233A ASN* 2.4 27.3 + - - -
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Residues in contact with GLU 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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142A ARG* 5.2 7.8 + - - +
179A GLY 2.9 9.1 + - - +
180A LEU* 3.6 22.2 - - - +
181A LEU 3.1 0.2 - - - -
182A GLY* 1.3 72.1 - - - +
184A VAL* 1.3 69.7 + - + +
185A HIS* 4.6 5.0 + - - -
229A SER* 2.7 47.1 + - - +
232A CYS* 5.9 3.1 - - + -
233A ASN* 3.3 11.4 + - - +
274A LEU* 5.9 3.5 - - - +
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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