Contacts of the helix formed by residues 176 - 188 (chain A) in PDB entry 3OEE
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 GLY 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLN* 3.6 1.8 - - - +
175A THR* 1.3 80.8 - - - +
177A LYS* 1.3 64.6 + - - +
178A THR 3.5 2.9 - - - -
179A ALA* 3.2 16.3 + - - +
180A VAL* 3.1 23.2 + - - +
354A LEU* 4.2 6.5 - - - +
359A PHE* 4.9 6.2 - - - -
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Residues in contact with LYS 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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169A ILE* 3.7 23.5 - - + +
170A ILE 3.8 1.8 - - - -
171A GLY* 3.3 33.4 + - - +
172A ASP 3.0 25.1 + - - -
173A ARG* 4.0 8.1 - - - +
174A GLN 4.4 4.0 - - - +
175A THR* 3.6 12.3 + - - +
176A GLY* 1.3 75.6 - - - +
178A THR* 1.3 63.3 + - - +
180A VAL* 3.2 13.2 + - - +
181A ALA* 3.4 7.8 + - - +
271A ASP* 5.7 0.2 - - - -
272A ASP* 5.5 2.2 - - - -
328A VAL* 3.6 28.3 - - + +
329A ILE 3.6 10.5 - - - +
330A GLU* 4.1 13.8 + - - +
354A LEU* 4.0 15.5 - - + +
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Residues in contact with THR 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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176A GLY 3.5 0.4 - - - -
177A LYS* 1.3 75.5 - - - +
179A ALA* 1.3 52.9 + - - +
181A ALA* 3.0 8.4 + - - +
182A LEU* 2.8 40.3 + - + +
205A TYR* 3.8 16.1 + - + +
210A GLN* 5.4 0.2 + - - -
218A LEU* 4.1 20.2 - - + -
271A ASP* 2.5 32.4 + - - +
328A VAL* 5.8 0.2 - - - -
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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
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176A GLY* 3.2 19.7 + - - +
178A THR* 1.3 78.7 - - - +
180A VAL* 1.3 62.4 + - + +
182A LEU* 4.1 6.1 - - - -
183A ASP* 2.9 32.2 + - - +
434A GLN* 3.4 35.0 - - + +
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Residues in contact with VAL 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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150A THR* 6.0 1.1 - - + -
152A LEU* 3.9 26.3 - - + +
155A VAL* 4.7 3.1 - - + -
169A ILE* 3.6 22.7 - - + -
176A GLY 3.1 13.0 + - - +
177A LYS 3.2 7.1 + - - +
179A ALA* 1.3 77.5 - - + +
181A ALA* 1.3 57.6 + - - +
182A LEU 3.3 0.2 + - - -
183A ASP 3.6 0.2 + - - -
184A THR* 2.8 35.0 + - - +
326A LEU* 5.3 1.1 - - + -
352A ILE* 4.4 21.3 - - + -
354A LEU* 3.9 26.2 - - + -
365A PRO* 4.6 12.3 - - + -
367A ILE* 5.0 2.5 - - + -
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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
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169A ILE* 3.7 17.0 - - + +
177A LYS 3.4 4.7 + - - +
178A THR* 3.0 12.7 + - - +
180A VAL* 1.3 78.5 - - - +
182A LEU* 1.3 57.2 + - - +
184A THR* 3.1 19.4 - - - +
185A ILE* 3.2 17.7 + - - +
205A TYR* 5.2 4.9 - - + -
269A VAL* 3.7 35.9 - - + +
326A LEU* 4.2 8.3 - - + -
328A VAL* 5.5 0.9 - - + -
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Residues in contact with LEU 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 THR* 2.8 21.8 + - + +
179A ALA* 3.7 5.2 - - - +
180A VAL 3.1 0.2 - - - -
181A ALA* 1.3 75.5 - - - +
183A ASP* 1.3 60.4 + - - +
184A THR 3.1 1.8 - - - -
185A ILE* 3.3 13.0 + - + +
186A LEU* 3.0 35.1 + - + +
205A TYR* 5.8 3.4 - - + -
218A LEU* 3.7 32.8 - - + -
221A THR* 4.3 9.4 - - + -
222A LEU* 3.7 30.5 - - + -
434A GLN* 5.0 5.8 - - - +
435A TYR* 3.9 31.0 - - + +
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Residues in contact with ASP 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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150A THR 3.5 3.6 - - - +
152A LEU* 3.9 32.0 - - + +
179A ALA* 2.9 21.8 + - - +
180A VAL 4.3 0.2 - - - +
182A LEU* 1.3 76.2 - - - +
184A THR* 1.3 56.1 + - - +
186A LEU* 3.4 7.8 + - - +
187A ASN* 2.9 29.6 + - - +
433A ASN 4.5 2.0 - - - +
434A GLN* 4.1 12.9 - - - +
435A TYR* 2.9 46.9 + - - -
436A SER 4.6 3.1 - - - -
437A PRO* 3.7 10.6 - - + +
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Residues in contact with THR 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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148A VAL* 4.4 7.2 - - + -
150A THR* 3.4 42.2 + - + +
152A LEU* 4.5 1.6 - - - +
161A ILE* 6.2 0.2 - - + -
180A VAL* 2.8 17.9 + - - +
181A ALA* 3.1 13.4 - - - +
183A ASP* 1.3 75.7 - - - +
185A ILE* 1.3 63.9 + - - +
187A ASN* 3.2 7.6 + - - +
188A GLN* 2.8 33.0 + - - +
267A LEU* 3.8 24.2 - - + -
326A LEU* 4.6 11.0 - - + +
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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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181A ALA 3.2 15.4 + - - +
182A LEU* 3.3 16.8 + - + +
184A THR* 1.3 75.8 - - - +
186A LEU* 1.3 52.9 + - - +
188A GLN* 3.4 5.4 + - - +
203A CYS* 3.7 32.5 - - + -
204A VAL 5.3 1.1 - - - +
205A TYR* 4.4 24.0 - - + -
222A LEU* 3.9 21.5 - - + -
227A ALA* 4.5 0.2 - - + -
230A TYR* 2.7 34.4 + - + -
231A SER* 3.6 23.1 - - - +
267A LEU* 4.4 8.1 - - + -
269A VAL* 4.3 16.8 - - + -
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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
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182A LEU* 3.0 18.6 + - + +
183A ASP* 3.4 14.8 - - - +
185A ILE* 1.3 75.1 - - - +
187A ASN* 1.3 62.8 + - - +
188A GLN 3.1 2.9 + - - -
189A LYS* 3.4 20.9 + - - +
221A THR* 5.1 2.7 - - + +
222A LEU* 4.0 13.9 - - + +
225A HIS* 3.6 44.2 - - + +
227A ALA* 3.8 17.3 - - + -
230A TYR* 3.3 10.2 + - - -
435A TYR* 3.8 41.1 - - + +
437A PRO* 4.3 8.8 - - + +
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Residues in contact with ASN 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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149A GLN* 3.0 25.8 + - - +
150A THR 3.2 20.4 - - - +
151A GLY* 3.2 20.6 - - - +
183A ASP 2.9 9.4 + - - +
184A THR 3.2 6.2 + - - +
186A LEU* 1.3 77.2 - - - +
188A GLN* 1.3 59.2 + - - +
189A LYS* 3.1 3.4 + - - -
190A ARG* 2.8 45.4 + - - +
191A TRP* 3.3 23.1 - - - -
437A PRO* 3.4 11.4 - - + +
438A LEU 4.3 2.0 + - - -
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Residues in contact with GLN 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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148A VAL* 4.4 1.6 - - - +
149A GLN 3.0 27.7 + - - +
163A ARG* 4.3 4.2 + - - -
184A THR* 2.8 31.3 + - - +
185A ILE* 3.7 9.6 - - - +
186A LEU 3.1 2.4 - - - -
187A ASN* 1.3 75.8 - - - +
189A LYS* 1.3 59.0 + - - +
190A ARG 3.0 3.4 + - - -
191A TRP* 3.3 22.8 + - + -
192A ASN* 2.9 50.8 + - - +
201A LEU* 3.6 39.3 - - + +
203A CYS* 4.2 10.5 - - - -
230A TYR* 3.8 0.9 - - + -
267A LEU* 5.3 0.7 - - + -
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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