Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 3OAA
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.9 0.8 - - - +
173A THR* 1.3 81.1 - - - +
175A LYS* 1.3 59.8 + - - +
176A THR 3.6 1.6 - - - -
177A ALA* 3.8 10.5 - - - +
178A LEU* 2.9 32.8 + - - +
355A LEU* 3.5 6.8 - - - +
360A PHE* 4.3 7.6 - - - -
365A ARG 5.7 0.7 - - - -
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Residues in contact with LYS 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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167A ILE* 4.0 19.0 - - + +
168A ILE 4.7 0.7 - - - -
169A GLY 3.1 31.6 - - - +
170A ASP 3.0 29.4 + - - -
172A GLN* 4.4 8.1 - - - +
173A THR* 3.7 10.7 + - - +
174A GLY* 1.3 73.0 - - - +
176A THR* 1.3 71.5 + - - +
178A LEU* 2.9 14.0 + - - +
179A ALA* 3.0 10.6 + - - +
262A ASP* 5.9 1.6 + - - -
329A ILE* 3.6 33.7 - - + +
330A ILE 3.7 6.3 - - - +
331A GLU* 4.1 18.3 + - - +
355A LEU* 3.5 9.8 - - + +
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Residues in contact with THR 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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174A GLY 3.6 0.2 - - - -
175A LYS* 1.3 77.0 - - - +
177A ALA* 1.3 52.3 + - - +
179A ALA* 2.6 24.0 + - - +
180A ILE* 2.7 38.5 + - + -
195A TYR* 3.9 9.9 - - + +
200A GLN* 5.0 2.8 + - - -
204A THR* 5.7 6.5 - - + -
208A VAL* 5.5 1.8 - - + -
261A ASP* 2.5 38.2 + - - +
329A ILE* 4.0 10.3 - - - +
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Residues in contact with ALA 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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150A TYR* 4.7 1.3 - - - +
174A GLY* 3.8 13.7 - - - +
176A THR* 1.3 76.6 - - - +
178A LEU* 1.3 71.9 + - - +
179A ALA 2.8 2.3 + - - -
180A ILE* 3.8 13.0 - - + -
181A ASP* 2.8 25.7 + - - +
435A GLN* 3.2 32.8 - - + +
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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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148A THR* 4.7 7.6 - - + -
150A TYR* 3.9 29.6 - - + -
153A VAL* 3.9 28.5 - - + -
167A ILE* 4.1 18.8 - - + -
174A GLY 2.9 19.6 + - - +
175A LYS* 2.9 5.4 + - - +
177A ALA* 1.3 81.2 - - - +
179A ALA* 1.3 63.9 + - - +
181A ASP* 3.1 2.6 + - - +
182A ALA* 3.0 22.7 + - + -
327A LEU* 5.7 0.7 - - + -
353A ILE* 4.8 16.6 - - + -
355A LEU* 4.9 11.9 - - + -
368A VAL* 5.5 0.7 - - + -
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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
----------------------------------------------------------
167A ILE* 4.0 17.7 - - + -
175A LYS 3.0 9.3 + - - +
176A THR 2.6 13.9 + - - +
178A LEU* 1.3 84.4 - - - +
180A ILE* 1.3 56.0 + - - +
182A ALA* 2.8 28.2 + - - +
183A ILE* 3.1 12.1 + - - +
259A ILE* 3.2 26.5 - - + -
327A LEU* 4.7 0.9 - - - -
329A ILE* 4.2 8.3 - - + -
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Residues in contact with ILE 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 THR* 2.7 30.0 + - + +
177A ALA* 3.5 11.2 - - - +
179A ALA* 1.3 73.5 - - - +
181A ASP* 1.3 53.0 + - - +
183A ILE* 3.0 12.6 + - + +
184A ILE* 2.7 40.5 + - + +
195A TYR* 3.6 30.3 - - + -
207A ASN* 5.8 1.6 - - - +
208A VAL* 3.6 34.1 - - + -
211A LYS* 2.9 40.4 - - + +
212A LEU* 5.6 6.7 - - + -
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Residues in contact with ASP 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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148A THR 3.6 4.1 - - - +
150A TYR* 3.1 28.0 + - + +
177A ALA 2.8 23.1 + - - +
178A LEU 3.3 4.3 - - - +
180A ILE* 1.3 77.5 - - - +
182A ALA* 1.3 57.1 + - - +
184A ILE* 3.7 12.7 - - - +
185A ASN* 3.0 28.9 + - - +
211A LYS* 3.7 13.2 + - - -
435A GLN* 2.7 41.2 - - - +
436A TYR* 3.5 12.3 - - - -
438A PRO* 5.0 9.0 - - + +
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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
----------------------------------------------------------
148A THR* 3.9 26.0 + - + +
178A LEU* 3.0 16.5 + - + +
179A ALA* 2.8 15.5 + - - +
181A ASP* 1.3 74.8 - - - +
183A ILE* 1.3 60.2 + - - +
185A ASN* 3.4 4.7 + - - +
186A GLN* 2.7 28.2 - - - +
257A LEU* 4.1 10.1 - - + +
327A LEU* 4.2 20.9 - - + -
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Residues in contact with ILE 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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179A ALA 3.1 29.4 + - - +
180A ILE* 3.0 12.7 + - + +
182A ALA* 1.3 75.4 - - - +
184A ILE* 1.3 62.0 + - - +
186A GLN* 2.8 25.6 + - - +
187A ARG* 3.8 2.6 + - - -
193A CYS* 3.7 27.4 - - + -
194A ILE 4.7 8.7 - - - +
195A TYR* 5.0 5.6 - - + -
212A LEU* 3.9 16.4 - - + -
217A ALA 4.9 1.7 - - - +
220A ASN* 5.3 0.7 + - - -
221A THR* 3.6 32.3 - - + +
257A LEU* 4.5 4.0 - - + -
259A ILE* 3.5 40.4 - - + -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 2.7 23.3 + - + +
181A ASP* 3.7 18.2 - - - +
183A ILE* 1.3 73.3 - - - +
185A ASN* 1.3 57.5 + - - +
186A GLN 3.2 3.8 + - - -
187A ARG* 3.2 51.9 + - - +
211A LYS* 3.8 34.5 - - + +
212A LEU* 4.5 22.0 - - + +
215A HIS* 4.4 25.4 - - + +
216A GLY* 4.6 2.0 - - - +
217A ALA 5.6 4.0 - - - +
436A TYR* 5.1 5.8 - - + +
438A PRO* 5.1 9.4 - - + -
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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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147A GLN* 2.8 30.6 - - - +
148A THR 3.7 8.7 - - - +
149A GLY* 3.4 18.4 + - - -
181A ASP 3.0 18.4 + - - +
182A ALA 3.8 5.2 - - - +
183A ILE 3.1 1.0 - - - -
184A ILE* 1.3 76.2 - - - +
186A GLN* 1.3 63.1 + - - +
187A ARG* 3.4 6.2 + - - +
188A ASP 4.8 0.5 + - - -
189A SER* 4.2 7.4 + - - -
438A PRO* 3.3 28.7 - - + +
439A MET 4.4 7.6 + - - +
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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