Contacts of the helix formed by residues 171 - 187 (chain A) in PDB entry 6AU8
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 ASP 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLN* 2.9 38.8 + - + +
151A LEU* 4.8 5.0 - - - +
166A PHE* 3.6 18.5 + - + +
169A SER* 2.9 17.3 + - - +
170A ALA* 1.3 74.0 - - - +
172A GLY* 1.3 61.1 + - - +
173A GLU* 3.5 7.3 + - - +
174A GLY* 3.0 22.4 + - - -
175A CYS* 3.1 17.7 + - - +
203A PHE* 5.1 2.5 - - - -
211A SER* 4.2 0.2 + - - -
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Residues in contact with GLY 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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170A ALA 3.5 6.5 + - - -
171A ASP* 1.3 74.5 - - - +
173A GLU* 1.3 58.5 + - - +
175A CYS* 3.4 7.4 + - - +
176A ALA* 2.9 28.6 + - - +
203A PHE* 4.7 2.2 - - - -
211A SER* 3.9 30.3 + - - +
214A VAL* 3.8 11.4 - - - +
215A VAL* 3.5 8.0 - - - -
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Residues in contact with GLU 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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171A ASP* 3.2 6.1 + - - +
172A GLY* 1.3 74.3 - - - +
174A GLY* 1.3 66.4 + - - +
176A ALA* 3.3 2.6 + - - +
177A ASN* 3.1 42.7 + - - +
214A VAL* 3.4 19.9 - - + +
218A THR* 4.0 17.7 - - + +
222A LYS* 4.6 6.7 + - - -
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Residues in contact with GLY 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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151A LEU* 5.5 1.3 - - - -
154A TRP* 3.9 10.5 - - - -
166A PHE* 3.6 13.9 - - - -
171A ASP* 3.0 25.5 + - - -
173A GLU* 1.3 73.5 - - - +
175A CYS* 1.3 66.5 + - - +
177A ASN* 3.2 6.1 + - - +
178A MET* 2.9 25.1 + - - +
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Residues in contact with CYS 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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163A ARG* 5.2 6.1 - - - -
166A PHE* 3.6 36.1 - - + -
167A LEU* 5.1 2.0 - - - -
171A ASP 3.1 18.9 + - - +
172A GLY* 3.5 9.6 - - - +
174A GLY* 1.3 77.8 - - - +
176A ALA* 1.3 57.9 + - - +
178A MET* 3.3 4.8 + - - +
179A LEU* 2.9 52.0 + - - +
199A ALA* 5.0 2.5 - - - -
203A PHE* 4.1 20.4 - - + -
215A VAL* 4.2 3.8 - - + -
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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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172A GLY 2.9 17.6 + - - +
173A GLU 3.7 0.2 - - - +
174A GLY 3.2 0.2 - - - -
175A CYS* 1.3 77.0 - - - +
177A ASN* 1.3 57.7 + - - +
179A LEU* 3.1 5.3 + - - +
180A VAL* 2.9 34.6 + - - +
215A VAL* 3.6 24.7 - - + +
218A THR* 3.5 30.7 - - + -
219A TYR* 3.6 9.7 - - + +
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Residues in contact with ASN 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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154A TRP* 3.7 23.6 - - + -
173A GLU* 3.1 36.9 + - - +
174A GLY* 3.2 3.1 + - - +
176A ALA* 1.3 75.8 - - - +
178A MET* 1.3 63.1 + - - +
180A VAL* 3.4 8.1 + - - +
181A GLU* 3.3 19.9 + - - +
218A THR* 4.1 2.2 - - - +
222A LYS* 3.2 46.6 + - - +
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Residues in contact with MET 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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154A TRP* 3.7 42.3 - - + +
159A TYR* 3.9 24.4 - - + +
162A SER* 3.8 8.3 - - - +
163A ARG* 3.5 42.6 - - + +
166A PHE* 3.9 16.4 - - + -
174A GLY 2.9 17.0 + - - +
175A CYS* 3.6 3.6 - - - +
177A ASN* 1.3 78.5 - - - +
179A LEU* 1.3 76.7 + - + +
181A GLU* 3.1 5.2 + - - +
182A TYR* 2.9 29.5 + - - -
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Residues in contact with LEU 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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163A ARG* 4.1 22.9 - - - +
175A CYS* 2.9 31.9 + - - +
176A ALA 3.7 3.6 - - - +
178A MET* 1.3 91.1 - - + +
180A VAL* 1.3 60.7 + - - +
182A TYR* 3.8 16.3 - - + +
183A SER* 2.8 33.3 + - - -
195A PHE* 4.1 23.6 - - + +
196A VAL* 5.1 0.4 - - - -
199A ALA* 3.7 30.7 - - + -
215A VAL* 4.5 7.4 - - + -
219A TYR* 3.8 15.9 - - + -
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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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176A ALA 2.9 20.0 + - - +
177A ASN* 3.6 9.9 - - - +
178A MET 3.2 0.2 - - - -
179A LEU* 1.3 76.6 - - - +
181A GLU* 1.3 60.0 + - - +
183A SER* 3.0 18.9 + - - -
184A THR* 2.9 22.3 + - + +
219A TYR* 3.8 23.6 - - + +
222A LYS* 4.2 14.1 - - + +
223A HIS* 4.2 22.0 - - + +
224A PRO* 4.1 25.8 - - + -
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Residues in contact with GLU 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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154A TRP* 2.9 31.4 + - - +
157A GLN* 4.3 9.0 + - - +
159A TYR* 2.5 33.5 + - + +
177A ASN 3.3 8.7 + - - +
178A MET 3.1 9.9 + - - +
180A VAL* 1.3 80.8 - - - +
182A TYR* 1.3 56.1 + - - +
184A THR* 3.2 5.5 + - - -
185A SER* 2.6 41.2 + - - +
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Residues in contact with TYR 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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159A TYR* 3.3 55.2 - + + -
160A CYS* 4.0 9.9 + - - +
163A ARG* 4.8 10.1 - - - -
178A MET* 2.9 20.6 + - + +
179A LEU* 3.8 24.2 - - + +
181A GLU* 1.3 71.8 - - - +
183A SER* 1.3 61.0 + - - +
185A SER* 4.6 1.8 - - - -
186A ARG* 2.8 39.9 + - + -
187A GLY 3.3 4.5 + - - -
195A PHE* 4.2 9.4 - + - -
1035C ALA* 3.1 36.3 + - + -
1038C SER* 2.6 26.8 + - - -
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Residues in contact with SER 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 LEU 2.8 26.3 + - - -
180A VAL 3.0 9.4 + - - -
182A TYR* 1.3 74.6 - - - +
184A THR* 1.3 57.8 + - - +
187A GLY* 3.1 27.4 + - - +
188A PHE 5.0 2.4 - - - +
192A VAL* 5.2 6.0 - - - +
195A PHE* 3.7 30.9 - - - -
219A TYR* 3.4 16.7 + - - -
223A HIS* 3.1 20.8 + - - -
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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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180A VAL* 2.9 23.4 + - + +
181A GLU* 3.2 8.3 + - - -
183A SER* 1.3 76.9 + - - +
185A SER* 1.3 63.5 + - - +
187A GLY 4.8 3.6 - - - +
223A HIS* 3.6 28.9 - - + +
224A PRO* 4.1 18.8 - - + -
225A SER* 5.6 0.4 - - - +
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Residues in contact with SER 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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159A TYR* 4.3 8.2 + - - -
181A GLU* 2.6 33.7 + - - +
182A TYR* 4.6 0.7 - - - -
184A THR* 1.3 81.0 + - - +
186A ARG* 1.3 78.2 + - - +
187A GLY 5.0 0.4 - - - -
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Residues in contact with ARG 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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157A GLN* 3.7 26.9 + - - +
159A TYR* 3.6 30.6 - - + +
182A TYR* 2.8 29.0 + - + +
185A SER* 1.3 88.5 - - - +
187A GLY* 1.3 66.7 + - - +
188A PHE* 4.6 5.9 - - - -
1033C SER* 4.2 7.3 - - - -
1035C ALA* 3.6 24.6 + - + +
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Residues in contact with GLY 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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182A TYR 3.3 3.6 + - - -
183A SER 3.1 21.2 + - - +
184A THR 4.8 3.6 - - - +
185A SER 5.0 0.5 - - - -
186A ARG* 1.3 82.4 + - - +
188A PHE* 1.3 67.4 + - - -
191A GLU* 3.7 2.7 - - - -
195A PHE* 4.0 13.9 - - - -
1033C SER* 3.7 13.0 - - - -
1035C ALA* 4.0 0.6 - - - +
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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