Contacts of the helix formed by residues 172 - 186 (chain Y) in PDB entry 3EXG
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 GLN 172 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1771 GLU* 3.9 3.4 + - - -
572 ILE* 3.2 23.2 + - - +
592 GLU* 3.2 13.7 + - - -
882 GLN* 2.9 41.2 + - - +
138Y VAL* 3.2 31.1 + - + +
139Y GLY* 4.0 7.4 - - - -
169Y ALA 3.1 16.7 + - - +
170Y ALA 3.6 0.8 - - - -
171Y ASN* 1.3 76.4 - - - +
173Y GLY* 1.3 69.3 + - - +
174Y GLN* 3.1 19.9 - - + +
175Y ILE* 3.0 28.0 + - + +
176Y PHE* 3.7 4.5 - - - -
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Residues in contact with GLY 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1731 GLY* 3.4 33.2 - - - -
1741 GLN 4.4 0.2 - - - -
1771 GLU* 2.9 37.4 + - - +
172Y GLN* 1.3 71.3 + - - +
174Y GLN* 1.3 62.4 + - - +
175Y ILE 3.0 1.9 + - - -
176Y PHE* 3.0 19.6 + - - +
177Y GLU 3.6 1.7 + - - -
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Residues in contact with GLN 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882 GLN* 3.5 7.5 + - - -
139Y GLY 3.3 8.8 - - - +
140Y ALA* 3.2 29.8 - - - +
143Y PRO* 3.3 16.3 - - + +
172Y GLN* 3.4 25.1 + - + +
173Y GLY* 1.3 70.3 - - - +
175Y ILE* 1.3 68.1 + - - +
176Y PHE 3.3 0.2 - - - -
177Y GLU* 3.3 15.4 + - - +
178Y ALA* 3.2 18.0 + - - +
60Z MET* 3.2 50.4 - - + +
91Z ASP* 3.6 9.3 + - - -
92Z GLN* 3.2 10.4 + - - -
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Residues in contact with ILE 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Y GLY* 4.9 3.8 - - - +
142Y VAL* 3.5 39.0 - - + -
165Y TYR* 3.9 22.9 - - + -
169Y ALA* 3.0 30.3 - - + +
170Y ALA* 4.2 5.6 - - - +
172Y GLN* 3.0 18.4 + - + +
174Y GLN* 1.3 77.4 - - - +
176Y PHE* 1.3 64.8 + - + +
178Y ALA* 2.8 21.3 + - - +
179Y TYR* 3.1 46.6 + - + +
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Residues in contact with PHE 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1711 ASN* 5.2 1.1 - - - +
1731 GLY* 5.0 0.4 - - - -
1761 PHE* 3.5 70.1 - + + -
2161 ARG* 5.2 2.4 + - - -
170Y ALA 4.0 12.3 - - - -
171Y ASN* 4.4 6.3 - - - -
172Y GLN 3.7 16.2 - - - -
173Y GLY* 3.0 9.7 + - - +
175Y ILE* 1.3 79.2 - - + +
177Y GLU* 1.3 60.4 + - - +
179Y TYR* 3.6 30.2 + + - +
180Y ASN* 3.4 19.9 + - - +
216Y ARG* 3.3 53.4 - - + -
219Y PHE* 5.6 0.7 - - - -
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Residues in contact with GLU 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711 ASN 3.0 23.9 - - - +
1721 GLN* 3.4 7.6 + - - -
1731 GLY* 2.9 30.6 + - - +
173Y GLY 3.6 1.8 + - - +
174Y GLN* 3.3 11.4 + - - +
175Y ILE 3.1 1.0 - - - -
176Y PHE* 1.3 76.7 - - - +
178Y ALA* 1.3 65.2 + - - +
180Y ASN* 3.9 4.6 - - - +
181Y MET* 3.2 31.0 + - - +
58Z SER* 3.3 34.3 - - - +
60Z MET* 3.8 9.8 + - - +
61Z GLY* 2.9 29.6 + - - -
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Residues in contact with ALA 178 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y VAL* 3.8 22.9 - - + -
143Y PRO* 4.0 11.4 - - + -
146Y ALA* 4.0 22.4 - - + +
174Y GLN 3.2 8.7 + - - +
175Y ILE 2.8 9.9 + - - +
177Y GLU* 1.3 77.9 - - - +
179Y TYR* 1.3 58.8 + - - +
181Y MET* 4.3 5.3 - - - +
182Y ALA* 2.8 34.0 + - - +
191Y PHE* 3.7 4.7 - - + -
61Z GLY* 5.3 0.4 - - - -
65Z ILE* 5.1 1.8 - - + -
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Residues in contact with TYR 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Y TYR* 2.5 29.0 + - - -
170Y ALA 5.6 1.2 + - - -
175Y ILE* 3.1 30.8 + - + +
176Y PHE* 3.7 39.0 - + - +
177Y GLU 3.3 0.2 - - - -
178Y ALA* 1.3 76.2 - - - +
180Y ASN* 1.3 66.8 + - - +
182Y ALA* 3.7 0.2 - - - +
183Y ALA* 2.9 17.5 + - - +
191Y PHE* 3.9 24.5 - + - -
216Y ARG* 3.7 27.3 - - + +
217Y GLY* 4.6 3.6 - - - +
219Y PHE* 4.0 9.4 - - + -
220Y ILE* 3.2 33.2 - - + +
252Y LEU* 3.7 26.7 - - + +
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Residues in contact with ASN 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711 ASN* 3.4 35.3 - - + +
2071 ALA 3.5 17.6 + - - -
2081 ALA* 3.6 2.5 - - - +
2091 ALA* 3.1 27.8 + - - +
2161 ARG* 4.2 3.5 + - - +
176Y PHE 3.4 13.8 + - - +
177Y GLU* 3.9 6.5 - - - +
178Y ALA 3.3 0.2 - - - -
179Y TYR* 1.3 78.3 - - - +
181Y MET* 1.3 53.6 + - - +
183Y ALA* 2.8 5.2 + - - +
184Y LEU* 2.7 37.2 + - - +
219Y PHE* 3.7 16.7 - - + -
56Z PRO* 3.7 15.2 - - - +
58Z SER* 5.7 0.2 - - - +
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Residues in contact with MET 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177Y GLU 3.2 23.9 + - - +
178Y ALA 4.3 0.4 - - - +
180Y ASN* 1.3 80.5 - - - +
182Y ALA* 1.3 64.3 + - - +
184Y LEU* 3.4 7.2 - - + +
185Y TRP* 3.0 66.7 + - + +
187Y LEU* 4.7 0.4 - - - -
56Z PRO* 3.8 27.6 - - + -
58Z SER* 3.5 20.0 - - - -
61Z GLY* 3.6 9.4 - - - -
62Z PHE* 3.3 42.2 - - - +
65Z ILE* 3.9 15.0 - - + -
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Residues in contact with ALA 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Y ALA* 5.0 1.1 - - + +
178Y ALA 2.8 24.5 + - - +
179Y TYR 3.7 2.0 - - - +
181Y MET* 1.3 71.8 - - - +
183Y ALA* 1.3 58.3 + - - +
186Y LYS* 2.8 24.4 + - - -
187Y LEU* 2.9 36.2 + - + +
189Y CYS* 4.8 1.8 - - + -
191Y PHE* 3.5 28.5 - - + -
250Y PRO* 3.7 13.3 - - + +
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Residues in contact with ALA 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091 ALA* 3.6 11.4 - - + -
179Y TYR 2.9 11.8 + - - +
180Y ASN 2.8 13.8 + - - +
182Y ALA* 1.3 69.6 - - - +
184Y LEU* 1.3 68.2 + - - +
186Y LYS* 3.0 17.5 + - - +
219Y PHE* 3.6 25.4 - - + +
220Y ILE* 4.1 7.6 - - + -
250Y PRO* 3.8 11.4 - - + +
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Residues in contact with LEU 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2061 ARG* 3.6 27.8 - - - +
2071 ALA 3.3 23.1 - - - +
2081 ALA 4.1 6.1 - - - +
2091 ALA* 3.9 25.4 - - + +
180Y ASN* 2.7 26.4 + - - +
181Y MET* 3.4 6.5 - - - +
183Y ALA* 1.3 76.4 - - - +
185Y TRP* 1.3 81.0 + - + +
186Y LYS* 4.4 6.9 - - - +
56Z PRO* 4.3 13.5 - - + -
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Residues in contact with TRP 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Y LEU* 4.4 20.6 - - + -
153Y LYS* 3.2 25.6 + - - +
181Y MET* 3.0 56.2 + - + +
184Y LEU* 1.3 94.0 - - + +
186Y LYS* 1.3 76.2 + - - +
187Y LEU* 4.1 17.7 - - + -
26Z LEU* 4.7 7.9 - - + -
53Z ILE* 3.8 30.0 - - + +
54Z ASP 3.9 15.8 + - - -
55Z THR* 4.4 7.6 - - + -
56Z PRO* 4.4 7.0 - - + -
65Z ILE* 4.1 22.2 - - + -
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Residues in contact with LYS 186 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y LYS* 3.9 14.8 - - - +
182Y ALA 2.8 10.8 + - - -
183Y ALA 3.0 15.1 + - - +
184Y LEU 4.4 6.1 - - - +
185Y TRP* 1.3 83.1 - - - +
187Y LEU* 1.3 60.8 + - - +
188Y PRO* 3.9 2.6 - - - +
247Y GLY 3.8 21.6 + - - +
248Y LYS* 4.7 12.3 + - - +
249Y GLY* 4.1 15.9 - - - -
250Y PRO* 4.4 1.3 - - + -
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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