Contacts of the helix formed by residues 178 - 189 (chain D) in PDB entry 4GTU
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 PRO 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D LEU 3.8 0.4 - - - -
175D ASP 3.9 8.3 - - - +
176D ALA 3.5 8.7 - - - +
177D PHE* 1.3 87.1 - - - +
179D ASN* 1.3 62.7 + - + +
181D LYS* 3.0 28.6 + - + +
182D ASP* 3.0 21.5 - - - +
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Residues in contact with ASN 179 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D SER* 2.8 50.2 + - - +
141D LEU* 3.5 15.1 - - - +
142D GLY* 2.8 37.9 + - - +
177D PHE 2.9 1.1 + - - -
178D PRO* 1.3 79.6 - - + +
180D LEU* 1.3 63.7 + - - +
182D ASP* 3.9 7.8 + - - +
183D PHE 3.9 7.1 + - - -
186D ARG* 4.9 2.4 + - - -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D MET* 3.8 25.8 - - + +
137D PHE* 4.0 11.9 - - + -
138D SER* 3.4 29.2 - - - +
141D LEU* 4.1 5.2 - - + -
147D PHE* 4.1 21.3 - - + -
163D LEU* 4.2 20.9 - - + -
174D LEU* 4.5 14.6 - - + -
177D PHE* 2.8 24.8 + - + +
179D ASN* 1.3 82.3 - - - +
181D LYS* 1.3 58.4 + - - +
182D ASP 3.2 2.0 - - - -
183D PHE* 2.8 26.3 + - - +
184D ILE* 3.0 17.1 - - + +
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ARG* 5.6 5.6 + - - +
174D LEU* 3.1 41.0 - - + +
175D ASP* 3.3 31.2 + - - +
177D PHE 3.6 0.2 + - - -
178D PRO* 3.0 19.4 + - + +
180D LEU* 1.3 79.4 - - - +
182D ASP* 1.3 58.3 + - - +
184D ILE* 3.5 12.0 + - - +
185D SER* 2.7 28.8 + - - +
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Residues in contact with ASP 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D PRO* 3.0 22.1 + - - +
179D ASN* 4.3 7.0 - - - +
180D LEU 3.2 0.6 - - - -
181D LYS* 1.3 77.4 - - - +
183D PHE* 1.3 55.6 + - - +
185D SER* 3.3 13.7 + - - -
186D ARG* 2.8 54.3 + - + +
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Residues in contact with PHE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.8 19.5 - - + -
145D PRO 3.7 17.0 - - - -
146D TRP* 3.9 16.0 - + - -
147D PHE* 3.3 27.8 - + - -
156D ASP* 3.1 51.8 - - + -
159D ALA* 3.9 7.4 - - + -
160D TYR* 3.9 9.6 - - + -
163D LEU* 3.4 29.4 - - + -
179D ASN 3.9 2.4 + - - -
180D LEU* 2.8 15.5 + - - +
182D ASP* 1.3 77.3 - - - +
184D ILE* 1.3 63.7 + - + +
186D ARG* 3.6 11.8 + - - +
187D PHE* 3.3 20.9 + + - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D TYR* 3.3 34.8 - - + +
163D LEU* 3.9 26.2 - - + -
164D ASP* 5.3 1.8 - - + +
167D ARG* 4.0 22.4 - - - +
174D LEU* 3.4 32.1 - - + -
180D LEU 3.0 29.2 - - - +
181D LYS 3.9 6.5 - - - +
182D ASP 3.2 0.2 - - - -
183D PHE* 1.3 75.2 - - + +
185D SER* 1.3 60.0 + - - +
187D PHE* 3.2 6.3 + - - +
188D GLU* 2.9 43.8 + - - +
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Residues in contact with SER 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A SER* 2.7 28.7 + - - -
181D LYS 2.7 21.5 + - - -
182D ASP* 3.1 20.9 + - - -
184D ILE* 1.3 79.9 - - - +
186D ARG* 1.3 56.5 + - - +
188D GLU* 3.5 7.8 + - - +
189D GLY 3.4 10.2 + - - -
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A SER* 3.5 8.5 + - - +
188A GLU* 6.1 0.9 - - - +
141D LEU* 4.6 4.9 - - - +
144D ARG 4.4 4.4 + - - -
145D PRO* 3.1 46.4 + - - +
146D TRP* 4.3 19.4 - - + -
179D ASN 4.9 2.0 + - - -
182D ASP* 2.8 35.2 + - + +
183D PHE* 3.8 23.5 - - - +
185D SER* 1.3 70.2 - - - +
187D PHE* 1.3 68.5 + - - +
189D GLY* 3.0 11.6 + - - -
190D LEU* 3.4 17.5 + - + +
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Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.5 5.8 - - + -
146D TRP* 3.8 19.9 - + - -
152D ILE* 4.8 2.9 - - + -
156D ASP* 3.6 31.6 - - + -
157D PHE* 3.4 44.4 - + - -
160D TYR* 3.9 43.7 - + + -
183D PHE* 3.3 13.1 + + - +
184D ILE 3.2 8.9 + - - +
186D ARG* 1.3 78.1 - - - +
188D GLU* 1.3 57.4 + - - +
189D GLY 3.0 5.9 + - - -
190D LEU* 3.1 26.1 + - + +
193D ILE* 3.3 39.7 - - + +
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Residues in contact with GLU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP* 4.7 13.0 - - - +
185A SER* 5.6 0.2 - - - -
186A ARG* 4.9 4.5 + - - +
160D TYR* 3.9 21.8 + - + +
167D ARG* 3.5 27.2 + - - -
184D ILE* 2.9 28.8 + - + +
185D SER* 3.9 7.5 - - - +
186D ARG 3.3 0.2 - - - -
187D PHE* 1.3 73.7 - - - +
189D GLY* 1.3 56.6 + - - +
190D LEU 3.5 0.2 - - - -
193D ILE* 5.0 0.7 - - - -
194D SER* 3.0 19.0 + - - -
197D MET* 4.3 23.7 - - - +
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Residues in contact with GLY 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP 5.4 0.4 - - - -
185A SER* 3.5 30.1 - - - -
186A ARG* 3.4 26.0 - - - +
189A GLY* 3.5 2.9 - - - -
185D SER 3.4 3.4 + - - -
186D ARG 3.0 8.8 + - - -
187D PHE 3.0 0.4 + - - -
188D GLU* 1.3 77.6 - - - +
190D LEU* 1.3 66.0 + - - +
191D GLU* 3.1 5.2 + - - -
194D SER* 3.4 6.8 + - - -
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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