Contacts of the helix formed by residues 182 - 192 (chain D) in PDB entry 3GTU
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ASP 3.9 4.4 - - - +
180D GLU 3.6 8.5 - - - +
181D PHE* 1.4 87.6 - - - +
183D ASN* 1.3 65.5 + - + +
185D LYS* 3.6 21.9 - - - +
186D ALA* 3.1 24.1 + - - +
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Residues in contact with ASN 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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142D SER* 2.8 48.6 + - - +
145D LEU* 3.8 14.4 - - - +
146D GLY* 2.9 31.5 + - - +
148D PHE 5.2 1.6 - - - +
182D PRO* 1.3 85.9 - - + +
184D LEU* 1.3 62.3 + - - +
186D ALA* 3.4 6.9 + - - +
187D PHE* 3.3 17.5 + - - +
190D ARG* 5.0 2.1 + - - -
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Residues in contact with LEU 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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138D LEU* 3.7 46.2 - - + +
141D PHE* 4.1 10.1 - - + -
142D SER* 3.9 27.1 - - - +
145D LEU* 4.3 8.3 - - + -
151D PHE* 4.2 19.5 - - + -
167D LEU* 4.4 12.6 - - + -
178D LEU* 4.1 14.6 - - + -
181D PHE* 3.0 22.2 + - + +
183D ASN* 1.3 77.0 - - - +
185D LYS* 1.3 66.3 + - - +
187D PHE* 3.0 9.8 + - + +
188D MET* 3.0 26.0 + - - +
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Residues in contact with LYS 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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178D LEU* 3.4 33.7 - - + +
179D ASP* 3.3 41.1 + - - +
181D PHE 3.3 1.7 + - - +
182D PRO* 3.6 21.8 - - - +
183D ASN 3.4 0.2 - - - -
184D LEU* 1.3 74.4 - - - +
186D ALA* 1.3 63.8 + - - +
188D MET* 3.1 12.6 + - - +
189D CYS* 3.1 27.6 + - - -
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Residues in contact with ALA 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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182D PRO 3.1 12.8 + - - +
183D ASN* 3.4 12.6 - - - +
185D LYS* 1.3 73.8 - - - +
187D PHE* 1.3 65.7 + - - +
189D CYS* 3.3 7.3 + - - +
190D ARG* 2.9 40.6 + - - +
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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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145D LEU* 4.0 13.2 - - + -
149D SER 4.2 6.5 - - - -
150D TRP* 3.5 24.9 - + - -
151D PHE* 4.0 24.0 - + - -
160D ASP* 3.3 46.9 - - + -
164D TYR* 4.1 28.7 - - + -
167D LEU* 4.2 9.9 - - + -
183D ASN 3.3 9.3 + - - +
184D LEU* 3.0 11.3 + - - +
186D ALA* 1.3 77.8 - - - +
188D MET* 1.3 72.2 + - - +
190D ARG* 3.2 14.6 + - - +
191D PHE* 2.8 36.5 + - + +
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Residues in contact with MET 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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164D TYR* 3.8 19.7 - - + +
167D LEU* 3.5 36.1 - - + +
168D ASP* 3.5 16.2 - - - +
171D ARG* 3.1 41.5 - - - +
178D LEU* 3.8 18.2 - - + -
184D LEU 3.0 14.2 + - - +
185D LYS* 3.1 8.7 + - - +
187D PHE* 1.3 88.9 - - - +
189D CYS* 1.3 59.1 + - - +
191D PHE* 3.2 5.4 + - - +
192D GLU* 2.9 35.9 + - - +
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Residues in contact with CYS 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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185D LYS* 3.1 16.6 + - - -
186D ALA* 3.8 8.3 - - - +
188D MET* 1.3 79.7 - - - +
190D ARG* 1.3 58.6 + - - +
192D GLU* 3.8 8.1 - - - +
193D ALA* 2.9 35.1 + - + +
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Residues in contact with ARG 190 (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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145D LEU* 4.9 3.8 - - - +
148D PHE 3.9 6.7 + - - -
149D SER* 2.8 47.7 + - - +
150D TRP* 3.5 21.6 - - + -
183D ASN* 5.0 1.6 + - - -
186D ALA* 2.9 41.3 + - - +
187D PHE* 3.4 23.8 - - - +
189D CYS* 1.3 76.2 - - - +
191D PHE* 1.3 61.9 + - - +
193D ALA* 3.7 10.8 + - - +
194D LEU* 3.7 14.9 + - - +
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Residues in contact with PHE 191 (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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22D LEU* 4.3 4.3 - - + -
150D TRP* 4.2 17.0 - + + -
156D LEU* 4.7 1.3 - - + -
160D ASP* 4.3 9.4 - - + -
161D PHE* 3.4 62.6 - + - -
164D TYR* 3.4 46.7 - + + -
187D PHE* 2.8 22.7 + + + +
188D MET* 3.2 4.2 + - - +
190D ARG* 1.3 73.1 - - - +
192D GLU* 1.3 65.7 + - - +
193D ALA 3.1 1.3 - - - -
194D LEU* 3.2 41.7 + - + +
197D ILE* 3.7 27.9 - - + +
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Residues in contact with GLU 192 (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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164D TYR* 3.4 33.1 + - + +
171D ARG* 3.1 37.6 + - - -
188D MET* 2.9 27.7 + - - +
189D CYS* 4.1 6.8 + - - +
191D PHE* 1.3 71.0 - - - +
193D ALA* 1.3 56.6 + - - +
194D LEU 3.2 2.1 + - - -
197D ILE* 4.1 7.9 - - - -
198D ALA* 3.2 30.0 + - - +
201D LEU* 3.7 15.3 - - + +
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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