Contacts of the helix formed by residues 185 - 196 (chain A) in PDB entry 1GCA
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 THR 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASN* 4.4 6.7 + - - -
183A TRP 4.1 1.2 + - - -
184A ASP* 1.3 76.4 + - - +
186A ALA* 1.3 64.3 + - - +
188A ALA* 3.3 2.3 + - - +
189A LYS* 3.0 20.4 + - + +
213A ALA* 2.9 38.8 + - - +
216A MET* 4.0 12.3 - - + +
217A GLY* 3.5 11.9 - - - +
220A GLU* 3.7 23.8 - - - +
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Residues in contact with ALA 186 (chain A).
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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184A ASP* 3.4 11.5 + - - +
185A THR* 1.3 80.1 - - - +
187A GLN* 1.3 62.1 + - + +
189A LYS* 3.4 10.3 + - - +
190A ASP* 3.2 25.1 + - - +
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Residues in contact with GLN 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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180A THR 4.5 2.6 - - - +
181A ALA* 3.5 25.2 - - + +
182A MET* 3.4 34.4 - - - +
184A ASP* 3.0 24.8 + - - +
185A THR 3.4 0.2 - - - -
186A ALA* 1.3 75.8 - - + +
188A ALA* 1.3 58.4 + - - +
190A ASP* 3.4 7.4 + - - +
191A LYS* 3.1 32.8 + - + +
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Residues in contact with ALA 188 (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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146A LEU* 4.2 13.0 - - + +
181A ALA* 3.6 11.6 - - + +
184A ASP 3.1 17.1 + - - +
185A THR 3.5 4.5 - - - +
187A GLN* 1.3 76.7 - - - +
189A LYS* 1.3 59.2 + - - +
191A LYS* 3.3 1.7 + - - +
192A MET* 2.9 31.4 + - - +
214A MET* 3.3 40.4 - - + +
217A GLY* 4.3 2.5 - - - -
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Residues in contact with LYS 189 (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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185A THR* 3.0 12.7 + - + +
186A ALA* 3.6 12.8 - - - +
188A ALA* 1.3 73.5 - - - +
190A ASP* 1.3 62.3 + - - +
192A MET 3.4 0.2 + - - -
193A ASP* 2.9 32.1 + - + +
217A GLY* 3.4 24.1 - - - +
220A GLU* 3.4 41.8 + - + +
221A ALA* 3.7 12.1 - - + +
224A ALA* 6.0 2.9 - - - -
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Residues in contact with ASP 190 (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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186A ALA 3.2 13.7 + - - +
187A GLN* 3.7 9.8 - - - +
188A ALA 3.3 0.2 - - - -
189A LYS* 1.3 84.6 - - - +
191A LYS* 1.3 63.6 + - + +
193A ASP* 3.4 10.8 + - - +
194A ALA* 3.1 22.9 + - - +
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Residues in contact with LYS 191 (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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146A LEU* 4.1 14.8 - - + -
179A ASP* 2.8 49.0 + - + +
180A THR 4.0 14.1 - - - +
181A ALA* 4.9 2.2 - - + -
187A GLN* 3.1 19.8 + - + +
188A ALA 3.3 4.0 + - - +
190A ASP* 1.3 73.7 - - + +
192A MET* 1.3 65.0 + - - +
194A ALA* 3.3 10.3 + - - +
195A TRP* 3.1 52.2 + - + +
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Residues in contact with MET 192 (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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144A VAL* 4.3 6.3 - - + -
146A LEU* 4.9 2.4 - - + +
188A ALA 2.9 17.6 + - - +
191A LYS* 1.3 76.0 - - - +
193A ASP* 1.3 62.8 + - - +
195A TRP* 3.2 23.4 + - + +
196A LEU* 2.9 57.5 + - + +
204A ILE* 4.2 18.4 - - + -
207A VAL* 4.0 26.9 - - + -
218A ALA* 3.9 30.7 - - + +
221A ALA* 3.5 23.1 - - + -
222A LEU* 4.3 6.5 - - + -
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Residues in contact with ASP 193 (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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189A LYS* 2.9 20.7 + - + +
190A ASP* 3.6 12.9 - - - +
192A MET* 1.3 76.1 - - - +
194A ALA* 1.3 60.5 + - - +
196A LEU* 3.3 2.8 + - - +
197A SER* 2.8 34.7 + - - -
221A ALA* 3.8 10.7 - - + +
225A HIS* 2.9 27.7 + - + -
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Residues in contact with ALA 194 (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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190A ASP 3.1 14.0 + - - +
191A LYS* 3.5 17.3 - - - +
193A ASP* 1.3 77.5 - - - +
195A TRP* 1.3 66.2 + - + +
197A SER* 3.1 16.0 + - - -
198A GLY* 3.2 12.0 + - - -
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Residues in contact with TRP 195 (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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144A VAL* 3.7 29.8 - - + -
145A LEU 3.6 22.0 - - - -
146A LEU* 3.8 31.4 - - + -
177A ALA* 3.5 30.2 - - + +
178A LEU* 4.0 2.0 - - - -
179A ASP* 3.8 15.0 - - + -
191A LYS* 3.1 42.1 + - + +
192A MET* 3.2 21.7 + - + +
194A ALA* 1.3 77.8 - - + +
196A LEU* 1.3 60.8 + - - +
197A SER 3.1 0.9 + - - -
198A GLY* 3.3 11.0 + - - +
200A ASN* 4.6 3.1 + - + +
201A ALA* 3.8 16.6 + - - +
204A ILE* 4.4 17.1 - - + +
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Residues in contact with LEU 196 (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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192A MET* 2.9 41.7 + - + +
193A ASP 3.3 1.5 + - - +
195A TRP* 1.3 73.7 - - - +
197A SER* 1.3 58.1 + - - +
198A GLY 3.5 0.7 - - - -
201A ALA* 3.4 27.2 - - + +
204A ILE* 4.4 11.9 - - + -
221A ALA* 3.4 33.4 - - + +
222A LEU* 4.0 19.3 - - + -
225A HIS* 3.6 38.2 + - + +
227A LYS* 4.6 15.0 - - + -
230A ILE* 6.3 0.4 - - + -
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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