Contacts of the helix formed by residues 185 - 195 (chain A) in PDB entry 2GAO
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 GLY 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A PHE* 4.3 8.8 - - - +
177A MET 3.7 19.9 - - - +
178A CYS* 3.6 6.7 - - - +
184A GLN* 1.3 72.7 - - - +
186A TYR* 1.3 61.2 + - - +
187A GLY 3.5 2.1 + - - +
188A GLU* 3.7 16.8 + - - +
189A GLY 3.8 6.1 + - - -
602A UNX 3.8 13.9 - - - -
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Residues in contact with TYR 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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18A PHE* 3.7 25.8 - + - -
41A LEU* 3.8 26.2 - - + -
44A MET* 3.4 23.1 + - + +
45A LEU* 4.2 9.9 - - + -
132A LEU* 4.0 31.9 - - + +
178A CYS* 3.5 7.1 - - + +
179A SER 4.6 0.2 - - - -
180A VAL* 3.8 33.7 - - + -
183A ARG* 3.8 37.1 + - - +
184A GLN 3.4 9.5 + - - -
185A GLY* 1.3 72.1 - - - +
187A GLY* 1.3 80.0 + - - +
188A GLU 3.2 2.0 - - - -
189A GLY* 3.0 3.3 + - - -
190A PHE* 3.0 34.7 + + + -
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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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18A PHE* 3.5 33.6 - - - +
185A GLY 3.5 0.8 - - - -
186A TYR* 1.3 82.8 - - - +
188A GLU* 1.3 57.4 + - - +
190A PHE* 3.4 6.1 + - - +
191A ARG* 3.0 44.0 + - - +
602A UNX 4.0 4.3 - - - -
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Residues in contact with GLU 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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160A LYS* 6.3 0.2 - - - -
176A PHE* 3.8 21.2 - - + -
185A GLY* 3.7 12.9 + - - +
186A TYR 3.2 0.4 - - - -
187A GLY* 1.3 76.6 - - - +
189A GLY* 1.3 55.8 + - - +
191A ARG* 3.5 25.0 + - + +
192A TRP* 3.0 27.0 + - - +
602A UNX 3.8 7.5 - - - -
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Residues in contact with GLY 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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130A LEU* 3.5 19.5 - - - +
132A LEU* 5.1 0.2 - - - -
176A PHE* 3.6 31.1 - - - -
185A GLY 3.8 3.4 + - - -
186A TYR* 3.0 9.4 + - - -
188A GLU* 1.3 76.5 - - - +
190A PHE* 1.3 58.5 + - - +
192A TRP* 3.3 6.4 + - - +
193A LEU 2.9 23.7 + - - -
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Residues in contact with PHE 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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19A LEU* 3.3 48.1 - - + +
21A LEU* 4.5 4.1 - - + +
28A LEU* 4.0 29.2 - - + -
30A PHE* 3.7 31.4 - + - -
41A LEU* 4.0 21.1 - - + -
45A LEU* 4.5 5.6 - - + -
71A PHE* 4.5 6.7 - + - -
97A VAL* 4.1 10.5 - - + -
130A LEU* 4.1 15.3 - - + -
132A LEU* 4.5 4.9 - - + -
186A TYR* 3.0 35.3 + + - -
187A GLY 3.8 6.1 - - - +
189A GLY* 1.3 71.6 - - - +
191A ARG* 1.3 54.5 + - - +
193A LEU* 3.2 6.6 + - + +
194A SER* 2.7 32.6 + - - -
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Residues in contact with ARG 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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17A GLN 4.7 3.4 - - - -
18A PHE* 2.8 60.7 + - - +
19A LEU 3.6 12.1 - - - -
20A GLY* 3.9 5.2 - - - +
162A ASN* 5.5 1.2 - - - +
187A GLY 3.0 31.1 + - - +
188A GLU* 3.6 27.2 - - + +
190A PHE* 1.3 76.1 - - - +
192A TRP* 1.3 62.8 + - - +
194A SER* 2.6 22.5 + - - +
195A GLN* 3.8 3.5 + - - +
602A UNX 4.0 9.7 - - - -
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Residues in contact with TRP 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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129A ILE 3.4 18.8 - - - -
130A LEU* 4.0 15.0 - - + -
158A THR* 4.1 4.3 - - - -
159A GLY 3.1 19.5 + - - -
160A LYS* 3.5 28.5 - - - +
161A GLY 4.2 0.2 + - - -
162A ASN* 5.7 0.7 - - - -
172A PRO* 4.0 6.7 - - + -
173A MET* 3.6 16.2 - - - -
174A GLU* 3.3 38.8 - - + +
176A PHE* 3.7 13.9 - + + -
188A GLU 3.0 14.8 + - - +
189A GLY 3.4 12.8 - - - +
190A PHE 3.3 0.2 - - - -
191A ARG* 1.3 76.0 - - - +
193A LEU* 1.3 97.0 + - + +
194A SER 3.2 0.5 + - - -
195A GLN* 3.0 47.9 + - - +
196A TYR* 3.8 22.0 + + - -
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Residues in contact with LEU 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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28A LEU* 4.2 23.1 - - + -
95A GLY* 4.8 1.1 - - - -
96A ILE 4.4 4.0 - - - +
97A VAL* 4.0 27.8 - - + -
128A PRO* 3.5 45.1 - - + +
130A LEU* 4.0 12.6 - - + +
189A GLY 2.9 19.0 + - - +
190A PHE* 3.2 7.8 + - + +
192A TRP* 1.3 95.4 - - + +
194A SER* 1.3 63.1 + - - +
196A TYR* 3.0 22.3 + - + +
197A ILE* 3.7 11.0 - - + +
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Residues in contact with SER 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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19A LEU 3.6 8.3 - - - -
20A GLY* 3.2 32.7 + - - -
21A LEU* 3.8 7.6 - - - -
24A LYS* 3.3 19.5 + - - -
190A PHE 2.7 18.8 + - - -
191A ARG* 2.6 19.6 + - - +
193A LEU* 1.3 73.4 - - - +
195A GLN* 1.3 61.9 + - - +
196A TYR 3.1 0.9 + - - -
197A ILE* 3.1 19.7 + - - +
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Residues in contact with GLN 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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24A LYS* 5.0 4.4 + - - +
161A GLY 3.0 22.2 + - - -
162A ASN* 3.3 24.1 + - - +
163A VAL 3.2 30.5 + - - +
164A THR* 5.2 0.3 - - - -
191A ARG 3.8 1.5 + - - +
192A TRP* 3.0 36.4 + - - +
193A LEU 3.2 0.2 - - - -
194A SER* 1.3 79.8 + - - +
196A TYR* 1.3 80.4 - - + +
197A ILE 3.5 2.2 + - - +
198A ASP 5.3 1.9 - - - +
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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