Contacts of the helix formed by residues 185 - 195 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ILE* 6.3 0.2 - - - -
176B PHE* 4.2 8.5 - - - +
177B MET 3.6 19.1 - - - +
178B CYS* 3.7 6.3 - - - -
183B ARG 4.4 0.2 + - - -
184B GLN* 1.3 70.4 - - - +
186B TYR* 1.3 60.8 + - - +
187B GLY 3.4 2.6 + - - +
188B GLU* 3.8 7.7 + - - +
189B GLY 3.7 11.4 + - - -
601B UNX 3.5 18.6 - - - -
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Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.2 22.0 - + - -
19B LEU* 4.4 7.0 - - + -
41B LEU* 3.8 22.9 - - + -
44B MET* 3.4 25.3 + - + +
45B LEU* 4.8 5.8 - - + -
132B LEU* 3.9 30.2 - - + +
178B CYS* 3.5 8.0 - - + +
180B VAL* 3.9 32.8 - - + -
183B ARG* 3.7 38.9 + - - +
184B GLN 3.3 9.3 + - - -
185B GLY* 1.3 76.0 - - - +
187B GLY* 1.3 57.9 + - - +
189B GLY* 2.9 3.6 + - - -
190B PHE* 2.8 46.2 + + + -
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 3.8 23.0 - - - +
19B LEU* 4.2 7.4 - - - -
185B GLY 3.4 1.0 - - - +
186B TYR* 1.3 84.9 - - - +
188B GLU* 1.3 51.5 + - - +
190B PHE* 3.2 2.9 + - - +
191B ARG* 2.8 55.2 + - - +
601B UNX 3.9 3.1 - - - -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LYS* 4.3 14.0 - - - +
176B PHE* 3.2 25.7 - - + -
185B GLY* 4.0 9.0 - - - +
186B TYR 3.3 0.2 - - - -
187B GLY* 1.3 74.4 - - - +
189B GLY* 1.3 59.2 + - - +
191B ARG* 3.4 22.6 + - + +
192B TRP* 2.9 28.2 + - - +
601B UNX 3.4 11.9 - - - -
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Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 3.4 21.7 - - - +
132B LEU* 4.8 0.7 - - - -
176B PHE* 3.6 32.1 - - - -
185B GLY 3.7 3.4 + - - -
186B TYR 2.9 9.6 + - - -
188B GLU* 1.3 77.7 - - - +
190B PHE* 1.3 62.7 + - - +
192B TRP* 3.4 5.7 + - - +
193B LEU* 3.1 17.5 + - - +
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Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.3 48.7 - - + +
21B LEU* 4.5 7.4 - - + +
28B LEU* 4.1 16.6 - - + -
30B PHE* 3.7 34.5 - + - -
41B LEU* 4.1 30.7 - - + -
45B LEU* 4.9 3.4 - - + -
71B PHE* 4.6 4.9 - + - -
97B VAL* 4.0 18.2 - - + -
130B LEU* 4.1 8.7 - - + -
132B LEU* 4.4 5.8 - - + -
186B TYR* 2.8 36.2 + + + -
187B GLY 3.6 7.0 - - - +
189B GLY* 1.3 72.3 - - - +
191B ARG* 1.3 63.5 + - - +
193B LEU* 3.1 7.4 + - + +
194B SER* 3.0 19.8 + - - -
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN 5.1 2.2 - - - -
18B PHE* 2.9 53.0 + - - +
19B LEU 3.6 12.3 - - - -
20B GLY* 3.7 6.7 - - - +
162B ASN* 5.5 2.3 + - - -
187B GLY 2.8 31.9 + - - +
188B GLU* 3.5 34.4 - - + +
190B PHE* 1.3 71.7 - - - +
192B TRP* 1.3 62.6 + - - +
194B SER* 2.6 22.9 + - - +
195B GLN* 3.7 3.8 + - - +
601B UNX 4.1 5.9 - - - -
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Residues in contact with TRP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO* 5.0 0.9 - - + -
129B ILE 3.5 27.4 - - - -
130B LEU* 3.8 18.6 - - + -
158B THR* 4.3 3.8 + - - -
159B GLY 2.9 25.2 + - - -
160B LYS* 3.4 21.1 - - - +
161B GLY 3.6 1.5 + - - -
162B ASN* 5.9 0.9 - - - +
172B PRO* 3.9 18.4 - - + -
173B MET* 3.7 16.2 - - - -
174B GLU* 3.5 22.7 - - + -
176B PHE* 3.4 31.0 - + + -
188B GLU 2.9 11.1 + - - +
189B GLY 3.5 8.7 - - - +
190B PHE 3.2 0.2 - - - -
191B ARG* 1.3 76.3 - - - +
193B LEU* 1.3 89.0 + - + +
195B GLN* 2.8 52.2 + - - +
196B TYR* 4.0 10.5 + + - -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 6.2 1.1 - - + -
28B LEU* 4.0 23.3 - - + -
95B GLY* 4.5 2.2 - - - -
96B ILE 4.6 3.6 - - - +
97B VAL* 4.0 27.1 - - + -
128B PRO* 3.5 42.4 - - + +
130B LEU* 4.1 12.6 - - + -
189B GLY 3.1 12.9 + - - +
190B PHE* 3.1 11.2 + - + +
192B TRP* 1.3 92.8 - - + +
194B SER* 1.3 56.8 + - - +
196B TYR* 3.0 24.6 + - + +
197B ILE* 3.6 17.2 - - + +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 3.9 0.2 - - - -
20B GLY* 3.3 35.2 + - - -
21B LEU* 3.7 10.1 - - - +
24B LYS* 3.3 18.6 - - - -
190B PHE 3.0 12.3 + - - -
191B ARG* 2.6 23.7 + - - +
193B LEU* 1.3 72.0 - - - +
195B GLN* 1.3 64.7 + - - +
196B TYR 3.0 2.5 - - - -
197B ILE* 3.0 22.2 + - - +
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Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 5.5 0.4 + - - +
161B GLY 3.3 19.0 + - - -
162B ASN* 3.0 29.9 + - - +
163B VAL 3.1 21.8 + - - +
191B ARG 4.7 1.6 - - - +
192B TRP* 2.8 41.6 + - - +
194B SER* 1.3 82.6 + - - +
196B TYR* 1.3 88.5 + - + +
197B ILE 3.5 3.2 + - - +
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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