Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 2GAU
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 ASP 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ARG 3.8 9.4 - - - +
209A MET* 3.2 12.2 + - - +
219A ILE* 4.0 2.9 - - - -
220A ILE* 1.3 79.3 - - - +
222A CYS* 1.3 58.2 + - - +
223A ASP* 3.7 8.8 + - - +
224A ARG* 2.4 63.3 + - + +
225A LEU* 3.0 27.4 + - - +
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Residues in contact with CYS 222 (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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162A LEU* 4.0 9.2 - - - -
165A LYS* 3.8 35.7 - - - -
170A PHE* 5.4 3.1 - - + -
219A ILE* 3.6 19.2 + - + +
220A ILE 4.0 0.8 - - - -
221A ASP* 1.3 72.0 + - - +
223A ASP* 1.3 62.0 + - - +
225A LEU* 3.1 3.2 + - - +
226A GLN* 2.8 60.4 + - - +
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Residues in contact with ASP 223 (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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221A ASP* 3.4 8.4 + - - +
222A CYS* 1.3 77.7 - - - +
224A ARG* 1.3 58.4 + - + +
226A GLN* 3.4 18.8 + - - +
227A LYS* 3.1 25.5 + - - +
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Residues in contact with ARG 224 (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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207A GLU* 2.7 32.1 + - - +
208A ARG* 3.6 17.2 + - - +
209A MET* 2.9 30.9 - - + +
221A ASP* 2.4 52.3 + - - +
222A CYS 3.2 0.4 - - - -
223A ASP* 1.3 76.6 - - + +
225A LEU* 1.3 59.5 - - - +
227A LYS* 3.1 16.1 + - + +
228A THR* 2.9 31.5 + - - -
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Residues in contact with LEU 225 (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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158A ALA* 3.7 27.4 - - + +
161A LEU* 4.3 14.4 - - + -
162A LEU* 3.8 26.0 - - + -
204A PHE* 4.2 21.1 - - + -
209A MET* 3.1 19.1 - - + +
210A LEU* 4.4 11.7 - - + -
219A ILE* 4.0 30.5 - - + -
221A ASP 3.0 18.3 + - - +
222A CYS* 3.5 5.6 - - - +
224A ARG* 1.3 76.0 - - - +
226A GLN* 1.3 57.1 + - - +
228A THR* 3.1 5.3 + - - -
229A ALA* 2.9 27.5 + - - +
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Residues in contact with GLN 226 (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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162A LEU* 3.5 28.5 - - + -
165A LYS* 5.1 4.2 - - - +
222A CYS* 2.8 43.8 + - - +
223A ASP* 3.5 20.1 + - - +
225A LEU* 1.3 73.2 - - - +
227A LYS* 1.3 64.6 + - - +
229A ALA* 3.3 2.6 + - - +
230A ARG* 3.0 41.0 + - - +
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Residues in contact with LYS 227 (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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223A ASP 3.1 13.9 + - - +
224A ARG* 3.1 20.0 + - + +
226A GLN* 1.3 74.5 - - - +
228A THR* 1.3 54.2 + - - +
230A ARG* 4.6 3.8 - - - +
231A SER* 2.6 56.7 + - - +
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Residues in contact with THR 228 (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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154A ARG* 3.9 34.7 + - + +
155A GLY* 3.6 4.7 - - - -
158A ALA* 4.1 2.9 - - + -
204A PHE* 4.0 15.0 - - + -
209A MET* 3.3 17.2 - - - +
224A ARG 2.9 13.8 + - - -
225A LEU* 3.1 11.0 + - - -
227A LYS* 1.3 73.8 - - - +
229A ALA* 1.3 61.9 + - - +
231A SER* 5.2 0.2 - - - -
232A GLY* 2.9 51.9 + - - +
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Residues in contact with ALA 229 (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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151A LYS* 2.6 36.9 + - - +
155A GLY* 3.8 6.3 - - - -
158A ALA* 3.6 8.2 - - + +
159A GLU* 3.8 22.7 - - + +
162A LEU* 3.6 26.7 - - + -
225A LEU 2.9 7.9 + - - +
226A GLN 3.3 8.3 + - - +
228A THR* 1.3 76.1 - - - +
230A ARG* 1.3 58.8 + - + +
232A GLY 4.7 0.2 + - - -
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Residues in contact with ARG 230 (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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151A LYS* 4.4 10.9 - - - +
226A GLN* 3.0 31.2 + - - +
227A LYS* 3.9 3.4 - - - +
229A ALA* 1.3 83.6 - - + +
231A SER* 1.3 65.5 + - - +
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Residues in contact with SER 231 (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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227A LYS* 2.6 37.4 + - - +
230A ARG* 1.3 78.9 - - - +
232A GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 232 (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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152A HIS* 6.0 6.1 - - - -
154A ARG* 3.7 31.3 + - - -
155A GLY* 4.6 8.5 - - - -
228A THR* 2.9 41.1 + - - +
229A ALA 4.7 0.2 - - - -
230A ARG 3.7 0.6 - - - -
231A SER* 1.3 82.1 - - - +
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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