Contacts of the helix formed by residues 224 - 232 (chain A) in PDB entry 2G9Y
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PHE 3.5 12.1 - - - -
212A ALA* 3.3 20.0 - - - +
213A GLU 3.1 7.0 - - - -
214A THR* 3.7 11.9 - - + +
223A LYS* 1.3 76.5 - - - +
225A LEU* 1.3 58.7 + - - +
226A ARG* 2.9 6.2 + - - +
227A GLU* 2.9 41.3 + - - +
228A GLN* 2.9 26.2 + - - +
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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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171A PRO* 3.8 24.9 - - + -
192A THR* 3.5 31.4 - - + -
193A GLU* 3.7 23.1 - - + +
196A LEU* 3.6 14.0 - - + +
210A THR* 3.9 11.7 - - + +
211A PHE* 3.2 22.6 + - + +
213A GLU 2.8 19.4 + - - +
215A ALA* 4.5 12.8 - - + +
224A THR* 1.3 73.4 - - - +
226A ARG* 1.3 59.7 + - - +
228A GLN* 3.6 26.9 - - - +
229A ALA* 3.1 19.1 + - - +
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Residues in contact with ARG 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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208A ALA* 4.5 12.9 + - - +
211A PHE* 3.0 31.3 + - + +
212A ALA* 5.7 0.7 - - - -
224A THR* 2.9 6.0 - - - +
225A LEU* 1.3 77.3 - - - +
227A GLU* 1.3 66.5 + - + +
229A ALA* 3.2 6.1 + - - +
230A GLN* 3.0 22.0 + - - +
236A LEU* 3.8 32.8 - - + +
237A VAL 5.2 1.6 + - - -
238A SER* 4.8 15.8 - - - -
258A LEU* 3.4 31.6 - - + +
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Residues in contact with GLU 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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222A GLY 4.8 0.2 - - - +
223A LYS* 3.4 25.9 - - + +
224A THR* 2.9 47.3 + - - +
226A ARG* 1.3 77.7 - - + +
228A GLN* 1.3 51.4 + - - +
230A GLN* 3.2 7.5 + - - +
231A ALA* 2.8 37.4 + - - +
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Residues in contact with GLN 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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193A GLU* 4.8 9.6 + - - +
196A LEU* 3.8 16.6 - - + +
215A ALA* 4.5 8.1 - - - +
220A TRP* 3.6 49.0 - - + +
223A LYS* 4.8 1.2 + - - +
224A THR 2.9 11.2 + - - +
225A LEU* 3.6 28.8 - - - +
226A ARG 3.2 0.2 - - - -
227A GLU* 1.3 76.1 - - - +
229A ALA* 1.3 51.8 + - - +
231A ALA* 3.1 1.8 + - - -
232A ARG* 2.8 77.9 + - - +
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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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196A LEU* 3.7 21.8 - - + -
211A PHE* 5.2 0.7 - - + -
225A LEU 3.1 10.9 + - - +
226A ARG* 3.2 10.7 + - - +
228A GLN* 1.3 78.7 - - - +
230A GLN* 1.3 63.1 + - - +
232A ARG* 3.2 6.7 + - - +
234A TYR* 3.0 47.6 + - + +
236A LEU* 4.3 7.2 - - + -
256A LEU* 4.3 12.1 - - + -
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Residues in contact with GLN 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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226A ARG 3.0 13.1 + - - +
227A GLU* 3.5 11.2 - - - +
229A ALA* 1.3 76.3 - - - +
231A ALA* 1.3 62.4 + - - +
233A GLY* 3.2 13.7 + - - -
234A TYR 4.2 15.1 + - - +
236A LEU* 3.7 26.0 - - + +
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Residues in contact with ALA 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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220A TRP* 4.2 21.3 + - + +
223A LYS* 5.1 10.5 - - + +
227A GLU 2.8 20.2 + - - +
228A GLN 3.6 4.7 - - - +
230A GLN* 1.3 74.0 - - - +
232A ARG* 1.3 58.7 + - - +
233A GLY 3.2 3.2 + - - -
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Residues in contact with ARG 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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193A GLU 4.8 0.2 + - - -
196A LEU* 4.2 19.2 + - - +
197A ASN* 3.0 40.2 + - - +
199A ARG* 3.0 37.1 + - - +
220A TRP* 3.4 44.3 - - + -
228A GLN* 2.8 53.3 + - - +
229A ALA* 3.2 4.4 + - - +
230A GLN 3.2 0.8 - - - -
231A ALA* 1.3 77.0 - - - +
233A GLY* 1.3 56.5 + - - +
234A TYR* 3.4 8.2 + - + -
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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