Contacts of the helix formed by residues 309 - 315 (chain A) in PDB entry 2G27
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ASP 3.1 19.5 - - - -
222A ALA* 3.4 8.3 - - - -
223A SER 4.3 0.2 - - - -
224A TYR 3.5 12.3 + - - -
225A ILE* 4.5 1.4 - - - +
307A ALA 3.2 8.7 + - - -
308A LEU* 1.3 73.5 - - - +
310A ALA* 1.3 66.5 + - - -
311A THR 3.3 2.5 - - - -
312A PHE* 3.1 4.7 + - - +
313A ILE* 3.0 26.8 + - - +
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Residues in contact with ALA 310 (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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12A ASP 4.9 0.4 - - - +
15A TYR* 4.2 2.5 - - + -
157A TYR* 3.7 28.2 - - + -
219A ASP 4.3 0.2 + - - -
222A ALA 2.8 15.7 + - - +
223A SER* 2.9 24.5 + - - +
309A GLY* 1.3 70.1 - - - -
311A THR* 1.3 55.6 + - - +
313A ILE* 4.2 1.1 - - - +
314A ARG* 2.8 50.6 + - - +
804A 4LG 4.0 7.0 - - - -
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Residues in contact with THR 311 (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 SER 3.2 7.4 + - - -
224A TYR* 3.8 0.5 - - - -
225A ILE* 3.7 16.6 - - + -
272A LEU* 3.6 26.4 - - + +
276A ASP* 3.3 27.4 - - - +
277A TYR* 4.5 4.9 - - + -
292A ALA* 3.0 38.5 + - + +
293A ILE* 5.6 0.4 - - + -
309A GLY 3.3 0.8 - - - -
310A ALA* 1.3 79.4 - - - +
312A PHE* 1.3 64.1 + - - +
314A ARG* 3.5 23.3 + - - +
315A LYS* 4.0 3.3 + - - +
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Residues in contact with PHE 312 (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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218A VAL* 6.0 0.2 - - + -
225A ILE* 4.3 8.4 - - + +
263A PHE* 4.1 18.2 - + - -
265A LEU* 4.0 2.9 - - + -
270A TYR* 3.4 39.7 - + + -
272A LEU* 4.4 8.7 - - + -
308A LEU* 3.7 48.2 - - + -
309A GLY 3.1 9.0 + - - +
311A THR* 1.3 79.0 - - - +
313A ILE* 1.3 65.9 + - + +
315A LYS* 2.9 19.4 + - - +
316A PHE* 3.0 39.7 + + + -
329A PHE* 3.3 39.3 - + - -
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Residues in contact with ILE 313 (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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155A PHE* 4.5 14.6 - - + +
156A TYR* 5.3 0.2 - - - -
157A TYR* 3.7 38.4 + - + +
218A VAL* 5.1 6.5 - - + -
219A ASP 4.3 0.9 - - - +
220A THR* 3.6 43.1 - - + +
308A LEU 4.4 7.0 - - - +
309A GLY 3.0 21.8 + - - +
310A ALA 3.8 3.4 - - - +
312A PHE* 1.3 75.7 - - + +
314A ARG* 1.3 67.8 + - - +
315A LYS 3.2 0.5 + - - -
316A PHE 3.3 24.4 + - - +
317A TYR* 4.1 1.9 + - - -
318A THR* 4.0 16.6 - - - +
332A ALA* 4.6 1.2 - - - +
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Residues in contact with ARG 314 (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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12A ASP* 2.6 58.3 + - - +
15A TYR* 3.3 34.5 + - - +
156A TYR* 5.4 0.3 - - - -
157A TYR* 3.3 24.0 - - + +
158A ASN 3.9 4.3 - - - +
159A ARG* 4.1 27.7 + - - +
223A SER 4.3 2.8 + - - -
224A TYR* 5.5 0.6 - - - -
276A ASP 5.0 5.5 + - - -
279A PHE* 4.6 4.6 - - - -
292A ALA* 4.2 10.9 - - - +
310A ALA* 2.8 25.8 + - - +
311A THR* 3.5 36.4 + - - +
312A PHE 3.1 0.2 + - - -
313A ILE* 1.3 74.8 - - - +
315A LYS* 1.3 61.3 + - - +
332A ALA* 3.6 11.8 - - - +
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Residues in contact with LYS 315 (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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159A ARG* 3.6 22.1 + - - +
271A THR* 2.8 29.3 + - - +
272A LEU* 4.0 7.4 - - + -
273A THR* 3.7 15.7 - - - +
276A ASP* 2.9 31.5 + - + +
311A THR 4.0 2.0 + - - +
312A PHE 2.9 8.6 + - - +
314A ARG* 1.3 82.4 - - - +
316A PHE* 1.3 79.2 + - + +
331A LEU* 3.8 19.9 - - + +
332A ALA* 2.8 23.8 + - - +
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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