Contacts of the helix formed by residues 278 - 286 (chain A) in PDB entry 2GTI
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 LEU 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A VAL* 4.1 2.1 + - + -
264A VAL* 4.0 18.8 - - + +
276A LEU* 3.7 0.8 - - - +
277A HIS* 1.3 81.2 - - + +
279A LEU* 1.3 66.0 + - - +
280A ILE* 4.1 13.0 - - + -
281A GLY* 2.9 15.3 + - - +
282A LEU* 3.1 13.8 - - - +
322A VAL* 4.1 0.2 - - - -
323A ILE* 3.4 26.9 - - + +
325A LEU* 4.5 16.2 - - + +
327A LEU* 3.4 32.8 - - + -
330A PHE* 3.6 47.1 - - + -
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Residues in contact with LEU 279 (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 3.3 30.7 - - - +
227A LEU 4.7 0.4 - - - +
228A LEU* 4.3 26.0 - - + +
231A PHE* 3.9 14.1 - - + -
278A LEU* 1.3 71.6 - - - +
280A ILE* 1.3 64.2 + - - +
282A LEU* 2.8 22.4 + - + -
283A ALA* 2.9 9.9 + - - +
306A TYR* 5.6 6.3 - - + +
322A VAL* 3.7 20.4 - - + +
323A ILE 3.0 9.0 + - - +
324A ASP* 3.5 40.8 - - + +
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Residues in contact with ILE 280 (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* 5.1 1.1 - - - +
231A PHE* 3.4 31.4 - - + -
238A GLU* 3.7 48.0 - - + +
241A PHE* 3.7 24.2 - - + -
242A MSE 3.4 20.7 - - + +
264A VAL* 4.7 1.1 - - + -
278A LEU* 4.1 25.3 - - + +
279A LEU* 1.3 77.5 - - - +
281A GLY* 1.3 59.8 - - - +
283A ALA* 3.1 2.7 + - - +
284A ARG 2.9 24.3 + - - -
324A ASP* 4.8 1.0 + - - -
325A LEU 5.2 3.5 + - - +
327A LEU* 4.2 12.8 - - + -
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Residues in contact with GLY 281 (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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241A PHE* 4.1 10.8 - - - -
264A VAL* 3.2 25.9 - - - +
265A TYR* 4.8 3.3 - - - +
276A LEU* 4.0 8.6 - - - +
278A LEU* 2.9 8.9 + - - +
280A ILE* 1.3 81.5 - - - +
282A LEU* 1.3 65.2 + - - +
284A ARG* 3.3 3.3 + - - +
285A ARG* 3.2 21.5 + - - +
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Residues in contact with LEU 282 (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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228A LEU* 3.7 14.6 - - + +
276A LEU* 3.6 28.9 - - + +
278A LEU 3.1 23.8 - - - +
279A LEU* 2.8 20.4 + - + +
281A GLY* 1.3 76.0 - - - +
283A ALA* 1.3 62.4 + - - +
285A ARG* 3.3 3.1 + - - +
286A GLN* 3.0 23.2 + - - +
291A LEU* 3.8 20.1 - - + +
293A ILE* 4.1 27.8 - - + -
306A TYR* 4.7 4.9 - - + -
308A ILE* 4.2 4.9 - - + -
322A VAL* 4.1 25.4 - - + -
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Residues in contact with ALA 283 (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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228A LEU* 3.4 13.6 - - + +
231A PHE* 3.5 43.5 - - + -
242A MSE 4.3 6.6 - - - +
279A LEU 2.9 10.5 + - - +
280A ILE 3.2 10.1 - - - +
282A LEU* 1.3 78.6 - - - +
284A ARG* 1.3 61.1 + - - +
286A GLN* 3.3 16.4 + - - +
287A GLN* 3.6 9.4 + - - +
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Residues in contact with ARG 284 (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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241A PHE* 3.1 32.4 + - + +
242A MSE 3.2 26.5 + - + +
244A LEU 3.4 18.4 + - - -
245A ASP* 3.9 5.3 + - - +
246A ASP* 3.7 16.6 + - - +
265A TYR* 3.3 35.9 - - - -
280A ILE 2.9 9.3 + - - +
281A GLY* 3.7 5.6 - - - +
282A LEU 3.2 0.2 - - - -
283A ALA* 1.3 74.7 - - - +
285A ARG* 1.3 65.0 + - - +
287A GLN* 3.1 36.0 + - - +
288A LYS* 4.2 10.2 + - - +
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Residues in contact with ARG 285 (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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265A TYR 5.5 1.6 - - - +
268A PHE* 3.5 50.3 - - + +
276A LEU* 5.3 0.2 - - + -
281A GLY 3.2 11.2 + - - +
282A LEU 3.3 8.0 + - - +
284A ARG* 1.3 74.2 - - - +
286A GLN* 1.3 57.6 + - - +
287A GLN 2.9 8.4 + - - -
288A LYS* 2.9 26.1 + - - +
289A SER* 2.8 42.6 + - - +
291A LEU* 3.9 17.0 - - + -
310A ASP* 2.8 43.7 + - - +
312A ASN* 3.9 9.7 - - - +
313A SER* 4.3 3.8 - - - -
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Residues in contact with GLN 286 (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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228A LEU* 3.5 31.3 - - + +
282A LEU 3.0 8.8 + - - +
283A ALA 3.4 13.0 - - - +
285A ARG* 1.3 76.1 - - - +
287A GLN* 1.3 61.6 + - - +
288A LYS 3.3 0.4 + - - -
289A SER 3.2 11.3 + - - +
290A ASN* 3.6 10.6 - - - +
291A LEU* 2.9 58.5 + - - +
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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