Contacts of the helix formed by residues 275 - 285 (chain A) in PDB entry 7JDW
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 TYR 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PHE* 5.5 4.3 - + - -
248A GLU* 3.0 25.7 + - + +
269A ARG* 3.5 37.2 - - + +
274A ASN* 1.3 72.6 - - - +
276A LEU* 1.3 60.3 + - - +
278A ILE* 4.0 5.4 - - + +
279A GLU* 3.0 30.5 + - - +
293A ILE* 3.9 36.8 - - + +
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Residues in contact with LEU 276 (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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248A GLU* 2.9 41.5 + - + +
249A PHE 4.5 1.6 - - - +
250A GLU* 4.0 17.9 - - - -
251A PRO* 3.9 21.5 - - + +
274A ASN* 3.2 7.8 - - - +
275A TYR* 1.3 77.0 - - - +
277A GLY* 1.3 56.6 + - - +
279A GLU* 3.4 11.1 + - + +
280A TRP* 3.0 28.2 + - - +
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Residues in contact with GLY 277 (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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251A PRO* 3.9 5.6 - - - +
252A CYS 3.7 17.7 - - - -
253A PHE* 3.7 23.2 - - - -
274A ASN* 2.8 20.3 - - - +
276A LEU* 1.3 78.1 - - - +
278A ILE* 1.3 60.3 + - - +
280A TRP* 3.3 6.0 + - - +
281A MET* 3.2 17.7 + - - +
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Residues in contact with ILE 278 (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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258A PHE* 4.2 13.5 - - + -
267A ALA* 4.3 8.5 - - + -
268A GLN 3.8 21.8 - - - +
269A ARG* 3.9 22.4 - - + +
273A THR* 3.6 15.0 - - + -
274A ASN 3.1 13.7 + - - +
275A TYR* 4.0 13.7 - - + +
277A GLY* 1.3 72.1 - - - +
279A GLU* 1.3 56.2 + - - +
281A MET* 3.2 3.8 + - - +
282A ARG* 2.8 33.6 + - + +
291A VAL* 3.9 20.3 - - + +
293A ILE* 3.9 31.6 - - + -
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Residues in contact with GLU 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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275A TYR 3.0 18.7 + - - +
276A LEU* 3.6 14.6 - - + +
277A GLY 3.3 0.2 - - - -
278A ILE* 1.3 74.1 - - - +
280A TRP* 1.3 56.4 + - - +
282A ARG* 3.0 46.6 + - - -
283A ARG* 2.7 67.6 + - - +
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Residues in contact with TRP 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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180A ILE* 4.7 2.5 - - + -
211A THR* 3.9 17.7 - - + -
212A THR 4.8 1.8 - - - -
213A ALA* 3.6 29.6 - - + -
214A PRO* 3.4 36.8 - - + +
251A PRO* 4.7 13.0 - - + -
253A PHE* 4.2 9.4 - + + -
276A LEU 3.0 14.0 + - - +
277A GLY* 3.3 12.8 - - - +
278A ILE 3.2 0.4 - - - -
279A GLU* 1.3 77.8 - - - +
281A MET* 1.3 68.1 + - - +
283A ARG* 3.7 4.3 - - + +
284A HIS* 2.8 73.5 + + + +
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Residues in contact with MET 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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173A ILE* 4.2 28.9 - - + -
175A VAL* 5.2 0.7 - - + -
180A ILE* 4.3 13.7 - - + -
253A PHE* 3.6 31.9 - - + -
258A PHE* 3.7 41.5 - - + -
265A ILE* 5.7 2.2 - - + -
277A GLY 3.2 4.6 + - - +
278A ILE 3.2 8.3 + - - +
280A TRP* 1.3 90.8 - - + +
282A ARG* 1.3 58.5 + - - +
284A HIS* 3.3 1.4 + - - -
285A LEU* 2.9 58.5 + - + +
291A VAL* 4.2 7.0 - - + -
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Residues in contact with ARG 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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278A ILE* 2.8 19.7 + - + +
279A GLU* 3.0 39.7 + - - +
281A MET* 1.3 76.6 - - - +
283A ARG* 1.3 78.0 + - - +
285A LEU* 4.5 0.5 - - - +
286A ALA* 3.1 38.0 + - - +
289A TYR 5.1 1.7 - - - +
290A ARG* 6.0 0.2 - - - -
291A VAL* 3.7 39.2 - - + +
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Residues in contact with ARG 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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279A GLU* 2.7 53.2 + - - +
280A TRP* 3.8 5.2 - - + +
282A ARG* 1.3 86.9 - - - +
284A HIS* 1.3 62.9 + - - +
285A LEU 3.6 0.2 + - - -
286A ALA* 3.9 14.2 + - - +
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Residues in contact with HIS 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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178A GLU* 2.7 32.3 + - - -
180A ILE* 4.4 6.0 - - + +
211A THR* 4.0 16.7 + - + +
280A TRP* 2.8 52.3 + + + +
281A MET* 3.3 3.3 + - - +
283A ARG* 1.3 80.3 - - - +
285A LEU* 1.3 76.5 + - + +
286A ALA 4.2 3.3 - - - +
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Residues in contact with LEU 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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175A VAL* 4.2 21.1 - - + -
178A GLU* 4.0 15.3 - - - +
180A ILE* 4.3 5.8 - - + -
265A ILE* 3.9 26.9 - - + -
281A MET* 2.9 42.2 + - + +
282A ARG 4.5 0.9 - - - +
284A HIS* 1.3 94.7 - - + +
286A ALA* 1.3 67.4 + - - +
287A PRO* 4.5 0.2 - - - +
288A ASP* 3.5 5.2 + - - +
289A TYR* 3.3 39.6 + - + +
291A VAL* 4.4 9.4 - - + -
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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