Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 1JD5
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 GLU 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLN* 6.3 0.2 - - - +
273A TRP* 4.4 0.2 - - - -
276A ASN 3.6 7.3 + - - +
277A ASP* 1.3 74.4 - - - +
279A PRO* 1.3 73.8 - - + +
280A TRP* 3.3 3.4 - - + +
281A GLU* 3.1 46.4 + - + +
282A GLN* 3.0 26.0 + - - +
301A TYR* 5.1 1.2 + - - -
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Residues in contact with PRO 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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242A GLN* 4.1 8.7 - - + -
246A GLN* 3.8 44.2 - - + +
247A LEU* 3.9 24.2 - - + -
250A ALA* 3.7 22.4 - - + -
252A PHE* 3.8 5.5 - - + -
273A TRP* 3.8 12.7 - - + -
277A ASP 3.9 6.1 - - - +
278A GLU* 1.3 82.7 - - + +
280A TRP* 1.3 58.8 + - + +
282A GLN* 3.5 1.2 + - - +
283A HIS* 3.0 29.8 + - - +
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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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246A GLN 5.6 1.3 - - - -
249A GLU* 3.2 27.9 + - - +
250A ALA* 3.8 24.1 - - + +
278A GLU* 3.3 3.5 - - + +
279A PRO* 1.3 78.8 - - + +
281A GLU* 1.3 58.2 + - + +
283A HIS* 3.3 6.2 + - - +
284A ALA* 2.9 30.7 + - - +
292A PHE* 3.6 24.9 - + - -
293A VAL* 4.0 25.6 - - + -
296A MET* 3.6 26.7 - - + -
297A LYS* 3.6 38.3 - - + +
301A TYR* 3.4 18.4 + - + +
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Residues in contact with GLU 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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276A ASN 5.3 1.2 - - - +
278A GLU* 3.1 50.3 + - + +
280A TRP* 1.3 73.3 - - - +
282A GLN* 1.3 61.0 + - - +
284A ALA 3.3 0.5 + - - -
285A LEU* 2.8 37.5 + - - +
301A TYR* 3.3 18.7 - - + +
305A VAL* 3.5 13.9 - - + +
308A LYS* 3.7 22.0 - - - +
311A LEU* 3.9 30.2 - - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.0 12.8 - - + +
273A TRP* 3.7 26.9 - - + -
277A ASP* 3.5 27.7 + - + +
278A GLU 3.0 19.5 + - - +
279A PRO 3.9 1.1 - - - +
281A GLU* 1.3 73.8 + - - +
283A HIS* 1.3 66.6 + - - +
285A LEU* 4.3 4.1 - - - +
286A TRP* 3.1 36.2 + - + +
311A LEU* 3.7 17.4 - - - +
314A GLU* 2.7 40.6 + - - +
1B ALA* 3.1 14.0 + - + +
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Residues in contact with HIS 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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250A ALA 2.7 29.5 + - - -
251A GLY* 4.6 0.4 - - - -
252A PHE* 3.3 17.9 - + + -
263A CYS* 3.3 21.4 - - + +
270A LEU* 4.2 2.0 - - - +
279A PRO 3.0 18.0 + - - +
280A TRP* 3.4 10.5 - - + +
282A GLN* 1.3 78.1 - - - +
284A ALA* 1.3 57.6 + - - +
287A LEU* 2.9 54.3 + - + +
290A CYS* 4.3 0.7 - - - -
292A PHE* 4.8 2.7 - + - -
293A VAL* 3.6 22.1 - - + +
501A ZN 2.4 34.6 - - - -
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Residues in contact with ALA 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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280A TRP 2.9 17.2 + - - +
281A GLU 3.9 2.7 - - - +
283A HIS* 1.3 76.9 - - - +
285A LEU* 1.3 61.9 + - - +
288A SER* 3.3 29.0 - - - +
293A VAL* 3.8 25.1 - - + -
301A TYR* 3.9 17.7 - - + -
302A ILE* 4.1 19.8 - - + +
305A VAL* 4.3 7.2 - - + -
306A ALA* 6.1 0.3 - - - +
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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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281A GLU 2.8 19.4 + - - +
282A GLN* 3.8 5.4 - - - +
283A HIS 3.2 0.2 - - - -
284A ALA* 1.3 79.2 - - - +
286A TRP* 1.3 94.5 + - + +
288A SER* 4.5 5.0 + - - -
305A VAL* 3.9 7.2 - - + +
306A ALA* 4.2 22.8 - - + +
311A LEU* 3.9 37.5 - - + +
312A ALA* 5.3 0.4 - - - -
314A GLU* 4.2 6.5 - - - +
315A LYS* 3.7 46.8 - - + +
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Residues in contact with TRP 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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270A LEU* 3.8 20.0 - - + -
282A GLN* 3.1 28.5 + - + +
285A LEU* 1.3 87.6 - - + +
287A LEU* 1.3 70.7 + - + +
288A SER 3.7 1.3 - - - -
314A GLU* 3.0 56.8 + - + -
315A LYS* 3.6 30.9 - - + +
318A SER* 4.1 21.5 - - - -
1B ALA 3.1 17.5 + - - -
2B ILE* 4.7 6.3 - - + -
3B ALA* 3.9 29.8 - - + -
6B ILE* 4.0 26.4 - - + +
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Residues in contact with LEU 287 (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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252A PHE* 4.6 1.8 - - + -
266A CYS* 3.9 18.2 - - - -
268A GLY* 3.9 22.2 - - - +
270A LEU* 4.4 19.1 - - + -
283A HIS* 2.9 41.1 + - + +
286A TRP* 1.3 91.3 - - + +
288A SER* 1.3 57.4 + - - +
289A GLN 3.1 3.6 - - - -
290A CYS* 3.0 25.7 + - - +
293A VAL* 4.6 2.1 - - - +
3B ALA* 5.2 1.1 - - + -
5B PHE 4.1 6.3 - - - +
6B ILE* 4.2 7.2 - - + -
7B PRO* 3.4 33.4 - - + -
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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