Contacts of the helix formed by residues 283 - 289 (chain S) in PDB entry 5JPQ
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 SER 283 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137S ASP* 5.5 6.3 - - - -
278S LEU* 3.5 11.1 + - - +
281S ALA* 3.4 7.3 + - - +
282S GLY* 1.3 78.2 - - - +
284S LEU* 1.3 60.5 + - - +
285S ASP* 3.4 11.2 - - - -
286S GLU* 3.9 11.4 - - - +
287S LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 284 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137S ASP* 4.7 19.8 - - + +
261S VAL* 5.4 7.4 - - + +
262S ALA* 5.7 8.1 - - + -
278S LEU* 5.2 5.5 - - + +
283S SER* 1.3 72.3 - - - +
285S ASP* 1.3 60.6 + - - +
287S LEU* 3.1 9.0 + - - +
288S ALA* 2.8 30.3 + - - +
349S ALA* 5.0 1.6 - - - +
352S ASP* 6.2 2.5 - - + -
353S ALA* 4.3 13.2 - - + +
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Residues in contact with ASP 285 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283S SER* 3.4 6.4 - - - -
284S LEU* 1.3 77.5 - - - +
286S GLU* 1.3 58.7 + - - +
288S ALA* 3.8 7.3 + - - +
289S LYS* 3.5 20.6 + - - +
353S ALA* 4.5 8.0 - - + +
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Residues in contact with GLU 286 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281S ALA* 3.6 26.3 - - - +
282S GLY 5.0 0.4 - - - -
283S SER* 3.6 16.2 + - - +
284S LEU 3.2 0.6 - - - -
285S ASP* 1.3 77.9 - - - +
287S LEU* 1.3 65.8 + - - +
289S LYS* 3.3 15.7 + - - +
290S MET* 3.6 9.0 + - - +
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Residues in contact with LEU 287 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277S LEU* 4.9 7.6 - - + +
278S LEU* 5.3 3.4 - - - +
281S ALA* 3.8 16.1 - - + +
283S SER 3.1 14.3 + - - +
284S LEU* 3.1 12.2 + - - +
286S GLU* 1.3 77.2 - - - +
288S ALA* 1.3 63.5 + - - +
290S MET* 3.1 23.1 + - - +
346S ALA* 5.6 2.3 - - - -
349S ALA* 4.2 15.0 - - + +
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Residues in contact with ALA 288 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284S LEU 2.8 9.5 + - - +
285S ASP* 4.0 6.3 - - - +
287S LEU* 1.3 76.3 - - - +
289S LYS* 1.3 57.5 + - - +
290S MET 3.1 10.6 + - - +
346S ALA* 4.7 6.2 - - - +
349S ALA* 3.8 22.6 - - - +
350S ARG* 4.0 11.2 - - + +
353S ALA* 3.5 32.3 - - + -
68U HIS* 4.4 12.9 - - + +
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Residues in contact with LYS 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285S ASP 3.5 14.6 + - - +
286S GLU* 3.3 9.1 + - - +
287S LEU 3.3 1.0 - - - -
288S ALA* 1.3 77.2 - - - +
290S MET* 1.3 58.8 + - - +
291S PRO 3.9 0.9 - - - -
43U THR* 5.0 8.1 - - - -
68U HIS* 4.4 15.7 - - + +
72U LEU* 5.9 7.2 - - + -
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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