Contacts of the helix formed by residues 283 - 289 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137T ASP* 5.4 6.5 - - - -
278T LEU* 3.4 11.1 + - - +
281T ALA* 3.5 6.2 + - - +
282T GLY* 1.3 78.4 - - - +
284T LEU* 1.3 60.7 + - - +
285T ASP* 4.2 9.6 - - - -
286T GLU* 3.5 11.4 + - - +
287T LEU* 3.1 24.8 + - - +
119X LEU* 4.9 16.8 - - - -
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Residues in contact with LEU 284 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137T ASP* 4.6 21.0 - - + +
261T VAL* 5.4 7.6 - - + +
262T ALA* 5.5 8.5 - - + -
278T LEU* 5.1 5.1 - - + +
283T SER* 1.3 72.2 - - - +
285T ASP* 1.3 60.2 + - - +
287T LEU* 3.1 9.3 + - - +
288T ALA* 2.8 28.4 + - - +
349T ALA* 5.0 2.9 - - - +
352T ASP* 6.2 2.7 - - + -
353T ALA* 4.5 11.3 - - + +
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Residues in contact with ASP 285 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283T SER* 3.5 5.6 - - - -
284T LEU* 1.3 77.6 - - - +
286T GLU* 1.3 57.5 + - - +
288T ALA* 3.3 9.0 + - - +
289T LYS* 3.1 27.4 + - - +
353T ALA* 4.6 7.4 - - + +
115X ARG* 5.2 16.2 - - + +
116X GLU* 5.3 13.0 - - + -
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Residues in contact with GLU 286 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281T ALA* 3.5 27.5 - - + +
282T GLY 5.0 0.4 - - - -
283T SER* 3.5 16.2 + - - +
284T LEU 3.2 1.0 - - - -
285T ASP* 1.3 75.3 - - - +
287T LEU* 1.3 64.5 + - - +
289T LYS* 3.2 15.8 + - - +
290T MET* 3.6 10.2 + - - +
116X GLU* 6.1 2.2 - - + +
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Residues in contact with LEU 287 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277T LEU* 5.2 6.7 - - + +
278T LEU* 5.2 4.9 - - + -
281T ALA* 3.8 17.8 - - + +
283T SER 3.1 13.2 + - - +
284T LEU* 3.1 12.2 + - - +
286T GLU* 1.3 76.1 - - - +
288T ALA* 1.3 60.8 + - - +
290T MET* 3.3 21.7 + - - +
295T ILE* 6.1 0.2 - - - +
346T ALA* 5.4 3.3 - - - -
349T ALA* 4.1 17.4 - - + +
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Residues in contact with ALA 288 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284T LEU 2.8 11.1 + - - +
285T ASP* 3.5 7.4 - - - +
286T GLU 3.1 0.2 - - - -
287T LEU* 1.3 77.5 - - - +
289T LYS* 1.3 60.7 + - - +
290T MET 3.2 6.3 + - - +
346T ALA* 4.9 3.2 - - - +
349T ALA* 3.8 17.9 - - - +
350T ARG* 4.2 12.7 - - + +
353T ALA* 3.4 32.1 - - + -
68V HIS* 4.1 13.5 - - + +
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Residues in contact with LYS 289 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285T ASP 3.1 14.9 + - - +
286T GLU* 3.2 9.1 + - - +
288T ALA* 1.3 76.9 - - - +
290T MET* 1.3 60.6 + - - +
291T PRO 4.0 0.7 - - - -
43V THR* 4.9 9.2 - - - -
68V HIS* 4.4 15.7 - - + +
72V LEU* 5.8 7.6 - - + -
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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