Contacts of the helix formed by residues 288 - 295 (chain B) in PDB entry 5JLH
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 ILE 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLY* 4.1 20.4 - - - -
63A ILE* 4.9 3.6 - - + -
164B ILE 5.7 0.2 - - - -
165B TYR* 3.5 55.4 - - + -
170B LEU* 3.8 25.1 - - + -
284B CYS* 4.1 3.8 - - + -
285B ASP* 3.6 17.4 + - + +
287B ASP* 1.3 76.1 - - - +
289B ARG* 1.3 65.3 + - - +
290B LYS* 2.8 10.1 + - - +
291B ASP* 2.5 30.0 + - - +
292B LEU* 3.5 25.4 + - + -
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 2.7 53.4 + - - +
245A GLN* 5.3 1.0 + - - -
281B ILE* 2.9 37.0 + - + +
282B MET* 2.7 44.1 + - - +
284B CYS* 2.8 19.3 + - + -
285B ASP 3.5 11.7 - - - +
286B VAL* 3.6 30.0 - - - +
287B ASP 3.4 1.2 - - - -
288B ILE* 1.3 78.8 - - - +
290B LYS* 1.3 64.2 + - - +
292B LEU* 3.0 9.8 + - - +
293B TYR* 3.0 35.4 + - + -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER 5.1 6.9 + - - -
242A PRO* 3.7 27.4 + - + +
165B TYR* 5.3 6.7 + - - -
287B ASP* 3.6 31.1 + - - +
288B ILE* 2.8 8.6 + - - +
289B ARG* 1.3 75.1 - - - +
291B ASP* 1.3 79.0 + - + +
293B TYR* 3.6 5.2 + - - +
294B ALA* 3.4 18.4 + - - +
324B MET* 3.6 24.3 - - + +
325B LYS 5.0 1.2 - - - +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B THR* 3.1 27.2 + - - +
165B TYR* 3.2 22.1 - - - -
288B ILE 2.5 26.4 + - - +
290B LYS* 1.3 87.3 + - + +
292B LEU* 1.3 70.8 + - - +
294B ALA* 3.1 5.9 + - - +
295B ASN* 2.6 50.3 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B THR* 4.3 1.1 - - + -
149B GLY* 3.4 37.2 - - - +
150B ILE* 3.6 11.5 - - + +
163B PRO* 4.0 9.9 - - + -
164B ILE 3.7 14.4 - - - +
281B ILE* 4.2 21.3 - - + +
284B CYS* 3.8 23.1 - - + -
288B ILE* 3.7 33.0 - - + +
289B ARG* 3.0 11.0 + - - +
291B ASP* 1.3 89.9 + - - +
293B TYR* 1.3 65.6 + - - +
295B ASN* 3.1 9.8 + - - +
296B THR* 3.3 14.2 + - - -
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 4.1 11.0 + - - -
278B PHE* 3.9 21.4 - + - -
281B ILE* 3.8 32.3 - - + +
282B MET* 3.2 28.1 - - - +
289B ARG* 3.0 34.3 + - + -
290B LYS 3.7 6.3 - - - +
292B LEU* 1.3 77.2 - - - +
294B ALA* 1.3 58.1 - - - +
296B THR* 3.9 5.2 + - - -
316B ILE* 4.2 9.6 - - + -
320B ALA* 3.7 20.4 - - + -
321B PRO* 4.3 8.7 - - + +
324B MET* 3.5 20.9 - - - -
325B LYS 4.8 0.9 - - - +
326B ILE* 3.1 54.6 - - + +
327B LYS 3.3 7.3 - - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LYS 3.4 9.7 + - - +
291B ASP* 3.1 10.3 + - - +
293B TYR* 1.3 77.8 - - - +
295B ASN* 1.3 70.1 + - - +
325B LYS 3.8 15.0 - - - +
327B LYS* 2.9 46.5 - - + +
329B ILE* 5.2 0.5 - - - +
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ARG* 2.9 32.8 - - - +
148B THR* 3.5 22.4 - - - +
149B GLY* 3.3 19.3 - - - -
291B ASP* 2.6 42.0 + - - +
292B LEU 3.1 5.6 + - - -
294B ALA* 1.3 90.4 + - - +
296B THR* 1.3 62.8 + - - +
297B VAL* 3.2 10.6 + - - +
327B LYS* 4.3 5.2 - - - +
329B ILE* 4.2 4.7 - - - -
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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