Contacts of the helix formed by residues 289 - 297 (chain B) in PDB entry 5J63
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 GLY 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 3.8 13.9 - - - +
276B ILE* 3.6 28.3 - - - -
277B VAL 2.9 14.9 + - - -
287B MET 3.8 0.6 + - - -
288B GLN* 1.3 71.3 - - - +
290B SER* 1.3 51.5 + - - +
292B LEU* 3.0 9.5 + - - +
293B ALA* 2.7 35.7 + - - +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL 3.5 21.3 - - - +
263B ALA* 4.0 17.9 - - - +
264B PRO* 5.7 0.7 - - - -
265B LEU* 4.6 2.6 - - - +
288B GLN* 3.7 22.8 + - - +
289B GLY* 1.3 73.7 - - - +
291B GLN* 1.3 70.8 + - - +
293B ALA* 3.7 2.8 + - - +
294B GLN* 3.0 38.3 + - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B MET* 3.4 34.7 - - - +
288B GLN* 3.3 21.4 + - + +
290B SER* 1.3 80.1 + - - +
292B LEU* 1.3 62.5 + - - +
294B GLN* 3.6 13.1 + - + +
295B THR* 3.1 19.0 + - - +
55D PRO* 3.5 11.1 - - - +
56D VAL* 2.5 53.1 + - - +
57D TYR* 4.0 20.1 - - + +
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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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240B PHE* 4.2 20.2 - - + -
241B THR 4.2 0.2 - - - +
265B LEU* 4.8 2.9 - - + -
276B ILE* 4.1 18.6 - - + -
279B GLY* 3.8 26.0 - - - +
280B GLN* 3.7 7.6 - - - +
281B ALA* 3.6 28.9 - - + +
287B MET* 3.7 13.4 - - + -
288B GLN 2.8 14.6 + - - +
289B GLY* 3.0 11.0 + - - +
291B GLN* 1.3 73.2 - - - +
293B ALA* 1.3 68.5 + - - +
295B THR* 2.7 16.9 + - + -
296B LEU* 2.9 34.7 + - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL* 4.1 20.9 - - + +
265B LEU* 4.1 22.4 - - + +
289B GLY 2.7 18.4 + - - +
290B SER 3.8 5.4 - - - +
292B LEU* 1.3 71.6 - - - +
294B GLN* 1.3 52.4 + - + +
296B LEU 3.1 0.7 + - - -
297B GLY 2.6 32.2 + - - -
298B LEU* 2.9 34.1 + - + +
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Residues in contact with GLN 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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64A HIS* 5.0 2.3 + - - -
262B VAL* 5.1 5.3 + - + +
263B ALA* 5.8 1.8 - - - +
290B SER* 3.0 33.1 + - - +
291B GLN* 3.9 11.0 - - + +
292B LEU 3.1 0.8 - - - -
293B ALA* 1.3 78.8 - - + +
295B THR* 1.3 62.6 + - - +
297B GLY* 3.4 11.5 + - - +
298B LEU 5.3 2.5 - - - +
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Residues in contact with THR 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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64A HIS* 3.9 12.8 + - - -
281B ALA* 3.5 31.4 - - + -
287B MET* 4.0 19.9 - - + +
291B GLN* 3.1 13.6 + - - +
292B LEU* 2.7 16.5 + - + +
294B GLN* 1.3 73.7 - - - +
296B LEU* 1.3 60.6 + - + +
297B GLY 3.5 0.3 + - - -
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Residues in contact with LEU 296 (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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64A HIS* 3.3 17.4 - - - +
65A PRO* 5.8 0.3 - - - +
235B VAL* 3.8 39.4 - - + +
238B GLN* 4.2 18.8 - - + -
240B PHE* 3.9 23.8 - - + -
265B LEU* 5.5 0.9 - - + -
281B ALA* 3.6 30.1 - - + -
292B LEU* 2.9 34.9 + - + +
293B ALA 3.8 4.7 - - - +
295B THR* 1.3 77.9 - - + +
297B GLY* 1.3 60.7 + - - +
298B LEU* 3.6 24.4 + - + -
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 4.0 13.9 - - - -
65A PRO* 5.2 11.8 - - - +
235B VAL* 5.8 0.2 - - - -
293B ALA 2.6 13.0 + - - -
294B GLN* 3.4 9.1 + - - -
295B THR 3.2 3.4 - - - -
296B LEU* 1.3 76.4 - - - +
298B LEU* 1.3 63.3 + - - -
299B VAL* 3.7 8.9 + - - +
302B SER* 4.5 1.9 + - - -
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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