Contacts of the helix formed by residues 275 - 289 (chain A) in PDB entry 4OGB
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 LYS 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A SER* 3.9 16.6 + - - -
269A LEU* 3.9 18.4 - - - +
270A ALA 4.5 8.7 - - - +
272A ASP* 2.9 18.6 + - + +
274A SER* 1.3 88.8 + - - +
276A HIS* 1.3 63.9 + - - +
277A MET 3.5 1.8 - - - -
278A ASN* 3.3 13.9 + - - +
279A LEU* 3.0 23.6 + - + +
507A EDO 3.9 38.6 - - - +
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASP 3.9 1.0 + - - -
273A MET* 2.9 31.0 + - + +
274A SER 3.4 0.6 - - - -
275A LYS* 1.3 76.6 - - - +
277A MET* 1.3 89.4 + - + +
279A LEU* 3.3 5.3 + - - +
280A LEU* 2.9 48.6 + - + +
315A HIS* 2.9 37.4 + + + +
375A TYR 4.8 1.0 + - - -
376A ILE* 3.7 44.8 + - + +
380A LEU* 4.2 11.9 - - + -
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Residues in contact with MET 277 (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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273A MET 4.8 0.2 + - - -
274A SER 5.1 2.3 + - - +
275A LYS 3.5 0.4 - - - -
276A HIS* 1.3 98.2 - - + +
278A ASN* 1.3 60.6 + - - +
280A LEU* 3.4 10.5 + - - +
281A ALA* 2.9 30.2 + - - +
375A TYR* 4.7 12.6 - - + +
376A ILE* 5.1 5.6 - - + -
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Residues in contact with ASN 278 (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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274A SER 4.9 8.7 + - - -
275A LYS* 3.3 11.0 + - - +
276A HIS 3.3 0.4 - - - -
277A MET* 1.3 76.1 - - - +
279A LEU* 1.3 66.3 - - - +
281A ALA* 3.2 6.7 + - - +
282A ASP* 3.0 32.9 + - - +
507A EDO 3.6 18.9 + - - +
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Residues in contact with LEU 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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270A ALA* 3.5 32.1 - - + +
275A LYS 3.0 16.2 + - - +
276A HIS* 3.6 7.6 - - - +
278A ASN* 1.3 75.3 - - - +
280A LEU* 1.3 58.0 + - - +
282A ASP* 3.2 8.5 + - + +
283A LEU* 2.9 27.4 + - - +
308A GLN* 5.0 4.3 - - + -
311A GLN* 3.9 28.5 - - + +
312A ASN* 3.6 30.7 + - - +
315A HIS* 4.1 26.9 - - + +
507A EDO 4.1 20.1 + - - -
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Residues in contact with LEU 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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276A HIS* 2.9 43.2 + - + +
277A MET* 3.8 10.5 - - - +
279A LEU* 1.3 73.3 - - - +
281A ALA* 1.3 68.0 + - - +
283A LEU* 3.3 5.4 + - + +
284A LYS* 2.9 38.0 + - + +
312A ASN* 4.3 3.1 + - - -
315A HIS* 6.1 0.6 - - + -
375A TYR 6.0 0.2 - - - +
379A PRO* 4.0 23.1 - - + -
380A LEU* 3.8 21.3 - - + +
383A THR* 3.5 34.5 - - + +
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Residues in contact with ALA 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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277A MET 2.9 18.1 + - - +
278A ASN* 3.5 8.7 - - - +
280A LEU* 1.3 76.9 - - - +
282A ASP* 1.3 61.9 + - - +
284A LYS* 3.3 13.3 + - - +
285A THR* 3.0 32.7 + - - +
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Residues in contact with ASP 282 (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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278A ASN* 3.0 17.7 + - - +
279A LEU* 3.6 11.0 - - + +
281A ALA* 1.3 80.2 - - - +
283A LEU* 1.3 62.3 + - - +
285A THR* 3.3 9.5 + - - -
286A MET* 3.0 18.5 + - - +
308A GLN* 3.3 29.8 - - + +
507A EDO 5.4 2.9 + - - -
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Residues in contact with LEU 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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279A LEU 2.9 13.6 + - - +
280A LEU* 3.5 10.8 - - + +
282A ASP* 1.3 77.2 - - - +
284A LYS* 1.3 56.4 + - - +
286A MET* 3.3 3.9 + - + +
287A VAL* 2.9 32.5 + - + +
308A GLN* 3.6 20.7 - - - +
309A VAL* 5.2 1.6 - - + -
312A ASN* 3.8 32.3 - - + +
380A LEU* 4.3 12.8 - - + -
383A THR* 3.6 23.1 - - + -
384A TRP* 4.1 22.4 - - + +
387A LEU* 3.9 28.0 - - + -
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Residues in contact with LYS 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 LEU* 2.9 37.6 + - + +
281A ALA* 3.4 11.9 - - - +
283A LEU* 1.3 74.2 - - - +
285A THR* 1.3 67.3 + - - +
287A VAL* 2.8 16.4 + - - +
288A GLU* 2.9 27.1 + - + +
379A PRO* 5.3 6.2 - - - +
383A THR* 3.8 30.7 - - + +
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Residues in contact with THR 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 ALA* 3.0 15.1 + - - +
282A ASP* 3.3 13.5 + - - -
284A LYS* 1.3 76.8 - - - +
286A MET* 1.3 60.7 + - - +
288A GLU* 3.4 17.4 + - - +
289A THR* 3.0 32.7 + - + +
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Residues in contact with MET 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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282A ASP 3.0 12.4 + - - +
283A LEU* 3.6 8.3 - - + +
285A THR* 1.3 77.0 - - - +
287A VAL* 1.3 58.9 + - - +
289A THR* 3.4 6.7 - - - +
290A LYS* 2.8 38.5 + - + +
300A LEU* 3.9 13.7 - - + -
305A ASP* 3.4 43.5 - - + +
308A GLN* 3.2 30.3 - - - +
309A VAL* 3.5 25.1 - - - -
387A LEU* 4.4 16.2 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 2.9 19.0 + - + +
284A LYS* 2.8 11.0 + - + +
286A MET* 1.3 77.1 - - - +
288A GLU* 1.3 65.6 + - + +
290A LYS* 3.6 24.3 + - + +
383A THR* 3.6 30.3 - - + +
386A ASP* 3.9 28.7 - - + +
387A LEU* 4.0 22.4 - - + +
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Residues in contact with GLU 288 (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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284A LYS* 2.9 28.3 + - - +
285A THR* 3.6 17.2 + - - +
286A MET 3.2 0.2 - - - -
287A VAL* 1.3 82.2 - - + +
289A THR* 1.3 64.4 + - + +
290A LYS 3.7 0.5 + - - -
291A LYS* 5.1 2.3 + - - -
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Residues in contact with THR 289 (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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285A THR* 3.0 24.9 + - + +
286A MET* 3.4 7.4 + - - +
288A GLU* 1.3 83.3 - - + +
290A LYS* 1.3 65.5 + - - +
291A LYS* 3.0 20.7 + - - +
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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