Contacts of the helix formed by residues 273 - 288 (chain A) in PDB entry 5J1T
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 GLU 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TRP* 4.6 14.3 + - - -
228A ARG* 3.9 26.6 + - - +
272A LEU* 1.3 74.7 - - - +
274A TYR* 1.3 67.9 + - - +
275A LYS* 3.2 30.5 + - + +
276A HIS* 2.9 30.6 + - + +
277A LEU* 3.2 12.7 + - - +
305A PHE* 4.3 2.7 - - - -
312A VAL* 3.5 29.4 - - + +
313A PHE* 3.9 16.0 - - + -
405A BTB 6.4 0.2 - - - -
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Residues in contact with TYR 274 (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 GLU* 1.3 72.8 - - - +
275A LYS* 1.3 65.1 + - + +
277A LEU* 3.1 7.1 + - - +
278A LYS* 3.1 51.4 + - + +
298A SER* 3.1 33.3 + - - -
301A ALA* 3.4 42.8 - - + -
302A GLU* 3.5 22.2 + - - -
305A PHE* 3.7 18.5 - + + -
312A VAL 4.2 1.4 + - - -
405A BTB 3.6 47.4 + - - -
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Residues in contact with LYS 275 (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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228A ARG* 5.7 4.4 - - - +
229A GLU* 5.6 5.5 + - - -
273A GLU* 3.9 28.5 + - + +
274A TYR* 1.3 80.7 - - - +
276A HIS* 1.3 89.2 + - + +
278A LYS* 3.4 19.4 + - - +
279A MET* 3.2 28.4 + - + +
282A ARG* 5.0 0.5 + - - -
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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
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70A PHE* 4.6 5.1 - - + -
71A GLY* 3.6 24.9 - - - -
228A ARG* 3.6 37.1 + - - -
229A GLU* 5.5 2.4 + - - -
272A LEU* 3.9 26.1 - - + +
273A GLU* 2.9 39.5 + - + +
275A LYS* 1.3 96.7 - - + +
277A LEU* 1.3 68.0 + - - +
279A MET* 3.1 21.7 + - - +
280A CYS* 3.1 25.7 + - - -
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Residues in contact with LEU 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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272A LEU* 4.2 15.7 - - + -
273A GLU 3.2 8.5 + - - +
274A TYR* 3.1 7.7 + - - +
276A HIS* 1.3 79.4 - - - +
278A LYS* 1.3 62.5 + - - +
280A CYS* 3.1 6.9 + - - +
281A ILE* 2.9 32.1 + - + +
301A ALA* 3.9 20.6 - - + +
303A MET* 3.6 31.0 - - + -
305A PHE* 4.2 5.2 - - + -
314A SER* 3.9 20.2 - - - +
317A GLY 3.3 28.5 - - - +
318A CYS* 4.0 12.3 - - + -
321A VAL* 4.3 5.6 - - + -
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Residues in contact with LYS 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 TYR* 3.1 42.3 + - + +
275A LYS* 3.6 18.2 - - - +
276A HIS 3.2 0.2 - - - -
277A LEU* 1.3 75.4 - - - +
279A MET* 1.3 65.0 + - - +
281A ILE* 3.4 4.9 + - - +
282A ARG* 3.1 50.6 + - - +
294A GLU* 5.1 0.7 - - - +
297A VAL* 3.7 27.5 - - + +
298A SER* 4.2 16.0 + - - +
301A ALA* 3.8 14.8 - - + -
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Residues in contact with MET 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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70A PHE* 3.5 52.2 - - + -
275A LYS* 3.3 17.5 - - - +
276A HIS* 3.1 20.3 + - - +
278A LYS* 1.3 79.3 - - - +
280A CYS* 1.3 62.2 + - - +
282A ARG* 3.4 21.5 + - - +
283A VAL* 3.4 24.1 + - - +
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Residues in contact with CYS 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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70A PHE* 3.8 10.8 - - - -
272A LEU* 5.2 3.8 - - - -
276A HIS 3.1 19.7 + - - -
277A LEU* 3.1 5.4 + - - +
279A MET* 1.3 75.4 - - - +
281A ILE* 1.3 65.8 + - - +
283A VAL* 3.2 6.5 + - - +
284A GLU* 3.0 22.0 + - - +
318A CYS* 3.4 34.3 - - - -
322A PHE* 3.8 8.2 - - + -
401A ATP 3.6 40.2 - - - +
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Residues in contact with ILE 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 LEU* 2.9 22.1 + - + +
278A LYS* 3.4 5.8 + - - +
280A CYS* 1.3 76.0 - - + +
282A ARG* 1.3 58.7 + - - +
284A GLU* 3.2 2.4 + - - +
285A MET* 2.9 54.4 + - + +
297A VAL* 3.8 15.0 - - + +
300A VAL* 3.7 11.9 - - + -
301A ALA* 3.6 38.8 - - + +
321A VAL* 3.6 24.7 - - + -
322A PHE* 4.0 10.8 - - + -
325A LEU* 4.2 14.1 - - + -
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Residues in contact with ARG 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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275A LYS 5.0 0.4 + - - -
278A LYS* 3.1 52.4 + - - +
279A MET* 3.7 22.3 - - - +
280A CYS 3.2 0.2 - - - -
281A ILE* 1.3 76.6 - - - +
283A VAL* 1.3 62.4 + - + +
285A MET* 3.4 6.2 + - - +
286A GLN* 3.1 33.5 + - - +
292A ILE* 3.8 18.1 - - + +
294A GLU* 2.8 43.2 + - - +
297A VAL* 4.1 9.8 - - + +
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Residues in contact with VAL 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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68A ASN* 6.1 1.1 - - - +
70A PHE* 4.1 22.7 - - + -
279A MET 3.4 14.1 + - - +
280A CYS* 3.2 9.8 + - - +
282A ARG* 1.3 78.1 - - + +
284A GLU* 1.4 63.6 + - - +
286A GLN* 3.3 15.3 + - - +
287A SER* 3.0 24.6 + - - -
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Residues in contact with GLU 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 CYS 3.0 6.7 + - - -
281A ILE 3.2 6.5 + - - +
283A VAL* 1.4 76.3 - - - +
285A MET* 1.3 64.9 + - - +
287A SER* 2.8 25.8 + - - -
288A ARG* 2.8 48.3 + - - +
322A PHE* 3.7 47.8 - - + -
325A LEU* 3.7 14.8 - - + -
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Residues in contact with MET 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 ILE* 2.9 23.1 + - + +
282A ARG* 3.6 5.6 - - - +
283A VAL 3.3 0.2 - - - -
284A GLU* 1.3 77.0 - - - +
286A GLN* 1.3 63.1 + - - +
288A ARG* 3.2 6.9 + - - -
290A TYR* 3.0 49.1 + - + +
292A ILE* 3.9 25.4 - - + -
293A ASP 3.8 4.0 - - - +
296A ILE* 3.7 26.0 - - + -
297A VAL* 3.5 35.0 - - + +
325A LEU* 3.8 22.7 - - + -
329A TYR* 3.6 21.3 - - - +
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Residues in contact with GLN 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 ARG* 3.1 23.8 + - - +
283A VAL* 3.7 15.2 - - - +
285A MET* 1.3 74.6 - - - +
287A SER* 1.3 64.6 + - - +
289A GLY* 3.0 14.8 + - - +
290A TYR 4.5 6.1 - - - +
292A ILE* 3.7 24.0 - - + +
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Residues in contact with SER 287 (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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283A VAL* 3.0 15.1 + - - -
284A GLU* 2.8 36.5 + - - -
286A GLN* 1.3 78.3 - - - +
288A ARG* 1.3 60.8 + - - +
289A GLY 3.6 0.3 + - - -
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Residues in contact with ARG 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 GLU* 2.8 43.4 + - - +
285A MET 3.7 5.2 - - - +
286A GLN 3.1 0.4 - - - -
287A SER* 1.3 78.1 - - - +
289A GLY* 1.3 59.7 + - - +
290A TYR* 3.1 51.1 + - + -
322A PHE* 3.5 26.1 + - - +
323A THR* 5.4 0.4 - - - +
325A LEU* 3.8 17.6 - - - +
326A ASP* 3.4 20.6 + - - -
283B LYS* 3.4 13.2 - - - +
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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