Contacts of the helix formed by residues 275 - 292 (chain Q) in PDB entry 3J7Y
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 THR 275 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81Q ILE* 4.3 17.0 - - + -
82Q PRO 5.1 3.1 - - - +
273Q TYR* 3.0 38.4 + - + +
274Q ASP* 1.3 71.4 + - - +
276Q SER* 1.3 53.8 + - - +
277Q LYS 3.5 1.8 - - - -
278Q ILE* 3.3 26.8 + - + -
279Q GLU* 2.8 60.4 + - + +
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Residues in contact with SER 276 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274Q ASP* 3.5 20.8 + - - -
275Q THR* 1.3 75.8 - - - +
277Q LYS* 1.3 71.7 + - - +
279Q GLU* 3.2 12.9 + - - +
280Q ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 277 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274Q ASP* 5.2 8.9 + - - +
275Q THR 3.5 0.2 - - - -
276Q SER* 1.3 87.6 + - - +
278Q ILE* 1.3 61.1 + - + +
280Q ALA* 3.2 8.6 + - - +
281Q ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 278 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q PRO* 3.8 21.5 - - + -
273Q TYR* 3.9 28.0 - - + +
274Q ASP 4.2 16.6 - - - +
275Q THR* 3.3 14.1 + - + +
276Q SER 3.2 0.2 - - - -
277Q LYS* 1.3 77.9 - - + +
279Q GLU* 1.3 58.4 + - - +
281Q ALA* 3.2 9.2 + - + +
282Q ILE* 2.9 46.9 + - + +
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Residues in contact with GLU 279 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q LEU* 3.8 13.6 - - + +
81Q ILE* 3.3 35.2 - - + +
275Q THR* 2.8 43.2 + - - +
276Q SER* 3.4 10.3 + - - +
278Q ILE* 1.3 77.4 - - - +
280Q ALA* 1.3 57.6 + - - +
282Q ILE* 3.2 10.3 + - - +
283Q TRP* 2.9 36.8 + - + -
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Residues in contact with ALA 280 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG* 6.1 1.1 - - - +
276Q SER 2.9 12.5 + - - +
277Q LYS* 3.3 12.3 - - - +
279Q GLU* 1.3 75.9 - - - +
281Q ALA* 1.3 57.5 + - - +
283Q TRP* 3.2 10.7 + - - +
284Q LYS* 2.9 42.6 + - - +
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Residues in contact with ALA 281 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q ARG* 6.0 0.2 - - - +
277Q LYS 2.9 13.6 + - - +
278Q ILE* 3.3 12.8 - - + +
280Q ALA* 1.3 75.9 - - - +
282Q ILE* 1.3 59.7 + - + +
284Q LYS* 3.2 13.9 + - - +
285Q GLU* 2.9 41.4 + - - +
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Residues in contact with ILE 282 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q LEU* 4.2 8.5 - - + -
80Q PHE* 3.7 42.6 - - + +
81Q ILE* 3.8 21.3 - - + +
82Q PRO* 3.9 2.2 - - + -
96Q ARG* 3.7 23.7 - - - +
278Q ILE* 2.9 36.8 + - + +
279Q GLU* 3.2 7.8 + - - +
281Q ALA* 1.3 76.7 - - + +
283Q TRP* 1.3 56.6 + - - +
285Q GLU* 3.2 11.4 + - - +
286Q ILE* 2.9 46.8 + - + +
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Residues in contact with TRP 283 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG* 3.7 59.3 + - + +
75Q PHE* 5.1 2.2 - + - -
76Q LEU* 3.5 58.4 - - + +
279Q GLU* 2.9 23.4 + - + -
280Q ALA* 3.5 11.2 - - - +
282Q ILE* 1.3 76.7 - - - +
284Q LYS* 1.3 56.9 - - - +
286Q ILE* 3.2 35.1 + - + +
287Q GLU* 2.9 47.5 + - + +
290Q LYS* 5.1 8.3 - - - -
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Residues in contact with LYS 284 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Q ALA* 2.9 26.0 + - - +
281Q ALA* 3.3 14.1 - - - +
283Q TRP* 1.3 77.7 - - + +
285Q GLU* 1.3 57.9 + - + +
287Q GLU* 3.2 19.1 + - - +
288Q ALA* 2.9 28.6 + - - +
291Q ARG* 4.8 2.8 + - - +
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Residues in contact with GLU 285 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q GLN* 3.4 19.9 + - - +
96Q ARG* 3.0 47.0 + - - +
100Q LEU* 4.9 6.6 - - + +
281Q ALA* 2.9 33.3 + - - +
282Q ILE* 3.2 7.4 + - - +
284Q LYS* 1.3 78.2 - - + +
286Q ILE* 1.3 57.8 - - + +
288Q ALA* 3.2 8.9 + - - +
289Q SER* 2.9 29.0 + - - -
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Residues in contact with ILE 286 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q LEU* 4.1 11.2 - - + -
80Q PHE* 4.3 13.7 - - + -
96Q ARG* 6.2 0.4 - - - -
100Q LEU* 4.1 22.0 - - + -
282Q ILE* 2.9 38.5 + - + +
283Q TRP* 3.4 37.9 - - + +
285Q GLU* 1.3 75.5 - - + +
287Q GLU* 1.3 58.4 - - + +
289Q SER* 2.5 28.3 + - - +
290Q LYS* 2.9 36.3 + - + +
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Residues in contact with GLU 287 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG* 2.8 31.4 + - - +
283Q TRP* 2.9 31.7 + - + +
284Q LYS* 3.4 19.9 + - - +
286Q ILE* 1.3 76.8 - - + +
288Q ALA* 1.3 58.8 + - - +
290Q LYS* 3.2 12.1 + - + +
291Q ARG* 2.9 58.0 + - - +
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Residues in contact with ALA 288 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284Q LYS 2.9 13.8 + - - +
285Q GLU* 3.3 12.3 - - - +
287Q GLU* 1.3 76.7 - - - +
289Q SER* 1.3 55.9 + - - +
291Q ARG* 3.2 19.4 + - - +
292Q SER* 2.9 29.2 + - - -
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Residues in contact with SER 289 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q LEU* 3.6 37.5 - - - +
104Q LYS* 5.2 11.5 + - - -
285Q GLU 2.9 13.2 + - - -
286Q ILE 2.5 20.1 + - - -
288Q ALA* 1.3 75.1 - - - +
290Q LYS* 1.3 65.6 + - - +
292Q SER* 2.5 28.1 + - - -
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Residues in contact with LYS 290 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283Q TRP* 5.1 7.9 - - - -
286Q ILE* 2.9 29.6 + - + +
287Q GLU* 3.4 14.8 - - + +
289Q SER* 1.3 84.9 + - - +
291Q ARG* 1.3 65.2 + - + +
292Q SER 4.0 3.6 - - - -
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Residues in contact with ARG 291 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284Q LYS* 4.8 2.6 + - - +
287Q GLU* 2.9 48.8 + - - +
288Q ALA* 3.4 16.0 - - - +
290Q LYS* 1.3 80.0 - - + +
292Q SER* 1.3 62.7 + - - +
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Residues in contact with SER 292 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LYS* 5.0 9.7 + - - -
288Q ALA 2.9 13.8 + - - -
289Q SER* 2.5 29.6 + - - -
290Q LYS 4.0 3.6 - - - -
291Q ARG* 1.3 82.5 - - - +
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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