Contacts of the helix formed by residues 273 - 289 (chain A) in PDB entry 6EJ9
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 SER 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS* 1.3 81.0 - - - +
274A LYS* 1.3 64.1 + - - +
275A HIS* 4.1 9.4 - - - +
276A CYS* 3.0 17.3 + - - +
277A ARG* 3.2 23.5 + - - +
472A ASP* 2.6 31.9 + - - -
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Residues in contact with LYS 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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252A ASP* 5.7 9.9 - - - +
272A LYS 4.0 0.2 + - - -
273A SER* 1.3 69.7 - - - +
275A HIS* 1.3 68.2 + - - +
277A ARG* 3.3 26.3 + - - +
278A GLN* 3.0 26.8 + - + +
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Residues in contact with HIS 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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273A SER* 3.3 9.5 - - - +
274A LYS* 1.3 79.4 - - - +
276A CYS* 1.3 59.0 + - - +
278A GLN* 3.6 6.2 + - - +
279A GLU* 3.1 31.3 + - + +
471A CYS* 4.1 19.6 - - - -
472A ASP* 5.3 2.9 - - - -
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Residues in contact with CYS 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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271A ALA* 4.0 10.5 - - + -
273A SER* 3.0 24.3 + - - +
274A LYS 3.1 0.4 - - - -
275A HIS* 1.3 76.9 - - - +
277A ARG* 1.3 60.8 + - - +
279A GLU* 3.3 1.7 + - - +
280A ILE* 2.9 45.3 + - - +
471A CYS* 3.5 37.5 - - - -
472A ASP* 3.2 13.7 - - - +
476A TRP* 3.7 20.0 - - - -
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Residues in contact with ARG 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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252A ASP* 5.9 4.8 - - - +
268A LEU* 3.4 41.7 - - + +
271A ALA* 3.7 23.8 + - + -
272A LYS 3.1 26.9 + - - -
273A SER 3.2 10.6 + - - +
274A LYS* 3.3 29.4 + - - +
276A CYS* 1.3 76.4 - - - +
278A GLN* 1.3 63.0 + - - +
280A ILE* 3.5 2.2 + - - -
281A GLY* 3.0 19.4 + - - -
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Residues in contact with GLN 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 LYS* 3.0 21.2 + - + +
275A HIS* 3.8 7.4 - - - +
277A ARG* 1.3 78.5 - - - +
279A GLU* 1.3 57.6 + - - +
281A GLY* 3.2 2.9 + - - -
282A GLU* 3.0 48.1 + - + +
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Residues in contact with GLU 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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275A HIS* 3.1 26.8 + - + +
276A CYS 3.3 3.6 + - - +
278A GLN* 1.3 74.1 - - - +
280A ILE* 1.3 65.0 + - - +
282A GLU* 3.4 12.3 + - + +
283A THR* 3.0 33.3 + - - +
469A LEU* 3.8 26.0 - - + -
470A GLU 5.8 0.2 - - - +
471A CYS* 4.6 13.2 - - + -
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Residues in contact with ILE 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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264A ALA* 4.5 9.4 - - + +
267A ALA* 4.0 29.8 - - + +
268A LEU* 3.4 25.4 - - + -
271A ALA* 4.1 6.7 - - + -
276A CYS* 2.9 39.1 + - - +
277A ARG 3.6 4.0 - - - +
279A GLU* 1.3 77.1 - - - +
281A GLY* 1.3 62.0 + - - +
283A THR* 3.9 1.6 - - - -
284A TYR* 3.1 23.4 + - + +
469A LEU* 3.9 20.6 - - + -
476A TRP* 4.2 11.4 - - + -
478A LEU* 4.0 23.1 - - + +
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Residues in contact with GLY 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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255A PRO* 5.3 4.9 - - - -
256A LYS 6.2 0.9 - - - -
259A ILE* 4.3 21.3 - - - -
268A LEU* 5.0 1.3 - - - -
277A ARG 3.0 14.5 + - - -
278A GLN* 3.2 4.0 + - - -
280A ILE* 1.3 79.3 - - - +
282A GLU* 1.3 61.4 + - - +
284A TYR* 3.4 2.3 + - - +
285A CYS* 3.0 31.0 + - - -
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Residues in contact with GLU 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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256A LYS* 6.3 4.3 - - + -
278A GLN* 3.0 39.8 + - + +
279A GLU* 4.0 9.8 - - + +
280A ILE 3.4 0.2 - - - -
281A GLY* 1.3 75.3 - - - +
283A THR* 1.3 62.9 + - - +
285A CYS* 3.4 4.0 + - - +
286A ARG* 2.9 27.1 + - - +
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Residues in contact with THR 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 GLU* 3.0 21.5 + - - +
280A ILE 3.9 3.4 - - - -
282A GLU* 1.3 76.0 - - - +
284A TYR* 1.3 62.2 + - - +
286A ARG* 3.4 3.2 + - - +
287A HIS* 3.0 23.0 + - - +
292A LEU* 3.6 26.9 - - + +
467A LEU* 4.2 7.2 - - + -
469A LEU* 3.8 15.5 - - + +
478A LEU* 3.9 20.2 - - + -
523A TYR* 3.9 24.3 + - + -
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Residues in contact with TYR 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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257A CYS* 4.0 4.9 - - - -
258A ASP 3.6 19.1 - - - -
259A ILE* 3.7 20.4 - - + -
260A SER* 3.2 19.0 + - - -
261A GLY* 3.3 16.2 + - - -
264A ALA* 3.6 32.1 - - + -
280A ILE* 3.1 18.3 + - + +
281A GLY* 3.8 3.8 - - - +
283A THR* 1.3 77.9 - - - +
285A CYS* 1.3 61.9 + - - +
287A HIS* 3.4 6.8 + + - +
288A LYS* 2.8 60.2 + - + +
467A LEU* 5.5 2.0 - - - -
478A LEU* 4.2 19.7 - - + +
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 4.7 1.3 - - - -
256A LYS* 4.2 13.2 - - + -
257A CYS* 2.0 66.1 - - + +
259A ILE* 4.5 3.4 - - - -
281A GLY 3.0 22.6 + - - +
282A GLU* 4.1 4.3 - - - +
284A TYR* 1.3 78.7 - - - +
286A ARG* 1.3 65.0 + - - +
288A LYS* 3.2 4.0 + - - +
289A LEU* 3.2 29.9 + - + +
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Residues in contact with ARG 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 GLU 2.9 19.6 + - - +
283A THR* 3.8 3.8 - - - +
285A CYS* 1.3 75.5 - - - +
287A HIS* 1.3 60.1 + - - +
289A LEU* 3.3 11.6 + - - -
291A LEU* 3.1 47.4 + - - +
292A LEU* 3.7 33.7 - - + +
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Residues in contact with HIS 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 THR 3.0 17.0 + - - +
284A TYR* 3.7 5.4 - + - +
286A ARG* 1.3 73.1 - - - +
288A LYS* 1.3 64.8 + - - +
290A GLY* 3.0 15.6 + - - +
292A LEU* 3.7 12.8 - - + +
293A MET* 4.0 26.9 + - + +
467A LEU* 3.7 27.4 - - + -
479A GLY* 5.9 1.6 - - - -
480A ASP 3.0 25.0 + - - -
481A ARG* 3.9 18.9 - - + +
482A ARG 5.6 0.4 - - - -
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A CYS* 4.7 7.2 - - + -
258A ASP* 3.8 17.2 + - - -
260A SER* 3.5 15.4 + - - -
284A TYR* 2.8 47.3 + - + +
285A CYS* 3.3 15.9 - - - +
286A ARG 3.2 0.4 - - - -
287A HIS* 1.3 78.9 - - - +
289A LEU* 1.3 67.6 + - + +
290A GLY 3.4 0.7 + - - -
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Residues in contact with LEU 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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257A CYS* 6.1 3.8 - - + -
285A CYS* 3.2 17.7 + - + +
286A ARG* 3.3 6.5 + - - +
287A HIS 3.2 0.2 - - - -
288A LYS* 1.3 84.2 - - + +
290A GLY* 1.3 60.9 + - - +
291A LEU* 3.5 31.3 + - + +
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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