Contacts of the helix formed by residues 267 - 285 (chain E) in PDB entry 5X8Q
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 LEU 267 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E SER* 1.3 73.1 - - - +
268E THR* 1.3 61.4 + - + +
270E ILE* 3.7 8.4 - - - +
271E GLU* 3.0 46.8 + - - +
452E HIS* 5.5 9.0 - - + -
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Residues in contact with THR 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER* 3.1 11.6 + - - +
267E LEU* 1.3 77.9 - - + +
269E GLU* 1.3 59.8 + - - +
271E GLU* 3.8 10.6 - - - +
272E HIS* 2.9 52.1 + - - -
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Residues in contact with GLU 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER* 3.3 33.6 + - - +
268E THR* 1.3 79.9 + - - +
270E ILE* 1.3 64.3 + - + +
272E HIS* 4.1 9.6 - - - +
273E LEU* 3.8 14.2 + - - +
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Residues in contact with ILE 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER 3.3 18.1 + - - +
267E LEU* 3.7 8.5 - - - +
269E GLU* 1.3 83.9 - - + +
271E GLU* 1.3 60.8 + - - +
272E HIS 3.2 0.7 - - - -
273E LEU* 3.3 10.2 + - + +
274E VAL* 3.0 32.4 + - - +
445E ASN* 5.3 3.4 - - + +
448E LEU* 4.2 29.4 - - + +
449E ALA* 3.9 11.1 - - + +
452E HIS* 3.6 43.5 - - + +
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Residues in contact with GLU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E LEU* 3.0 34.4 + - - +
268E THR* 4.0 10.5 + - - +
270E ILE* 1.3 76.4 - - - +
272E HIS* 1.3 59.7 + - + +
274E VAL* 3.5 8.4 + - + +
275E GLN* 3.1 36.5 + - + +
452E HIS* 3.7 28.7 + - + +
456E LYS* 4.2 17.4 + - - +
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Residues in contact with HIS 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E THR* 2.9 40.1 + - - +
269E GLU* 4.2 9.7 - - - +
270E ILE 3.2 0.2 - - - -
271E GLU* 1.3 78.7 - - + +
273E LEU* 1.3 55.8 + - - +
275E GLN* 3.4 8.4 + - + +
276E SER* 2.9 30.5 + - - -
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Residues in contact with LEU 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E GLU 3.8 11.7 + - - +
270E ILE* 3.3 14.2 + - + +
272E HIS* 1.3 74.7 - - - +
274E VAL* 1.3 65.4 + - - +
276E SER* 3.3 8.5 + - - +
277E VAL* 3.0 41.1 + - + +
339E SER* 4.4 23.8 - - - +
419E LEU* 6.0 0.2 - - + -
445E ASN* 3.6 41.7 - - + +
446E LEU* 4.2 17.0 - - + +
449E ALA* 4.2 8.7 - - + -
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Residues in contact with VAL 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E ILE 3.0 20.5 + - - +
271E GLU* 3.7 10.8 - - + +
272E HIS 3.4 0.2 - - - -
273E LEU* 1.3 75.2 - - - +
275E GLN* 1.3 74.7 + - - +
277E VAL* 3.3 2.9 + - - +
278E CYS* 3.1 33.1 + - - -
415E ASP* 4.6 2.0 - - - +
419E LEU* 4.2 21.3 - - + +
449E ALA* 3.7 31.4 - - + +
452E HIS* 5.8 3.6 - - + -
453E HIS* 4.0 26.9 - - + +
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Residues in contact with GLN 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU* 3.1 24.8 + - + +
272E HIS* 3.9 9.0 - - + +
273E LEU 3.3 0.2 - - - -
274E VAL* 1.3 85.7 - - - +
276E SER* 1.3 57.4 + - - +
278E CYS* 3.5 11.7 + - - +
279E LYS* 3.0 29.0 + - - +
282E ARG* 4.9 2.3 + - - -
415E ASP* 4.9 4.3 - - - +
294G ARG* 4.2 28.9 + - - +
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Residues in contact with SER 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E HIS 2.9 18.7 + - - -
273E LEU* 3.5 14.5 + - - +
274E VAL 3.2 0.2 - - - -
275E GLN* 1.3 77.8 - - - +
277E VAL* 1.3 62.3 + - - +
279E LYS* 3.5 7.0 + - - +
280E SER* 2.8 30.7 + - - -
337E ARG 4.7 6.9 + - - -
338E LEU* 5.6 0.5 - - - -
339E SER* 5.0 9.6 + - - -
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Residues in contact with VAL 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E LEU* 3.0 27.6 + - + +
274E VAL 3.3 4.2 + - - +
276E SER* 1.3 77.3 - - - +
278E CYS* 1.3 59.2 + - - +
280E SER* 3.4 7.4 + - - -
281E TYR* 3.1 26.3 + - - +
334E PHE* 3.8 6.3 - - + -
338E LEU* 3.9 15.0 - - + -
339E SER 6.2 0.4 - - - +
418E ALA* 3.4 33.9 - - + +
419E LEU* 4.0 15.5 - - + +
422E ALA* 4.2 7.6 - - + -
446E LEU* 3.9 24.7 - - + -
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Residues in contact with CYS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E VAL* 3.1 23.7 + - - +
275E GLN* 3.7 12.3 - - - +
276E SER 3.3 0.2 - - - -
277E VAL* 1.3 75.6 - - - +
279E LYS* 1.3 64.0 + - - +
281E TYR* 3.1 3.3 + - - +
282E ARG* 2.9 43.8 + - - +
414E GLU* 4.0 6.4 - - - +
415E ASP* 3.5 46.0 - - - +
418E ALA* 4.0 11.4 - - - -
419E LEU* 5.4 1.3 - - - -
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Residues in contact with LYS 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLN 3.0 17.0 + - - +
276E SER* 3.7 8.3 - - - +
278E CYS* 1.3 76.5 - - - +
280E SER* 1.3 63.4 + - - +
282E ARG* 3.3 26.5 + - + +
283E GLU* 3.1 54.2 + - + +
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Residues in contact with SER 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E SER* 2.8 14.8 + - - -
277E VAL* 3.6 10.1 - - - -
278E CYS 3.2 0.2 - - - -
279E LYS* 1.3 80.7 - - - +
281E TYR* 1.3 53.8 + - - +
283E GLU* 3.3 11.1 + - - +
284E THR* 2.6 37.3 + - - +
334E PHE* 3.9 16.8 - - - -
337E ARG* 3.5 36.6 + - - +
338E LEU* 4.5 2.4 + - - +
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Residues in contact with TYR 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E VAL 3.1 6.3 + - - +
278E CYS* 3.1 7.2 + - - +
280E SER* 1.3 74.5 - - - +
282E ARG* 1.3 69.5 + - + +
284E THR* 3.1 5.5 + - - -
285E CYS* 3.0 44.3 + - + +
334E PHE* 3.8 8.4 - + + -
364E ARG* 3.7 36.8 - - + +
367E ARG* 3.7 28.1 + - - +
414E GLU* 4.2 26.5 - - + -
417E ILE* 3.4 34.4 - - + +
418E ALA* 3.6 31.0 - - + -
421E THR* 4.4 6.3 - - - -
9000E 82R 4.7 4.0 + - - -
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Residues in contact with ARG 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E GLN* 4.9 2.2 + - - -
278E CYS* 2.9 21.8 + - - +
279E LYS* 3.3 39.8 + - + +
281E TYR* 1.3 76.3 - - + +
283E GLU* 1.3 61.9 + - + +
284E THR 3.4 0.5 + - - -
285E CYS* 3.4 22.0 + - - -
286E GLN 5.3 0.2 + - - -
414E GLU* 2.6 54.6 + - + +
290G GLU* 5.6 4.3 + - - -
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Residues in contact with GLU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E LYS* 3.1 53.6 + - + +
280E SER* 3.6 7.9 + - - +
281E TYR 3.2 0.2 - - - -
282E ARG* 1.3 77.8 - - + +
284E THR* 1.3 60.6 + - - +
285E CYS 3.7 0.2 - - - -
286E GLN 5.4 0.5 + - - -
330E TYR* 5.2 4.3 - - - -
337E ARG* 2.8 42.1 + - - +
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Residues in contact with THR 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E SER 2.6 23.6 + - - +
281E TYR 3.1 0.6 + - - -
283E GLU* 1.3 81.7 - - - +
285E CYS* 1.3 60.5 + - - +
286E GLN 3.3 6.6 + - - -
330E TYR* 3.5 31.8 - - + +
333E GLU* 3.8 13.9 - - + -
334E PHE* 3.7 23.9 - - - +
337E ARG* 3.8 21.3 - - - +
364E ARG* 2.7 36.0 + - - -
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Residues in contact with CYS 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E TYR* 3.0 36.2 + - + +
282E ARG* 3.4 24.9 - - - -
283E GLU 3.7 1.2 - - - -
284E THR* 1.3 77.1 - - - +
286E GLN* 1.3 58.1 + - - +
287E LEU 2.9 32.1 + - - +
288E ARG* 5.1 4.3 - - - -
289E LEU 5.7 0.9 - - - -
364E ARG* 3.9 9.6 - - - +
9000E 82R 2.7 35.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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