Contacts of the helix formed by residues 270 - 286 (chain E) in PDB entry 6O81
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 270 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222E SER* 4.6 14.3 + - - -
225E ARG* 3.5 25.0 + - - +
269E LEU* 1.3 77.4 - - - +
271E ALA* 1.3 63.6 + - - +
272E SER* 2.8 25.6 + - - -
273E MET* 3.2 17.8 + - - +
274E HIS* 3.1 20.9 + - - -
406E HIS* 5.9 2.7 - - - -
415E MET* 5.6 2.2 - - - -
489E TYR* 4.0 17.9 - - - -
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Residues in contact with ALA 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E SER* 1.3 72.2 - - - +
272E SER* 1.3 60.8 + - - +
274E HIS* 3.3 13.1 + - + +
275E ASN* 2.9 39.3 + - - +
406E HIS 4.7 2.8 + - - +
407E ALA* 3.7 20.2 - - + +
415E MET* 4.8 10.8 - - + +
442E LYS* 4.9 1.8 - - - +
444E CYS* 3.6 31.0 - - - -
446E ARG* 5.1 3.6 - - - +
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Residues in contact with SER 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E SER* 3.6 19.6 + - - -
226E CYS* 4.0 10.1 - - - +
270E SER* 2.8 19.6 + - - -
271E ALA* 1.3 77.5 - - - +
273E MET* 1.3 54.8 + - - +
275E ASN* 3.5 7.1 + - - +
276E ALA* 2.9 29.6 + - - +
406E HIS 4.8 4.5 + - - -
441E TYR* 3.6 31.7 - - - -
442E LYS* 3.7 17.6 - - - +
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Residues in contact with MET 273 (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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214E TYR* 3.6 26.0 - - + -
225E ARG* 3.3 49.8 - - + +
226E CYS* 4.7 1.6 - - - +
229E LEU* 3.8 36.9 - - + +
263E LEU* 4.1 6.5 - - + -
269E LEU* 3.7 27.8 - - + -
270E SER* 3.2 20.1 + - - +
272E SER* 1.3 77.8 + - - +
274E HIS* 1.3 60.0 + - - +
276E ALA* 3.6 1.6 - - - +
277E ILE* 2.9 36.0 + - + +
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Residues in contact with HIS 274 (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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264E THR* 5.6 3.4 - - + -
269E LEU* 3.6 41.1 + - + +
270E SER 3.1 26.8 + - - -
271E ALA* 3.3 11.8 + - - +
273E MET* 1.3 76.8 - - - +
275E ASN* 1.3 58.5 + - - +
277E ILE* 3.3 11.6 + - - +
278E LYS* 2.9 39.9 + - - +
446E ARG* 6.0 5.2 - - - -
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Residues in contact with ASN 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E ALA* 2.9 27.8 + - - +
272E SER 3.9 2.5 - - - +
274E HIS* 1.3 74.0 - - - +
276E ALA* 1.3 60.1 + - - +
278E LYS* 3.1 29.1 + - - +
279E PHE* 2.9 30.0 + - - +
307E TYR* 4.5 5.1 + - - +
441E TYR* 2.8 30.1 + - - +
442E LYS 3.8 1.0 - - - -
443E PHE 2.7 30.5 + - - +
444E CYS* 5.1 1.5 - - - -
445E GLU* 4.2 3.6 - - - +
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Residues in contact with ALA 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E CYS* 4.0 9.6 - - - -
229E LEU* 4.2 7.4 - - + -
230E LEU* 3.7 30.1 - - + +
233E LEU* 5.6 2.4 - - + +
272E SER 2.9 18.5 + - - +
273E MET 3.6 4.5 - - - +
274E HIS 3.3 0.2 - - - -
275E ASN* 1.3 73.9 - - - +
277E ILE* 1.3 59.8 + - - +
279E PHE* 3.4 4.0 + - - +
280E LEU* 2.9 30.8 + - - +
307E TYR* 4.3 14.2 + - + +
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Residues in contact with ILE 277 (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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229E LEU* 5.0 7.2 - - + -
233E LEU* 5.8 3.1 - - + -
260E MET* 3.7 44.2 - - + -
269E LEU* 4.0 23.6 - - + -
273E MET* 2.9 26.2 + - + +
274E HIS* 3.3 12.3 + - - +
276E ALA* 1.3 76.8 - - - +
278E LYS* 1.3 59.5 + - + +
280E LEU* 3.4 7.4 + - + +
281E ASN* 2.9 50.6 + - - +
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Residues in contact with LYS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E HIS* 2.9 26.6 + - - +
275E ASN* 3.1 26.2 + - - +
276E ALA 3.3 0.4 - - - -
277E ILE* 1.3 79.3 - - + +
279E PHE* 1.3 57.1 + - - +
281E ASN* 3.4 8.6 + - - +
282E LYS* 2.9 29.3 + - - +
444E CYS* 5.8 0.6 - - - +
445E GLU* 3.0 29.6 + - - +
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Residues in contact with PHE 279 (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 ASN 2.9 18.9 + - - +
276E ALA* 3.9 5.6 - - - +
278E LYS* 1.3 75.9 - - - +
280E LEU* 1.3 60.7 + - + +
282E LYS* 3.4 25.5 + - - +
283E GLU* 2.9 62.2 + - + +
303E ALA* 4.7 8.5 - - + -
304E ILE* 5.6 5.4 - - + -
307E TYR* 3.5 58.8 - + + +
311E LYS* 6.0 2.5 - - - -
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Residues in contact with LEU 280 (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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233E LEU* 3.7 42.8 - - + -
237E ILE* 4.5 9.9 - - + -
256E LEU* 3.8 20.2 - - + -
260E MET* 6.1 0.2 - - + -
276E ALA 2.9 18.5 + - - +
277E ILE* 3.8 6.1 - - + +
279E PHE* 1.3 79.4 - - + +
281E ASN* 1.3 58.6 + - - +
283E GLU* 3.3 7.4 + - + -
284E ILE* 2.9 50.1 + - + +
300E LEU* 5.2 2.5 - - + -
304E ILE* 3.7 30.5 - - + -
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Residues in contact with ASN 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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253E VAL* 4.3 18.9 - - + +
256E LEU* 4.8 9.7 - - - +
257E LYS* 4.9 11.1 - - - +
277E ILE* 2.9 40.9 + - - +
278E LYS* 3.8 8.4 - - - +
280E LEU* 1.3 76.8 - - - +
282E LYS* 1.3 53.9 + - - +
284E ILE* 3.7 18.5 - - - +
285E THR* 2.3 41.3 + - - +
28L GLU* 5.8 7.4 - - - -
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Residues in contact with LYS 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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278E LYS 2.9 17.4 + - - +
279E PHE* 3.7 29.1 - - - +
280E LEU 3.3 0.2 - - - -
281E ASN* 1.3 76.3 - - - +
283E GLU* 1.3 66.0 + - - +
285E THR* 4.0 5.9 - - - -
286E SER* 3.2 22.9 + - - -
519E LYS 5.2 7.1 + - - -
520E SER* 5.4 4.9 - - - +
521E SER* 4.3 16.5 + - - +
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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 PHE* 2.9 56.2 + - + +
280E LEU* 3.3 9.1 + - + +
282E LYS* 1.3 83.9 - - - +
284E ILE* 1.3 61.8 + - + +
286E SER* 3.1 19.8 + - - -
287E VAL* 3.4 14.0 - - - +
300E LEU* 4.0 17.3 - - + +
303E ALA* 4.1 20.4 - - + +
304E ILE* 6.5 1.1 - - + -
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Residues in contact with ILE 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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248E LEU* 5.0 1.7 - - + +
249E SER* 3.3 26.4 + - - -
252E LEU* 3.8 34.8 - - + -
253E VAL* 3.7 25.8 - - + +
256E LEU* 4.0 13.0 - - + -
280E LEU* 2.9 34.9 + - + +
281E ASN* 3.7 18.8 - - - +
283E GLU* 1.3 73.8 - - - +
285E THR* 1.3 66.2 + - - +
287E VAL* 3.8 11.5 - - + +
300E LEU* 3.7 29.8 - - + -
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Residues in contact with THR 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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249E SER* 4.0 12.8 - - - -
253E VAL* 4.6 6.9 - - - +
281E ASN* 2.3 28.1 + - - +
282E LYS* 4.0 7.4 - - - -
283E GLU 3.2 0.2 - - - -
284E ILE* 1.3 78.9 - - - +
286E SER* 1.3 57.3 + - - +
287E VAL 3.2 11.8 + - - +
28L GLU 4.5 6.4 + - - +
29L MET* 3.7 41.9 + - + +
47L LEU* 6.4 1.6 - - + -
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Residues in contact with SER 286 (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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282E LYS 3.2 12.3 + - - -
283E GLU* 3.1 20.8 + - - -
284E ILE 3.4 0.4 - - - -
285E THR* 1.3 76.0 - - - +
287E VAL* 1.3 60.2 + - - +
288E GLY 3.6 2.6 + - - -
291E LYS* 4.6 5.9 + - - -
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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
------------------------------------------------------------
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