Contacts of the helix formed by residues 272 - 289 (chain E) in PDB entry 4K4I
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 ASP 272 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E TYR* 2.9 31.5 + - + +
270E GLN* 3.3 6.5 + - + +
271E GLY* 1.3 71.7 - - - +
273E LYS* 1.3 63.5 + - - +
274E TRP* 4.1 2.3 + - - +
275E ARG* 3.1 52.3 + - - +
276E ALA* 3.2 17.3 + - - +
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Residues in contact with LYS 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E SER* 5.4 3.4 - - - +
271E GLY 2.8 15.8 + - - +
272E ASP* 1.3 74.0 + - - +
274E TRP* 1.3 108.3 + - + +
276E ALA* 3.4 7.1 + - - +
277E LEU* 3.0 27.2 + - - +
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Residues in contact with TRP 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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272E ASP* 3.4 3.6 + - - +
273E LYS* 1.3 117.6 - - + +
275E ARG* 1.3 66.6 + - - +
277E LEU* 3.2 20.4 + - + +
278E GLY 3.0 18.0 + - - -
514E ARG* 5.1 2.0 - - - -
4F C 3.2 79.4 - + + +
5F G 4.0 6.1 - - - -
1H G 3.3 18.0 - - + -
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Residues in contact with ARG 275 (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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267E TYR* 3.6 37.3 - - + -
272E ASP* 3.1 40.4 + - - +
274E TRP* 1.3 78.0 - - - +
276E ALA* 1.3 61.6 + - - +
278E GLY* 3.1 3.5 + - - -
279E TYR* 3.0 28.6 + - + -
308E ARG* 5.1 1.2 - - - +
1H G 3.2 72.2 + - + +
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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
----------------------------------------------------------
264E ALA* 3.8 25.5 - - + +
267E TYR* 4.5 4.2 - - + +
268E SER* 3.9 20.6 - - - +
272E ASP 3.2 15.3 + - - +
273E LYS* 3.6 10.1 - - - +
274E TRP 3.3 0.2 - - - -
275E ARG* 1.3 74.1 - - - +
277E LEU* 1.3 58.7 + - - +
279E TYR* 3.2 8.5 + - - +
280E ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E LYS 3.0 13.8 + - - +
274E TRP* 3.5 32.1 - - + +
276E ALA* 1.3 77.4 - - - +
278E GLY* 1.3 56.3 + - - +
280E ALA* 3.1 4.7 + - - +
281E LYS* 2.8 67.7 + - + +
511E HIS* 4.2 11.0 - - - +
514E ARG* 3.9 41.3 - - - +
4F C 4.1 11.9 - - + +
5F G 3.9 8.7 - - - +
1H G 4.7 2.2 - - - +
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Residues in contact with GLY 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E TRP 3.0 11.1 + - - -
275E ARG 3.1 1.5 + - - -
277E LEU* 1.3 72.9 - - - +
279E TYR* 1.3 65.5 + - - +
281E LYS* 3.4 6.9 + - - +
282E ALA* 3.1 22.2 + - - +
304E GLY 4.8 2.3 - - - +
309E MET* 4.1 1.6 - - - +
1H G 3.3 38.3 - - - +
2H C 4.9 5.0 - - - +
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Residues in contact with TYR 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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260E LEU* 4.0 26.9 - - + -
263E LEU* 3.6 26.7 - - + +
264E ALA* 3.5 20.0 - - + -
267E TYR* 3.7 23.2 - + - -
275E ARG* 3.0 30.1 + - + -
276E ALA* 3.4 7.6 - - - +
278E GLY* 1.3 75.2 - - - +
280E ALA* 1.3 55.0 + - - +
282E ALA* 3.1 2.6 + - - +
283E ILE* 2.7 40.4 + - + +
309E MET* 3.8 25.4 - - + -
312E LYS* 3.3 18.1 + - + -
1H G 2.6 46.4 + - - -
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Residues in contact with ALA 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E ALA* 4.8 2.9 - - + +
276E ALA 2.8 17.7 + - - +
277E LEU* 3.1 12.5 + - - +
279E TYR* 1.3 72.5 - - - +
281E LYS* 1.3 63.2 + - - +
283E ILE* 3.4 10.6 + - - +
284E ASN* 3.1 29.6 + - - +
511E HIS* 3.6 31.0 - - + +
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Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E LEU* 2.8 52.6 + - + +
278E GLY* 3.7 7.4 - - - +
280E ALA* 1.3 78.9 - - - +
282E ALA* 1.3 57.4 + - - +
284E ASN* 3.4 7.2 + - - +
285E ALA* 3.0 27.5 + - - +
304E GLY* 5.0 11.0 - - - +
511E HIS* 5.1 10.1 - - + -
514E ARG* 5.4 6.5 - - - +
515E SER* 5.7 6.3 - - - +
577E GLU* 5.0 1.0 - - - +
4F C 4.8 8.9 + - - -
5F G 4.2 10.8 + - - -
1H G 5.4 2.9 + - - +
2H C 6.1 1.1 - - - +
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Residues in contact with ALA 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E LEU* 5.3 0.7 - - + -
278E GLY 3.1 13.3 + - - +
279E TYR 3.1 7.5 + - - +
281E LYS* 1.3 73.3 - - - +
283E ILE* 1.3 67.6 + - + +
285E ALA* 3.1 6.7 + - - +
286E LEU* 2.9 29.9 + - + +
304E GLY 3.7 19.9 + - - +
305E ILE* 4.4 3.7 - - + +
309E MET* 3.7 34.3 - - + -
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Residues in contact with ILE 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E THR* 3.8 15.2 - - - +
260E LEU* 3.9 26.5 - - + +
261E GLU* 3.5 58.6 - - + +
264E ALA* 4.0 8.3 - - + -
279E TYR* 2.7 30.6 + - + +
280E ALA* 3.6 8.5 - - - +
282E ALA* 1.3 69.5 - - - +
284E ASN* 1.3 66.3 + - - +
286E LEU* 3.0 8.4 + - - +
287E LYS* 3.0 39.0 + - + +
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Residues in contact with ASN 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E ALA* 3.1 20.8 + - - +
281E LYS* 3.7 6.8 - - - +
282E ALA 3.2 0.2 - - - -
283E ILE* 1.3 77.6 - - - +
285E ALA* 1.3 64.2 + - - +
287E LYS* 3.2 21.9 + - - +
288E SER* 3.1 23.7 + - - -
511E HIS* 3.5 40.9 + - - +
574E ASP 4.5 3.1 + - - +
575E TRP* 4.3 21.1 - - + +
577E GLU* 3.8 15.0 - - - +
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Residues in contact with ALA 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 LYS 3.0 14.3 + - - +
282E ALA* 3.1 10.5 + - - +
284E ASN* 1.3 77.3 - - - +
286E LEU* 1.3 63.4 + - - +
288E SER* 3.2 4.2 + - - -
289E PHE* 3.0 21.5 + - - +
302E ILE* 4.0 16.5 - - + +
303E PRO 3.5 24.5 - - - +
304E GLY* 4.9 1.1 - - - -
305E ILE* 4.9 3.1 - - + -
577E GLU* 3.5 19.9 + - - +
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Residues in contact with LEU 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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251E ASN* 4.2 0.9 - - - +
252E HIS 5.1 0.2 + - - -
253E ASN* 3.2 29.9 + - + +
256E ILE* 3.7 17.5 - - + -
257E THR* 3.6 14.8 - - + -
260E LEU* 3.7 30.3 - - + -
282E ALA* 2.9 19.1 + - + +
283E ILE* 3.0 6.0 + - - +
285E ALA* 1.3 77.0 - - - +
287E LYS* 1.3 60.4 + - - +
289E PHE* 3.2 10.9 + - - +
293E VAL* 3.7 29.2 - - + -
302E ILE* 4.5 1.6 - - + -
305E ILE* 3.6 23.1 - - + -
313E ILE* 4.0 13.5 - - + -
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Residues in contact with LYS 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E THR 3.5 19.9 - - - +
251E ASN* 3.8 33.9 - - + +
257E THR* 4.3 8.1 - - + -
261E GLU* 3.0 26.8 + - - -
283E ILE* 3.0 28.9 + - + +
284E ASN* 3.6 22.9 + - - +
285E ALA 3.2 0.4 - - - -
286E LEU* 1.3 77.0 - - - +
288E SER* 1.3 59.7 + - - +
289E PHE 3.6 1.9 + - - +
575E TRP* 3.7 30.7 - - + -
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Residues in contact with SER 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E THR 5.6 0.2 - - - -
284E ASN 3.1 8.9 + - - -
285E ALA 3.3 6.4 + - - -
286E LEU 3.2 0.2 - - - -
287E LYS* 1.3 74.9 - - - +
289E PHE* 1.3 68.6 + - - +
290E HIS* 3.5 2.6 + - - -
575E TRP* 3.1 41.1 - - - +
577E GLU* 3.3 35.4 + - - +
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Residues in contact with PHE 289 (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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250E THR 4.6 0.7 - - - +
252E HIS* 3.7 14.4 + - - -
253E ASN* 4.2 6.3 + - - +
285E ALA 3.0 11.4 + - - +
286E LEU* 3.2 16.0 + - - +
287E LYS 4.1 3.8 - - - +
288E SER* 1.3 81.2 - - - +
290E HIS* 1.3 88.8 + + - +
291E LYS* 3.2 32.0 + - + +
293E VAL* 4.0 12.1 - - + -
298E GLU* 3.5 35.0 - - + -
301E SER* 4.8 4.9 - - - -
302E ILE* 3.7 39.0 - - + -
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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
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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