Contacts of the helix formed by residues 272 - 289 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A TYR* 2.9 27.2 + - + +
268A SER* 5.3 0.2 - - - -
270A GLN* 3.4 5.4 + - + -
271A GLY* 1.3 74.0 - - - +
273A LYS* 1.3 58.0 + - - +
274A TRP* 4.2 3.5 + - - +
275A ARG* 2.6 56.0 + - - +
276A ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 273 (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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268A SER* 5.7 2.0 - - - +
271A GLY* 3.1 10.3 + - - +
272A ASP* 1.3 73.1 + - - +
274A TRP* 1.3 102.8 + - + +
276A ALA* 3.0 8.2 + - - +
277A LEU* 2.7 35.5 + - - +
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Residues in contact with TRP 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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272A ASP* 3.5 3.3 + - - +
273A LYS* 1.3 116.2 - - + +
275A ARG* 1.3 63.3 + - - +
277A LEU* 3.2 18.5 + - + +
278A GLY 2.9 19.1 + - - -
514A ARG* 4.4 6.1 - - - -
4B C 3.3 84.3 - + + +
5B G 3.8 10.8 - - - -
1D G 3.2 19.5 + - + -
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TYR* 3.3 40.3 - - + -
272A ASP* 2.6 51.2 + - - +
273A LYS 3.2 0.4 - - - -
274A TRP* 1.3 79.3 - - - +
276A ALA* 1.3 62.5 + - - +
278A GLY* 3.2 2.9 + - - -
279A TYR* 3.1 35.6 + - + -
1D G 3.0 68.8 + - + +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA* 4.2 7.7 - - - +
267A TYR* 4.4 6.1 - - - +
268A SER* 4.0 32.8 - - - +
272A ASP 3.0 15.6 + - - +
273A LYS* 3.0 12.0 + - - +
275A ARG* 1.3 76.6 - - - +
277A LEU* 1.3 60.6 + - - +
279A TYR* 3.3 6.6 + - - +
280A ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LYS 2.7 16.3 + - - +
274A TRP* 3.3 24.5 - - + +
276A ALA* 1.3 70.2 - - - +
278A GLY* 1.3 66.9 + - - +
280A ALA* 3.0 15.4 + - - +
281A LYS* 3.1 49.5 + - + +
511A HIS* 4.2 16.4 - - + +
514A ARG* 3.9 40.4 - - - +
4B C 3.9 22.2 - - - +
5B G 4.4 5.4 - - - +
1D G 4.6 1.6 - - - +
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TRP 2.9 11.5 + - - -
275A ARG 3.2 3.1 + - - -
277A LEU* 1.3 75.9 - - - +
279A TYR* 1.3 63.7 + - - +
281A LYS* 3.3 7.6 + - - +
282A ALA* 3.1 23.4 + - - +
304A GLY 4.5 2.6 - - - +
309A MET* 4.9 0.8 - - - +
1D G 3.6 35.1 + - - +
2D C 4.7 6.3 - - - +
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Residues in contact with TYR 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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260A LEU* 4.0 32.8 - - + -
263A LEU* 3.6 22.1 - - + +
264A ALA* 3.7 22.4 - - + -
267A TYR* 3.8 17.0 - + - -
275A ARG* 3.1 28.7 + - + +
276A ALA 3.7 4.9 - - - +
277A LEU 3.2 0.4 - - - -
278A GLY* 1.3 75.8 - - - +
280A ALA* 1.3 65.6 + - - +
282A ALA* 3.3 5.0 + - - +
283A ILE* 2.9 30.7 + - + +
309A MET* 3.9 26.0 - - + -
312A LYS* 3.5 17.8 + - + -
1D G 2.5 52.4 + - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA* 5.1 2.1 - - + +
276A ALA 3.0 13.9 + - - +
277A LEU* 3.0 11.0 + - - +
279A TYR* 1.3 77.9 - - - +
281A LYS* 1.3 57.3 + - + +
283A ILE* 3.4 8.9 + - - +
284A ASN 3.0 22.5 + - - -
511A HIS* 4.2 17.5 - - + +
575A TRP* 3.4 25.7 - - + -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.1 50.4 + - + +
278A GLY* 3.9 7.6 - - - +
280A ALA* 1.3 73.5 - - + +
282A ALA* 1.3 68.6 + - - +
283A ILE 3.1 0.3 + - - -
284A ASN* 3.2 3.2 + - - +
285A ALA* 2.9 25.0 + - - +
304A GLY* 4.7 11.4 - - - -
511A HIS* 5.3 4.0 - - - +
514A ARG* 6.3 2.2 - - - +
515A SER* 5.6 6.9 + - - -
575A TRP* 4.2 18.6 - - + -
577A GLU* 6.2 5.6 - - + -
4B C 5.5 2.4 + - - -
5B G 5.0 5.7 + - - -
1D G 5.9 1.9 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 5.5 0.9 - - + -
278A GLY 3.1 11.8 + - - +
279A TYR 3.5 8.1 - - - +
281A LYS* 1.3 76.4 - - - +
283A ILE* 1.3 64.7 + - + +
285A ALA* 3.2 4.5 + - - +
286A LEU* 3.0 27.0 + - + +
304A GLY 3.3 28.3 + - - +
305A ILE* 4.0 4.2 - - + +
309A MET* 3.9 33.7 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 4.2 6.7 - - + +
260A LEU* 3.7 31.0 - - + +
261A GLU* 3.6 43.3 - - + +
264A ALA* 4.3 5.4 - - + -
279A TYR* 2.9 25.8 + - + +
280A ALA* 3.6 7.6 - - - +
282A ALA* 1.3 75.3 - - + +
284A ASN* 1.3 67.6 + - - +
286A LEU* 3.1 9.4 + - - +
287A LYS* 3.1 49.3 + - + +
575A TRP* 6.4 0.4 - - + -
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Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA 3.0 8.9 + - - +
281A LYS* 3.2 5.4 + - - +
283A ILE* 1.3 76.1 - - - +
285A ALA* 1.3 64.4 + - - +
287A LYS* 3.0 20.6 + - - +
288A SER* 2.9 35.7 + - - -
574A ASP* 4.5 4.8 + - - -
575A TRP* 3.1 71.6 - - + +
577A GLU* 5.1 3.3 - - - +
578A HIS* 3.8 10.3 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS 2.9 12.5 + - - +
282A ALA* 3.4 11.2 - - - +
284A ASN* 1.3 76.6 + - - +
286A LEU* 1.3 61.4 + - - +
288A SER* 3.1 18.9 + - - -
289A PHE* 3.3 13.7 + - - +
302A ILE* 3.6 30.1 - - + +
303A PRO 3.7 13.7 - - - +
305A ILE* 4.5 0.7 - - + -
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Residues in contact with LEU 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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251A ASN* 4.2 1.4 - - - +
252A HIS 5.1 0.3 + - - -
253A ASN* 3.5 31.1 - - + +
256A ILE* 4.2 11.9 - - + -
257A THR* 4.0 13.7 - - + -
260A LEU* 3.6 31.6 - - + -
282A ALA* 3.0 19.5 + - + +
283A ILE* 3.1 7.4 + - - +
285A ALA* 1.3 74.4 - - - +
287A LYS* 1.3 63.5 + - - +
289A PHE* 3.3 12.8 + - - +
293A VAL* 3.9 25.6 - - + -
302A ILE* 4.6 2.0 - - + -
305A ILE* 3.5 21.5 - - + -
313A ILE* 3.8 21.3 - - + -
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Residues in contact with LYS 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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250A THR 3.6 18.5 - - - +
251A ASN* 3.7 37.8 - - + +
254A LEU* 6.0 0.9 - - - -
257A THR* 3.7 13.1 - - + -
261A GLU* 3.3 31.2 + - - -
283A ILE* 3.1 32.8 + - + +
284A ASN* 3.0 23.2 + - - +
286A LEU* 1.3 77.0 - - - +
288A SER* 1.3 61.3 + - - +
289A PHE 3.4 1.0 + - - +
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Residues in contact with SER 288 (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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250A THR 5.4 0.4 - - - -
284A ASN* 2.9 25.4 + - - -
285A ALA* 3.1 12.0 + - - -
287A LYS* 1.3 76.0 - - - +
289A PHE* 1.3 64.4 + - - +
290A HIS* 3.5 2.3 + - - -
577A GLU 5.3 1.2 + - - -
578A HIS* 3.5 37.6 + - - +
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Residues in contact with PHE 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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250A THR 4.5 1.9 - - - +
252A HIS* 3.2 18.7 + - - +
253A ASN* 4.3 2.2 - - - +
285A ALA 3.3 7.7 + - - +
286A LEU* 3.3 16.1 + - - +
287A LYS 3.2 3.3 - - - +
288A SER* 1.3 80.5 - - - +
290A HIS* 1.3 86.3 + + - +
291A LYS* 2.9 40.7 + - + +
293A VAL* 4.3 9.2 - - + -
298A GLU* 3.4 37.5 - - + -
301A SER* 5.5 1.8 - - - -
302A ILE* 3.7 36.8 - - + -
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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