Contacts of the helix formed by residues 271 - 292 (chain A) in PDB entry 3KCZ
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 THR 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS 3.4 15.0 - - - +
270A LEU* 1.3 75.7 - - - +
272A VAL* 1.3 64.5 + - - +
273A ALA* 3.5 8.9 + - - +
274A GLN* 2.9 44.2 + - - +
275A ILE* 3.2 16.4 + - - +
341A GLU* 4.5 7.0 - - - -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 1.3 73.9 - - - +
273A ALA* 1.3 60.9 + - + +
275A ILE* 3.3 11.8 + - + +
276A LYS* 2.9 29.5 + - - +
341A GLU* 3.4 34.6 + - + +
345A LYS* 4.7 5.6 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.2 8.9 + - - +
272A VAL* 1.3 84.2 - - + +
274A GLN* 1.3 62.5 + - - +
276A LYS* 3.3 9.8 + - + +
277A ALA* 2.9 24.1 + - - +
364B ASN* 5.9 0.9 - - - +
366B HIS* 3.8 31.6 - - + +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TYR* 5.4 1.2 + - - -
265A ALA* 6.0 3.6 - - - +
269A LYS* 3.6 16.6 + - - +
270A LEU* 3.1 19.6 - - + +
271A THR* 2.9 41.4 + - - +
273A ALA* 1.3 75.0 - - - +
275A ILE* 1.3 59.6 + - + +
277A ALA* 3.3 9.5 + - - +
278A GLY 3.0 21.7 + - - -
308A ARG* 4.9 12.2 - - - +
309A ILE* 3.8 10.5 - - + +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.8 25.4 - - + -
271A THR 3.2 16.0 + - - +
272A VAL* 3.8 11.0 - - + +
273A ALA 3.2 0.2 - - - -
274A GLN* 1.3 76.1 - - - +
276A LYS* 1.3 63.2 + - - +
278A GLY* 3.1 10.6 + - - +
279A TYR* 3.1 34.3 + - + -
309A ILE* 4.6 6.5 - - + -
334A LEU* 3.9 23.5 - - + +
337A LEU* 3.6 17.5 - - + +
338A GLY* 3.6 29.2 - - - +
341A GLU* 4.2 7.6 - - + -
447A HIS* 5.8 1.6 - - + -
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL 2.9 17.3 + - - +
273A ALA* 3.7 7.9 - - - +
275A ILE* 1.3 77.2 - - - +
277A ALA* 1.3 62.7 + - - +
279A TYR* 3.2 13.0 + - - +
280A GLN* 3.0 47.8 + - - +
447A HIS* 4.2 24.3 + - + +
449A GLU* 4.4 15.0 + - + +
440B SER 4.9 5.5 + - - -
441B HIS* 3.5 40.4 + - - +
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Residues in contact with ALA 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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273A ALA 2.9 13.6 + - - +
274A GLN* 3.5 12.1 - - - +
276A LYS* 1.3 76.6 - - - +
278A GLY* 1.3 63.0 + - - +
280A GLN* 3.2 14.9 + - - +
281A SER* 3.0 19.8 + - - -
308A ARG* 3.1 39.2 + - + +
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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
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274A GLN 3.0 10.5 + - - -
275A ILE 3.1 5.3 + - - -
277A ALA* 1.3 77.4 - - - +
279A TYR* 1.3 62.3 + - - +
281A SER* 3.1 2.5 + - - -
282A LEU* 3.0 24.1 + - - +
305A PHE* 3.6 8.1 - - - -
308A ARG* 4.6 4.5 - - - +
309A ILE* 3.9 26.7 - - - -
334A LEU* 3.5 7.9 - - - -
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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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275A ILE* 3.1 41.5 + - + -
276A LYS* 3.2 6.3 + - - +
278A GLY* 1.3 75.5 - - - +
280A GLN* 1.3 63.9 + - - +
282A LEU* 3.2 7.8 + - + +
283A LYS 2.9 19.4 + - - -
331A ILE* 4.5 13.5 - - + -
334A LEU* 3.3 24.5 + - + +
335A GLU* 3.3 34.5 + - - +
447A HIS* 3.5 40.9 + + + +
449A GLU* 3.6 24.6 - - + +
450A ALA* 3.6 31.2 - - + -
451A PRO* 4.4 5.5 - - + +
455A TYR* 4.8 0.9 - - - -
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Residues in contact with GLN 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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276A LYS* 3.0 40.7 + - - +
277A ALA* 3.4 24.0 + - - +
278A GLY 3.2 0.2 - - - -
279A TYR* 1.3 75.9 - - - +
281A SER* 1.3 61.3 + - - +
283A LYS* 3.2 10.3 + - - +
284A LYS* 3.1 29.1 + - - +
308A ARG* 4.2 10.0 + - - +
449A GLU* 3.6 27.5 + - + +
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA 3.0 4.4 + - - -
278A GLY 3.1 6.7 + - - -
280A GLN* 1.3 73.0 - - - +
282A LEU* 1.3 61.4 + - - +
284A LYS* 3.2 7.9 + - - +
285A ILE* 3.0 31.9 + - - +
301A ALA 4.7 2.6 - - - +
304A GLU* 2.6 29.5 + - - -
305A PHE* 3.7 26.5 - - - -
308A ARG* 3.1 25.1 + - - -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLY 3.0 8.1 + - - +
279A TYR* 3.2 8.3 + - + +
281A SER* 1.3 75.6 - - - +
283A LYS* 1.3 56.8 + - - +
285A ILE* 3.2 20.5 + - + +
286A GLU* 2.9 27.0 + - - +
305A PHE* 3.6 25.6 - - + -
321A ILE* 4.7 0.4 - - + -
327A LEU* 3.8 17.3 - - + +
330A LYS* 3.7 36.3 - - + -
331A ILE* 4.0 24.0 - - + +
334A LEU* 3.8 24.7 - - + -
451A PRO* 3.7 14.8 - - + +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR 2.9 13.3 + - - +
280A GLN* 3.4 12.1 - - - +
281A SER 3.2 0.2 - - - -
282A LEU* 1.3 73.9 - - - +
284A LYS* 1.3 60.3 + - + +
286A GLU* 3.2 26.5 + - - +
287A ASP* 2.9 59.2 + - - +
449A GLU* 3.9 20.0 - - - +
450A ALA 5.6 0.7 - - - +
451A PRO* 4.0 8.9 - - + +
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLN* 3.1 21.8 + - - +
281A SER 3.2 7.8 + - - +
283A LYS* 1.3 74.6 - - + +
285A ILE* 1.3 65.1 + - - +
287A ASP* 3.2 14.0 + - - +
288A CYS* 3.0 28.1 + - - -
301A ALA* 4.7 9.9 - - + -
304A GLU* 3.3 37.0 + - - +
308A ARG* 4.7 9.5 - - - +
411B GLY* 5.9 5.7 + - - -
414B GLU* 5.7 8.1 - - - +
415B ALA* 5.9 6.7 - - - -
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Residues in contact with ILE 285 (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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281A SER 3.0 19.0 + - - +
282A LEU* 3.2 28.9 + - + +
284A LYS* 1.3 75.2 - - - +
286A GLU* 1.3 63.2 + - - +
288A CYS* 3.1 6.3 + - - +
289A ILE* 3.0 31.4 + - + +
298A LEU* 3.9 6.1 - - + -
301A ALA* 3.8 35.9 - - + +
302A CYS* 4.0 11.4 - - - +
305A PHE* 3.9 12.3 - - + -
321A ILE* 3.8 34.1 - - + +
327A LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 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 LEU 2.9 13.3 + - - +
283A LYS* 3.2 30.6 + - - +
285A ILE* 1.3 76.3 - - - +
287A ASP* 1.3 62.7 + - - +
289A ILE* 3.3 12.6 + - + +
290A ARG* 2.9 50.6 + - + +
327A LEU* 4.1 9.2 - - + +
451A PRO* 3.3 10.2 - - + +
452A ILE* 3.2 11.8 + - - +
453A THR* 2.7 46.6 + - + +
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Residues in contact with ASP 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 LYS* 2.9 52.3 + - - +
284A LYS* 3.4 17.5 - - - +
285A ILE 3.2 0.2 - - - -
286A GLU* 1.3 77.9 - - - +
288A CYS* 1.3 57.1 + - - +
290A ARG* 3.3 14.0 + - - +
291A ALA* 3.0 30.0 + - - +
293A GLN* 5.0 0.2 - - - -
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Residues in contact with CYS 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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284A LYS 3.0 17.8 + - - -
285A ILE 3.1 7.6 + - - +
287A ASP* 1.3 72.3 - - - +
289A ILE* 1.3 65.7 + - - +
291A ALA 3.4 1.4 + - - -
292A GLY 3.0 5.0 + - - -
293A GLN* 2.8 63.6 + - - +
297A ALA* 4.1 27.1 - - - -
298A LEU* 4.2 8.5 - - + -
301A ALA* 4.2 11.7 - - - -
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Residues in contact with ILE 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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285A ILE* 3.0 31.4 + - + +
286A GLU* 3.7 9.4 - - + +
288A CYS* 1.3 74.7 - - - +
290A ARG* 1.3 64.1 + - - +
292A GLY* 3.1 14.9 + - - -
294A HIS* 3.7 20.5 - - + -
298A LEU* 4.2 16.4 - - + -
321A ILE 3.9 3.4 - - - +
322A ARG* 3.6 34.5 - - - +
323A THR 5.1 2.7 - - - +
327A LEU* 4.6 14.4 - - + -
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Residues in contact with ARG 290 (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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286A GLU* 2.9 48.7 + - + +
287A ASP* 3.5 13.1 + - - +
289A ILE* 1.3 78.1 - - - +
291A ALA* 1.3 57.1 + - - +
292A GLY 3.6 0.5 + - - -
452A ILE* 4.1 10.9 - - - +
453A THR* 3.6 17.4 - - - +
504A LYS* 5.5 9.2 - - - +
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Residues in contact with ALA 291 (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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287A ASP 3.0 16.6 + - - +
288A CYS 4.1 0.2 - - - +
289A ILE 3.3 0.2 - - - -
290A ARG* 1.3 75.5 - - - +
292A GLY* 1.3 62.7 + - - +
293A GLN* 3.5 28.0 + - - +
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Residues in contact with GLY 292 (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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288A CYS 3.0 2.8 + - - -
289A ILE 3.1 5.9 + - - -
290A ARG 3.3 1.4 + - - -
291A ALA* 1.3 79.6 - - - +
293A GLN* 1.3 61.4 + - - +
294A HIS* 3.7 27.1 + - - -
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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