Contacts of the helix formed by residues 268 - 285 (chain A) in PDB entry 1CJY
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 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU 4.8 5.1 + - - -
266A LEU 2.7 11.1 + - - -
267A LEU* 1.3 74.9 + - - +
269A PRO* 1.3 66.8 - - + +
270A GLN* 3.2 15.9 - - + +
271A LYS* 2.9 35.2 + - + +
272A VAL* 2.7 37.6 + - - +
468A MET* 4.1 0.7 - - - -
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Residues in contact with PRO 269 (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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267A LEU 4.7 0.4 - - - +
268A THR* 1.3 90.3 - - + +
270A GLN* 1.3 57.4 + - - +
272A VAL 3.5 0.2 + - - -
273A LYS* 2.8 47.7 + - - +
468A MET* 3.9 34.9 - - + -
472A LEU* 3.7 5.1 - - + +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.1 11.3 - - + +
269A PRO* 1.3 80.2 - - - +
271A LYS* 1.3 62.6 + - - +
273A LYS* 3.2 14.0 + - - +
274A ARG* 3.2 25.6 + - - +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU 4.5 1.8 + - - -
266A LEU* 2.8 52.9 + - + +
267A LEU* 5.3 1.1 - - + -
268A THR* 2.9 25.1 + - + +
270A GLN* 1.3 73.1 - - - +
272A VAL* 1.3 67.4 + - + +
274A ARG* 2.9 25.0 + - - +
275A TYR* 3.0 27.1 + - + +
301A GLU* 3.3 33.0 - - - +
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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
----------------------------------------------------------
267A LEU* 4.1 16.6 - - + -
268A THR 2.7 30.6 + - - +
271A LYS* 1.3 72.0 - - - +
273A LYS* 1.3 62.9 + - - +
275A TYR* 3.1 13.7 + - + +
276A VAL* 3.0 28.2 + - + +
294A ILE* 5.7 4.5 - - + -
468A MET* 3.9 20.2 - - + -
469A ILE* 4.0 26.7 - - + +
472A LEU* 3.5 33.4 - - + -
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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
----------------------------------------------------------
269A PRO* 2.8 43.4 + - - +
270A GLN* 3.3 12.3 - - - +
271A LYS 3.1 0.2 - - - -
272A VAL* 1.3 77.7 - - - +
274A ARG* 1.3 56.6 + - + +
276A VAL* 3.6 7.0 + - - +
277A GLU* 3.1 27.4 + - - +
472A LEU* 3.9 28.7 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLN* 3.2 16.6 + - - +
271A LYS* 2.9 20.7 + - + +
273A LYS* 1.3 73.0 - - + +
275A TYR* 1.3 65.6 + - + +
277A GLU* 3.2 6.8 + - - +
278A SER* 2.8 32.3 + - - -
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Residues in contact with TYR 275 (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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266A LEU* 5.2 0.9 - - - +
267A LEU* 4.2 18.2 - - + +
271A LYS* 3.0 29.2 + - + +
272A VAL* 3.3 15.7 - - + +
274A ARG* 1.3 79.8 - - + +
276A VAL* 1.3 59.2 + - + +
278A SER 3.2 1.0 + - - -
279A LEU* 2.8 33.4 + - + +
294A ILE* 4.1 21.5 - - + -
297A MET* 3.0 53.7 - - + +
298A LEU* 3.8 22.5 - - - +
301A GLU* 2.5 42.8 + - + +
308A MET* 5.9 2.5 - - + -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.0 30.8 + - + +
273A LYS* 3.9 7.2 - - - +
275A TYR* 1.3 73.9 - - + +
277A GLU* 1.3 57.8 + - - +
279A LEU* 3.4 1.8 + - - +
280A TRP* 3.0 38.5 + - + -
294A ILE* 5.0 5.2 - - + -
472A LEU* 4.7 9.4 - - + +
473A VAL* 4.7 13.2 - - + -
476A SER* 3.2 35.2 - - - +
478A LEU* 3.9 22.4 - - + -
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Residues in contact with GLU 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 LYS 3.1 19.0 + - - +
274A ARG* 3.4 7.9 - - - +
276A VAL* 1.3 75.6 - - - +
278A SER* 1.3 67.6 + - - +
280A TRP* 3.3 17.8 + - - +
281A LYS* 3.9 3.3 + - - +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG 2.8 20.2 + - - -
275A TYR 3.6 3.1 - - - -
277A GLU* 1.3 72.9 - - - +
279A LEU* 1.3 63.7 + - - +
281A LYS* 3.1 25.3 + - - +
282A LYS* 4.1 0.9 + - - +
297A MET* 3.9 17.1 - - - +
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Residues in contact with LEU 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 TYR 2.8 21.5 + - - +
276A VAL 3.9 3.4 - - - +
278A SER* 1.3 73.3 - - - +
280A TRP* 1.3 65.5 + - - +
281A LYS 3.0 0.2 - - - -
282A LYS* 3.0 18.0 + - + +
283A LYS* 3.0 20.4 + - - +
289A VAL* 4.0 7.4 - - + +
293A ASP* 3.7 39.9 - - + +
294A ILE* 3.8 26.2 - - + +
297A MET* 3.3 25.1 - - + -
387A HIS* 5.7 2.9 - - - +
478A LEU* 4.0 21.1 - - + -
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Residues in contact with TRP 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 VAL* 3.0 31.6 + - + +
277A GLU* 3.5 15.0 - - - +
278A SER 3.2 0.8 - - - -
279A LEU* 1.3 76.6 - - - +
281A LYS* 1.3 53.3 + - - +
283A LYS* 3.5 40.6 - - + -
284A SER* 2.7 49.9 + - - -
476A SER* 3.3 33.9 + - - -
477A ALA* 3.7 9.4 - - + -
478A LEU* 3.7 16.3 - - + +
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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
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277A GLU 3.9 3.1 + - - +
278A SER* 3.1 15.3 + - - +
279A LEU 3.0 0.8 - - - -
280A TRP* 1.3 78.3 - - - +
282A LYS* 1.3 64.0 + - + +
284A SER* 3.3 6.9 + - - -
285A SER* 3.1 23.1 + - - -
382A GLU* 3.5 34.2 + - - -
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Residues in contact with LYS 282 (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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278A SER 4.1 0.6 + - - +
279A LEU* 3.0 18.0 + - + +
281A LYS* 1.3 83.5 - - + +
283A LYS* 1.3 62.0 + - - +
285A SER* 2.6 26.2 + - - -
287A GLN* 3.3 37.7 + - + +
288A PRO 3.6 18.6 + - - -
289A VAL* 4.2 7.4 - - + -
293A ASP* 2.6 31.5 + - - +
384A ASN* 3.5 24.4 - - - +
385A PRO* 6.2 0.9 - - + -
388A PHE* 3.4 27.1 - - - -
488A LYS 5.5 0.4 + - - -
489A VAL* 6.1 0.6 - - - +
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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
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279A LEU 3.0 12.0 + - - +
280A TRP* 3.5 46.7 - - + +
282A LYS* 1.3 77.0 - - - +
284A SER* 1.3 56.0 + - - +
286A GLY* 2.8 27.0 + - - -
287A GLN 3.5 15.6 + - - +
288A PRO* 6.1 1.2 - - - +
289A VAL* 3.9 14.1 - - + +
477A ALA 3.5 13.8 + - - -
478A LEU* 3.0 32.0 + - + +
479A PHE* 5.0 1.6 - - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TRP* 2.7 38.2 + - - -
281A LYS* 3.4 9.0 - - - -
283A LYS* 1.3 74.0 - - - +
285A SER* 1.3 59.4 + - - +
286A GLY* 3.1 1.1 + - - -
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Residues in contact with SER 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 LYS* 3.1 11.4 + - - -
282A LYS* 2.6 21.5 + - - -
283A LYS 3.1 1.0 - - - -
284A SER* 1.3 76.2 - - - +
286A GLY* 1.3 56.4 + - - +
287A GLN* 3.4 9.9 + - - -
381A TYR* 2.9 43.3 + - - +
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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
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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