Contacts of the helix formed by residues 252 - 278 (chain N) in PDB entry 5KHU
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 LEU 252 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251N SER* 3.8 28.7 - - - +
253N LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 253 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252N LEU* 3.8 29.2 - - - +
254N GLU* 3.8 23.6 - - - +
256N VAL* 4.7 18.8 - - - +
257N SER* 4.7 10.8 - - - +
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Residues in contact with GLU 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N LEU* 3.8 25.1 - - - +
255N ARG* 3.8 29.6 - - - +
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Residues in contact with ARG 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N GLU* 3.8 29.8 - - - +
256N VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N LEU* 4.7 10.3 - - - +
255N ARG* 3.8 27.6 - - - +
257N SER* 3.8 28.9 - - - +
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Residues in contact with SER 257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N LEU* 4.7 14.4 - - - +
256N VAL* 3.8 28.9 - - - +
258N ALA* 3.8 27.4 - - - +
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Residues in contact with ALA 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N SER* 3.8 25.8 - - - +
259N GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 259 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N ALA* 3.8 29.4 - - - +
260N ALA* 3.8 28.0 - - - +
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Residues in contact with ALA 260 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259N GLU* 3.8 27.1 - - - +
261N VAL* 3.8 28.0 - - - +
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Residues in contact with VAL 261 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260N ALA* 3.8 27.6 - - - +
262N THR* 3.8 28.9 - - - +
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Residues in contact with THR 262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N VAL* 3.8 28.9 - - - +
263N THR* 3.8 25.4 - - - +
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Residues in contact with THR 263 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262N THR* 3.8 28.7 - - - +
264N THR* 3.8 27.8 - - - +
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Residues in contact with THR 264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263N THR* 3.8 25.8 - - - +
265N LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 265 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N THR* 3.8 26.7 - - - +
266N HIS* 3.8 30.3 - - - +
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Residues in contact with HIS 266 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265N LEU* 3.8 29.8 - - - +
267N GLN* 3.8 28.0 - - - +
269N THR* 4.5 16.2 - - - +
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Residues in contact with GLN 267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266N HIS* 3.8 25.6 - - - +
268N VAL* 3.8 28.9 - - - +
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Residues in contact with VAL 268 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267N GLN* 3.8 29.2 - - - +
269N THR* 3.8 26.5 - - - +
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Residues in contact with THR 269 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266N HIS* 4.5 17.9 - - - +
268N VAL* 3.8 26.2 - - - +
270N ARG* 3.8 28.9 - - - +
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Residues in contact with ARG 270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N THR* 3.8 28.5 - - - +
271N GLU* 3.8 27.4 - - - +
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Residues in contact with GLU 271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270N ARG* 3.8 24.5 - - - +
272N ARG* 3.8 29.6 - - - +
274N GLU* 4.6 15.9 - - - +
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Residues in contact with ARG 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N GLU* 3.8 24.7 - - - +
273N MET* 3.8 29.2 - - - +
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Residues in contact with MET 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272N ARG* 3.8 29.2 - - - +
274N GLU* 3.8 27.1 - - - +
277N CYS* 4.4 20.6 - - - +
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Residues in contact with GLU 274 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N GLU* 4.6 16.2 - - - +
273N MET* 3.8 27.4 - - - +
275N ASP* 3.8 29.2 - - - +
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Residues in contact with ASP 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274N GLU* 3.8 28.5 - - - +
276N ARG* 3.8 26.2 - - - +
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Residues in contact with ARG 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275N ASP* 3.8 29.4 - - - +
277N CYS* 3.8 29.2 - - - +
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Residues in contact with CYS 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273N MET* 4.4 17.5 - - - +
276N ARG* 3.8 25.4 - - - +
278N ARG* 3.8 28.7 - - - +
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Residues in contact with ARG 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N CYS* 3.8 28.5 - - - +
279N GLY* 3.8 23.8 - - - +
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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
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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