Contacts of the helix formed by residues 304 - 335 (chain Y) 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 304 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303Y TYR* 3.8 28.9 - - - +
305Y ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304Y LEU* 3.8 27.6 - - - +
306Y LYS* 3.8 29.6 - - - +
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Residues in contact with LYS 306 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Y ILE* 3.8 28.5 - - - +
307Y GLY* 3.8 28.9 - - - +
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Residues in contact with GLY 307 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306Y LYS* 3.8 29.4 - - - +
308Y MET* 3.8 25.8 - - - +
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Residues in contact with MET 308 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Y GLY* 3.8 26.9 - - - +
309Y ASP* 3.8 29.4 - - - +
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Residues in contact with ASP 309 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Y MET* 3.8 28.9 - - - +
310Y VAL* 3.8 28.3 - - - +
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Residues in contact with VAL 310 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Y ASP* 3.8 25.6 - - - +
311Y TYR* 3.8 29.6 - - - +
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Residues in contact with TYR 311 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310Y VAL* 3.8 29.4 - - - +
312Y GLY* 3.8 25.4 - - - +
314Y LEU* 4.5 17.0 - - - +
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Residues in contact with GLY 312 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311Y TYR* 3.8 29.8 - - - +
313Y TYR* 3.8 26.2 - - - +
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Residues in contact with TYR 313 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Y GLY* 3.8 29.4 - - - +
314Y LEU* 3.8 24.9 - - - +
316Y ALA* 4.4 17.3 - - - +
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Residues in contact with LEU 314 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311Y TYR* 4.5 18.2 - - - +
313Y TYR* 3.8 26.2 - - - +
315Y LEU* 3.8 29.6 - - - +
317Y ARG* 4.7 12.8 - - - +
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Residues in contact with LEU 315 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314Y LEU* 3.8 29.2 - - - +
316Y ALA* 3.8 25.1 - - - +
318Y GLU* 4.1 20.2 - - - +
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Residues in contact with ALA 316 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Y TYR* 4.4 17.3 - - - +
315Y LEU* 3.8 28.9 - - - +
317Y ARG* 3.8 24.7 - - - +
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Residues in contact with ARG 317 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314Y LEU* 4.7 13.5 - - - +
316Y ALA* 3.8 29.8 - - - +
318Y GLU* 3.8 25.1 - - - +
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Residues in contact with GLU 318 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315Y LEU* 4.1 18.2 - - - +
317Y ARG* 3.8 26.7 - - - +
319Y GLY* 3.8 28.7 - - - +
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Residues in contact with GLY 319 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Y GLU* 3.8 29.4 - - - +
320Y ARG* 3.8 28.7 - - - +
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Residues in contact with ARG 320 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Y GLY* 3.8 27.8 - - - +
321Y LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 321 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320Y ARG* 3.8 28.7 - - - +
322Y GLU* 3.8 29.6 - - - +
324Y VAL* 4.6 16.8 - - - +
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Residues in contact with GLU 322 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Y LEU* 3.8 29.4 - - - +
323Y ASP* 3.8 24.7 - - - +
325Y GLU* 4.5 15.7 - - - +
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Residues in contact with ASP 323 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Y GLU* 3.8 28.9 - - - +
324Y VAL* 3.8 25.4 - - - +
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Residues in contact with VAL 324 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Y LEU* 4.6 15.0 - - - +
323Y ASP* 3.8 24.9 - - - +
325Y GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 325 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Y GLU* 4.5 15.9 - - - +
324Y VAL* 3.8 28.9 - - - +
326Y ASN* 3.8 26.7 - - - +
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Residues in contact with ASN 326 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325Y GLU* 3.8 26.9 - - - +
327Y LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 327 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326Y ASN* 3.8 29.6 - - - +
328Y GLY* 3.8 25.6 - - - +
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Residues in contact with GLY 328 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327Y LEU* 3.8 28.9 - - - +
329Y CYS* 3.8 25.4 - - - +
331Y LEU* 4.6 16.4 - - - +
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Residues in contact with CYS 329 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328Y GLY* 3.8 29.4 - - - +
330Y ARG* 3.8 24.7 - - - +
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Residues in contact with ARG 330 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329Y CYS* 3.8 25.8 - - - +
331Y LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 331 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328Y GLY* 4.6 15.9 - - - +
330Y ARG* 3.8 29.4 - - - +
332Y PHE* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 332 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331Y LEU* 3.8 26.5 - - - +
333Y ASN* 3.8 29.4 - - - +
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Residues in contact with ASN 333 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332Y PHE* 3.8 29.8 - - - +
334Y ILE* 3.8 26.9 - - - +
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Residues in contact with ILE 334 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333Y ASN* 3.8 29.2 - - - +
335Y SER* 3.8 25.6 - - - +
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Residues in contact with SER 335 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334Y ILE* 3.8 28.5 - - - +
336Y ASP* 3.8 29.2 - - - +
----------------------------------------------------------
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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