Contacts of the helix formed by residues 338 - 369 (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 HIS 338 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337Y GLN* 3.8 28.7 - - - +
339Y ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 339 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338Y HIS* 3.8 29.4 - - - +
340Y GLU* 3.8 28.3 - - - +
365Y ALA* 4.5 22.0 - - - +
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Residues in contact with GLU 340 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339Y ALA* 3.8 29.2 - - - +
341Y PRO* 3.8 25.6 - - - -
343Y VAL* 4.3 18.4 - - - +
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Residues in contact with PRO 341 (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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340Y GLU* 3.8 25.4 - - - -
342Y TRP* 3.8 29.4 - - - -
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Residues in contact with TRP 342 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341Y PRO* 3.8 28.9 - - - -
343Y VAL* 3.8 25.6 - - - +
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Residues in contact with VAL 343 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340Y GLU* 4.3 17.9 - - - +
342Y TRP* 3.8 27.4 - - - +
344Y VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 344 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343Y VAL* 3.8 25.1 - - - +
345Y SER* 3.8 28.9 - - - +
347Y CYS* 4.5 16.2 - - - +
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Residues in contact with SER 345 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344Y VAL* 3.8 26.2 - - - +
346Y GLY* 3.8 29.8 - - - +
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Residues in contact with GLY 346 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345Y SER* 3.8 29.2 - - - +
347Y CYS* 3.8 26.0 - - - +
349Y SER* 4.4 18.2 - - - +
358Y ALA* 4.5 20.2 - - - +
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Residues in contact with CYS 347 (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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344Y VAL* 4.5 17.5 - - - +
346Y GLY* 3.8 29.4 - - - +
348Y HIS* 3.8 24.7 - - - +
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Residues in contact with HIS 348 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347Y CYS* 3.8 29.8 - - - +
349Y SER* 3.8 25.8 - - - +
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Residues in contact with SER 349 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346Y GLY* 4.4 18.4 - - - +
348Y HIS* 3.8 29.4 - - - +
350Y PHE* 3.8 26.5 - - - +
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Residues in contact with PHE 350 (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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349Y SER* 3.8 27.8 - - - +
351Y TYR* 3.8 29.6 - - - +
353Y LYS* 4.7 9.9 - - - +
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Residues in contact with TYR 351 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350Y PHE* 3.8 30.1 - - - +
352Y SER* 3.8 26.9 - - - +
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Residues in contact with SER 352 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351Y TYR* 3.8 28.9 - - - +
353Y LYS* 3.8 24.0 - - - +
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Residues in contact with LYS 353 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350Y PHE* 4.7 17.5 - - - +
352Y SER* 3.8 28.3 - - - +
354Y ARG* 3.8 29.6 - - - +
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Residues in contact with ARG 354 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353Y LYS* 3.8 28.3 - - - +
355Y TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 355 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354Y ARG* 3.8 29.2 - - - +
356Y SER* 3.8 27.4 - - - +
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Residues in contact with SER 356 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355Y TYR* 3.8 26.9 - - - +
357Y ARG* 3.8 29.2 - - - +
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Residues in contact with ARG 357 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356Y SER* 3.8 29.4 - - - +
358Y ALA* 3.8 25.8 - - - +
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Residues in contact with ALA 358 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346Y GLY* 4.5 20.2 - - - +
357Y ARG* 3.8 25.4 - - - +
359Y LEU* 3.8 29.4 - - - +
361Y LEU* 4.3 17.3 - - - +
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Residues in contact with LEU 359 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358Y ALA* 3.8 29.2 - - - +
360Y TYR* 3.8 26.7 - - - +
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Residues in contact with TYR 360 (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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359Y LEU* 3.8 24.9 - - - +
361Y LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 361 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358Y ALA* 4.3 17.9 - - - +
360Y TYR* 3.8 29.4 - - - +
362Y GLY* 3.8 27.4 - - - +
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Residues in contact with GLY 362 (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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361Y LEU* 3.8 28.9 - - - +
363Y ALA* 3.8 28.3 - - - +
379Y LYS* 4.3 22.9 - - - +
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Residues in contact with ALA 363 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362Y GLY* 3.8 29.2 - - - +
364Y LYS* 3.8 27.4 - - - +
366Y ILE* 4.7 15.3 - - - +
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Residues in contact with LYS 364 (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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363Y ALA* 3.8 26.9 - - - +
365Y ALA* 3.8 28.9 - - - +
367Y GLN* 4.5 15.7 - - - +
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Residues in contact with ALA 365 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339Y ALA* 4.5 21.8 - - - +
364Y LYS* 3.8 24.0 - - - +
366Y ILE* 3.8 29.6 - - - +
368Y LEU* 4.3 17.0 - - - +
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Residues in contact with ILE 366 (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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363Y ALA* 4.7 15.7 - - - +
365Y ALA* 3.8 29.2 - - - +
367Y GLN* 3.8 25.6 - - - +
369Y ASN* 4.5 6.5 - - - +
370Y SER* 3.9 26.0 - - - +
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Residues in contact with GLN 367 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364Y LYS* 4.5 16.2 - - - +
366Y ILE* 3.8 28.5 - - - +
368Y LEU* 3.8 24.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 368 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365Y ALA* 4.3 16.8 - - - +
367Y GLN* 3.8 29.2 - - - +
369Y ASN* 3.8 26.2 - - - +
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Residues in contact with ASN 369 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Y ILE* 4.5 8.1 - - - +
368Y LEU* 3.8 28.3 - - - +
370Y SER* 3.8 28.7 - - - +
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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