Contacts of the helix formed by residues 337 - 357 (chain A) in PDB entry 5HJP
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A VAL* 1.3 85.4 - - - +
338A ASN* 1.4 58.6 + - - +
339A ILE 3.3 0.7 - - - -
340A CYS* 3.3 12.2 + - + +
341A GLN* 3.0 39.0 + - + +
516A THR* 3.6 45.0 + - + +
517A PRO 5.0 5.6 - - - +
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Residues in contact with ASN 338 (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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336A VAL* 3.3 6.0 - - + +
337A THR* 1.4 76.0 - - - +
339A ILE* 1.4 59.1 + - - +
341A GLN* 3.6 22.9 + - - +
342A ALA* 2.9 31.9 + - - +
397A LEU* 4.0 10.4 - - + +
399A THR* 4.0 17.6 + - - +
401A LEU* 3.5 36.3 - - + +
403A VAL* 5.4 2.0 - - + -
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Residues in contact with ILE 339 (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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336A VAL* 3.5 29.9 + - - +
337A THR 3.3 0.8 - - - -
338A ASN* 1.4 75.3 - - - +
340A CYS* 1.4 58.6 + - - +
342A ALA* 3.8 1.2 - - - +
343A ALA* 2.9 35.6 + - + +
384A PHE* 5.4 6.4 - - + -
397A LEU* 4.4 18.7 - - + +
403A VAL* 4.2 28.3 - - + -
413A VAL* 5.5 11.7 - - + -
417A PHE* 5.5 8.3 - - + -
507A LEU* 5.4 11.4 - - + -
510A PHE* 6.4 3.4 - - + -
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Residues in contact with CYS 340 (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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336A VAL 4.3 9.4 + - - -
337A THR* 3.3 15.9 + - + +
339A ILE* 1.4 77.7 - - - +
341A GLN* 1.4 60.4 + - - +
343A ALA* 4.5 0.2 - - - -
344A ASP* 3.4 10.4 + - - +
507A LEU* 4.3 14.1 - - - -
510A PHE* 4.0 28.3 - - - -
516A THR 6.1 0.4 - - - -
518A ILE* 4.1 32.2 - - + +
519A ASP* 5.4 2.4 + - - +
522A LEU* 3.2 28.5 - - + +
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Residues in contact with GLN 341 (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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337A THR* 3.0 25.0 + - + +
338A ASN* 3.6 33.4 + - - +
339A ILE 3.3 0.2 - - - -
340A CYS* 1.4 74.9 - - - +
342A ALA* 1.4 57.9 + - - +
344A ASP* 3.2 9.1 + - - +
345A LYS* 3.1 27.8 + - - +
399A THR* 4.8 5.4 - - + -
519A ASP* 4.6 15.9 + - - +
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Residues in contact with ALA 342 (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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338A ASN 2.9 20.5 + - - +
339A ILE 4.0 0.4 - - - +
341A GLN* 1.4 71.7 - - - +
343A ALA* 1.4 59.7 + - - +
345A LYS* 3.7 3.2 - - - +
346A GLN* 3.2 30.8 + - - +
384A PHE* 4.2 5.2 - - + -
397A LEU* 3.8 37.5 - - + -
398A ALA* 4.6 3.6 - - - +
399A THR* 3.8 22.6 - - + +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 2.9 21.5 + - + +
340A CYS* 4.5 0.2 - - - -
341A GLN 3.2 0.2 - - - -
342A ALA* 1.4 73.5 - - - +
344A ASP* 1.3 65.3 + - - +
346A GLN* 3.3 4.2 + - - +
347A LEU* 3.1 28.3 + - - +
376A TRP* 5.5 2.5 - - + -
380A LEU* 3.8 12.8 - - + +
384A PHE* 4.4 14.1 - - + -
507A LEU* 5.7 4.7 - - + -
522A LEU* 3.7 24.2 - - + -
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Residues in contact with ASP 344 (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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340A CYS 3.4 11.7 + - - +
341A GLN* 3.2 10.3 + - - +
343A ALA* 1.3 76.7 - - - +
345A LYS* 1.4 62.4 + - - +
347A LEU* 3.4 19.0 + - - +
348A PHE* 3.2 29.1 - - - -
519A ASP* 3.3 31.1 - - + +
520A THR* 6.0 0.2 - - - +
521A PHE* 3.2 19.3 + - - +
522A LEU* 2.9 33.5 + - + +
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Residues in contact with LYS 345 (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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341A GLN 3.1 17.1 + - - +
342A ALA* 3.7 6.3 - - - +
343A ALA 3.3 0.2 - - - -
344A ASP* 1.4 76.7 + - - +
346A GLN* 1.3 76.1 + - - +
347A LEU 3.3 1.2 + - - -
348A PHE* 3.4 23.9 + - + +
349A THR* 3.4 11.8 + - - -
398A ALA* 4.7 11.9 + - + +
399A THR* 3.9 28.3 - - + +
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Residues in contact with GLN 346 (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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311A VAL* 4.5 8.0 - - - +
342A ALA 3.2 17.8 + - - +
343A ALA* 3.3 3.8 + - - +
345A LYS* 1.3 88.5 + - + +
347A LEU* 1.3 59.3 + - - +
348A PHE 3.3 0.4 - - - -
349A THR* 3.2 33.9 + - - +
350A LEU* 2.8 29.5 + - - +
380A LEU* 3.6 24.8 - - + +
383A SER* 5.5 2.0 + - - -
384A PHE* 4.2 5.6 - - + -
387A ARG* 3.2 32.4 - - - +
398A ALA* 3.3 29.0 - - + +
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Residues in contact with LEU 347 (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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343A ALA 3.1 14.3 + - - +
344A ASP* 3.5 15.7 - - - +
345A LYS 3.2 0.8 - - - -
346A GLN* 1.3 76.6 - - - +
348A PHE* 1.4 60.2 + - - +
350A LEU* 3.4 15.7 - - + +
351A VAL* 3.4 21.0 - - - +
376A TRP* 3.8 42.0 - - + -
380A LEU* 3.9 7.0 - - + -
521A PHE* 3.5 18.8 - - + -
522A LEU* 3.6 45.1 - - + +
525A MET* 3.7 19.3 - - + -
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Residues in contact with PHE 348 (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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344A ASP* 3.2 42.0 - - - -
345A LYS* 3.4 13.6 + - + +
346A GLN 3.3 0.2 - - - -
347A LEU* 1.4 71.9 - - - +
349A THR* 1.4 66.4 + - - +
351A VAL* 3.3 15.2 + - - +
352A GLU* 3.6 13.6 + - - +
520A THR* 5.8 4.7 - - + -
521A PHE* 3.6 34.1 - + + -
542A ILE* 3.8 19.3 - - + -
545A ARG* 5.4 4.3 - - - -
546A LEU* 4.1 24.8 - - + +
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Residues in contact with THR 349 (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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311A VAL* 3.8 41.0 - - + +
345A LYS* 3.4 13.5 + - - -
346A GLN* 3.2 31.6 + - - +
348A PHE* 1.4 76.5 - - - +
350A LEU* 1.4 56.8 + - - +
352A GLU* 2.9 32.9 + - + +
353A TRP* 3.1 11.5 + - - +
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Residues in contact with LEU 350 (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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346A GLN 2.8 17.2 + - - +
347A LEU* 3.4 13.0 - - + +
348A PHE 3.3 0.2 - - - -
349A THR* 1.4 75.1 - - - +
351A VAL* 1.3 56.3 + - + +
353A TRP* 3.3 18.5 + - + +
354A ALA* 3.0 27.2 + - - +
372A LEU* 3.9 15.7 - - + -
376A TRP* 3.7 40.2 - - + +
379A LEU* 3.8 22.7 - - + -
380A LEU* 4.5 10.1 - - + -
442A ARG* 3.5 27.6 - - - +
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Residues in contact with VAL 351 (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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347A LEU 3.4 17.0 - - - +
348A PHE 3.3 7.1 + - - +
349A THR 3.2 1.0 - - - -
350A LEU* 1.3 74.9 - - + +
352A GLU* 1.4 61.1 + - - +
354A ALA* 3.5 6.2 + - - +
355A LYS* 3.2 29.2 + - - +
360A PHE* 6.3 0.2 - - + -
372A LEU* 4.3 10.5 - - + -
521A PHE* 4.3 6.5 - - + -
543A LEU* 3.9 25.4 - - + +
546A LEU* 3.9 31.6 - - + +
547A LEU* 3.8 28.7 - - + -
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Residues in contact with GLU 352 (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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348A PHE* 3.6 12.6 + - - +
349A THR* 2.9 19.0 + - + +
351A VAL* 1.4 75.8 - - - +
353A TRP* 1.4 60.4 + - - +
355A LYS* 3.9 10.4 + - + +
356A ARG* 3.3 47.4 + - - +
546A LEU* 5.5 7.9 - - + -
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Residues in contact with TRP 353 (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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304A ILE 4.7 0.8 + - - -
307A ALA* 3.4 36.6 - - + +
308A GLU* 2.9 25.6 + - - +
311A VAL* 5.0 11.2 - - + -
349A THR 3.1 10.9 + - - +
350A LEU* 3.3 26.4 + - + +
352A GLU* 1.4 75.5 - - - +
354A ALA* 1.3 78.7 + - + +
356A ARG* 3.3 9.3 + - - +
357A ILE* 3.2 42.4 + - + +
379A LEU* 3.8 15.0 - - + -
439A GLY 4.0 4.4 + - - -
442A ARG* 3.2 61.5 - - + +
443A ALA* 3.8 5.2 - - - -
446A LEU* 3.6 27.4 - - + -
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Residues in contact with ALA 354 (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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350A LEU 3.0 16.2 + - - +
351A VAL* 3.7 5.8 - - - +
352A GLU 3.5 0.2 - - - -
353A TRP* 1.3 89.0 - - + +
355A LYS* 1.4 58.3 + - - +
357A ILE* 3.0 23.3 - - - +
360A PHE* 3.1 41.8 - - + +
372A LEU* 4.0 18.4 - - + -
446A LEU* 4.3 4.9 - - + -
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Residues in contact with LYS 355 (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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303A ARG* 4.7 5.7 + - - -
351A VAL* 3.2 23.6 + - + +
352A GLU* 4.0 10.3 - - + +
353A TRP 3.3 0.4 - - - -
354A ALA* 1.4 77.1 - - + +
356A ARG* 1.4 62.0 + - + +
357A ILE 3.6 5.4 + - - +
360A PHE* 4.4 6.1 - - + -
361A SER* 3.3 30.9 + - - +
368A GLN* 5.7 2.0 - - - +
546A LEU 3.1 27.1 + - - -
547A LEU* 3.2 33.6 + - + +
548A GLN* 3.7 11.9 + - - +
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Residues in contact with ARG 356 (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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303A ARG* 3.3 30.4 + - - +
306A GLU* 4.4 15.5 + - - +
307A ALA* 3.7 20.6 - - + +
310A ALA* 3.7 36.5 + - - +
311A VAL* 6.2 1.2 - - - +
352A GLU* 3.3 43.5 + - - +
353A TRP* 3.3 10.6 + - - +
354A ALA 3.3 0.4 - - - -
355A LYS* 1.4 76.3 - - + +
357A ILE* 1.4 63.2 + - - +
358A PRO* 4.0 0.9 - - - +
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Residues in contact with ILE 357 (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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299A MET* 6.0 0.2 - - - -
303A ARG* 4.5 1.7 + - - -
304A ILE* 4.7 14.8 - - + -
307A ALA* 3.9 14.1 - - + -
353A TRP* 3.2 38.0 + - + +
354A ALA* 3.0 24.9 - - - +
355A LYS 3.8 3.8 - - - +
356A ARG* 1.4 76.4 - - - +
358A PRO* 1.4 75.6 - - + +
359A HIS 3.5 0.2 + - - -
360A PHE* 3.4 15.9 + - + +
443A ALA* 5.1 7.0 - - + -
446A LEU* 3.5 21.3 - - + -
447A PHE* 3.4 35.9 - - + -
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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