Contacts of the helix formed by residues 343 - 363 (chain A) in PDB entry 5E92
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 SER 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 1.3 77.5 - - - +
344A TRP* 1.3 60.2 + - - +
345A GLU* 3.4 10.0 + - - +
346A ASP* 3.2 29.2 + - - +
347A LEU* 3.0 23.4 + - - +
461A CYS* 3.6 7.0 - - - -
462A ASN* 3.6 17.9 - - - +
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Residues in contact with TRP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 1.3 72.8 - - - +
345A GLU* 1.4 66.1 + - + +
347A LEU* 3.3 28.9 + - + +
348A ARG* 3.0 31.9 + - + +
461A CYS* 3.6 8.4 - - - -
462A ASN* 4.0 4.4 + - - +
463A ALA* 3.8 15.0 - - + -
507A HIS* 3.9 23.2 - + - +
509A GLY* 3.4 42.8 - - - -
510A ILE* 3.7 8.5 - - + -
513A VAL* 4.1 4.9 - - + -
541A LEU* 3.9 40.1 + - + -
543A HIS 5.6 4.6 + - - -
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 3.3 9.0 + - - +
344A TRP* 1.4 83.5 - - + +
346A ASP* 1.4 62.8 + - - +
348A ARG* 3.4 7.4 + - + +
349A LYS* 3.1 41.1 + - + +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 5.0 2.8 + - - -
342A ILE* 3.8 20.5 - - + +
343A SER* 3.2 31.1 + - - +
345A GLU* 1.4 78.6 - - - +
347A LEU* 1.3 56.7 + - - +
349A LYS* 3.3 13.6 + - - +
350A LEU* 2.9 36.5 + - + +
391A LEU* 3.7 35.7 - - + +
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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
----------------------------------------------------------
342A ILE* 3.9 9.6 - - + +
343A SER 3.0 13.1 + - - +
344A TRP* 3.3 21.5 + - + +
346A ASP* 1.3 74.1 - - - +
348A ARG* 1.4 58.3 + - - +
350A LEU* 4.7 1.6 - - - +
351A GLY* 2.9 28.9 + - - +
454A LEU* 4.7 1.3 - - + +
457A MET* 3.6 34.3 - - + -
458A THR* 3.9 21.8 - - - +
461A CYS* 3.8 14.6 - - + -
510A ILE* 3.6 30.7 - - + -
513A VAL* 4.7 14.4 - - + -
538A PHE* 4.0 4.0 - - + -
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A TRP* 3.0 32.4 + - + +
345A GLU* 3.7 11.0 - - + +
346A ASP 3.3 0.2 - - - -
347A LEU* 1.4 75.3 - - - +
349A LYS* 1.3 52.2 + - + +
352A SER* 2.6 39.5 + - - -
538A PHE* 3.7 15.4 - - + +
541A LEU* 5.1 9.2 - - + +
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Residues in contact with LYS 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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345A GLU* 3.1 34.5 + - + +
346A ASP* 3.6 13.6 + - - +
348A ARG* 1.3 74.2 - - + +
350A LEU* 1.3 53.8 + - - +
352A SER* 3.4 4.5 + - - -
353A SER* 2.7 38.9 + - - -
356A ARG* 4.9 0.5 + - - -
390A ASP 3.2 28.2 + - - -
391A LEU* 3.5 24.0 - - - +
392A THR* 4.3 14.5 - - + +
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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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333A LEU* 4.3 20.9 - - + -
336A TYR* 5.2 2.2 - - + -
337A LEU* 5.1 1.1 - - + -
342A ILE* 4.1 26.5 - - + -
346A ASP 2.9 22.9 + - - +
347A LEU 4.2 1.1 - - - +
349A LYS* 1.3 72.2 - - - +
351A GLY* 1.3 57.1 + - - +
353A SER* 3.1 5.5 + - - -
354A LEU* 2.9 27.2 + - - +
387A VAL* 4.4 11.0 - - + -
391A LEU* 3.4 37.0 - - + +
392A THR 4.0 10.5 - - - +
393A CYS* 3.3 25.1 - - - -
457A MET* 3.8 19.3 - - + -
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Residues in contact with GLY 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* 2.9 18.1 + - - -
350A LEU* 1.3 76.6 - - - +
352A SER* 1.4 59.7 + - - +
354A LEU* 3.5 3.1 + - - +
355A ALA* 3.2 22.0 + - - +
454A LEU* 3.7 20.9 - - - +
457A MET* 3.8 4.6 - - - -
538A PHE* 3.7 20.7 - - - -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG 2.6 25.9 + - - -
349A LYS* 3.4 6.4 + - - -
351A GLY* 1.4 74.1 - - - +
353A SER* 1.4 60.3 + - - +
355A ALA* 3.3 4.2 + - - +
356A ARG* 2.9 54.8 + - - +
535A ALA* 4.8 3.1 - - - +
538A PHE* 3.5 33.8 - - - -
539A SER* 5.3 0.7 - - - -
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASN* 3.3 35.7 - - - +
349A LYS 2.7 23.6 + - - -
350A LEU* 3.1 7.4 + - - -
352A SER* 1.4 71.8 + - - +
354A LEU* 1.3 64.8 + - - +
356A ARG* 3.6 17.0 - - - +
357A GLY* 3.1 18.4 + - - -
392A THR* 3.9 4.9 - - - -
393A CYS* 2.8 29.9 + - - -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 2.9 20.0 + - - +
351A GLY 3.6 4.0 - - - +
352A SER 3.3 0.2 - - - -
353A SER* 1.3 78.8 + - - +
355A ALA* 1.4 61.3 + - - +
357A GLY* 3.4 1.2 + - - -
358A ILE* 3.2 48.0 + - + +
380A LEU* 5.1 0.9 - - + -
385A ILE* 3.7 25.8 - - + -
393A CYS* 3.9 10.0 - - + +
395A LEU* 3.8 16.4 - - + +
450A MET* 4.0 21.1 - - + +
453A VAL* 3.6 30.5 - - + -
454A LEU* 4.4 9.2 - - + -
457A MET* 3.8 9.9 - - + -
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Residues in contact with ALA 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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351A GLY 3.2 14.6 + - - +
352A SER* 3.7 5.2 - - - +
354A LEU* 1.4 77.7 - - - +
356A ARG* 1.4 56.4 + - - +
358A ILE* 3.5 0.9 + - - -
359A ALA* 2.9 31.7 + - - +
450A MET* 4.2 13.7 - - - -
454A LEU* 6.2 0.2 - - + -
531A ALA* 3.8 8.3 - - - +
534A VAL* 3.8 18.4 - - + +
535A ALA* 3.7 30.5 - - - +
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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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301A HIS* 4.0 13.5 + - + +
302A GLU* 3.7 20.5 + - - -
303A ASN* 3.5 15.5 + - - +
349A LYS 4.9 0.6 + - - -
352A SER* 2.9 45.3 + - - +
353A SER* 3.6 26.7 - - - +
355A ALA* 1.4 77.1 - - - +
357A GLY* 1.3 55.8 + - - +
359A ALA* 3.6 6.8 + - - +
360A HIS* 3.0 27.9 + - - +
392A THR* 4.9 9.1 - - - +
535A ALA* 4.1 16.4 - - + +
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Residues in contact with GLY 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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301A HIS* 4.4 6.5 - - - -
303A ASN* 3.8 28.6 - - - +
304A ILE* 4.2 3.3 - - - +
353A SER 3.1 11.3 + - - -
354A LEU* 3.4 3.1 + - - -
356A ARG* 1.3 74.4 - - - +
358A ILE* 1.4 57.5 + - - +
360A HIS* 3.3 5.1 + - - +
361A LEU* 3.0 28.8 + - - +
395A LEU* 3.7 10.1 - - - +
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Residues in contact with ILE 358 (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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354A LEU* 3.2 30.9 + - + +
355A ALA 3.9 3.6 - - - +
357A GLY* 1.4 72.3 - - - +
359A ALA* 1.3 58.1 + - - +
361A LEU* 3.1 8.1 + - + +
362A HIS* 2.9 57.4 + - + +
380A LEU* 3.7 31.9 - - + -
395A LEU* 3.8 18.4 - - + +
446A ASP* 4.6 2.5 - - + +
447A VAL* 5.3 1.8 - - + -
450A MET* 3.6 29.8 - - + -
531A ALA* 3.7 12.6 - - + -
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Residues in contact with ALA 359 (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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355A ALA 2.9 19.5 + - - +
356A ARG* 3.7 7.0 - - - +
358A ILE* 1.3 74.0 - - - +
360A HIS* 1.4 57.5 + - - +
362A HIS* 3.3 5.4 + - - +
363A SER* 3.0 30.2 + - - -
531A ALA* 3.6 9.5 - - - +
532A GLN* 3.8 40.6 - - + +
535A ALA* 5.1 1.3 - - + -
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Residues in contact with HIS 360 (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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298A ASN 2.9 21.9 + - - -
299A LEU* 2.9 31.1 + - + -
300A LYS 3.8 9.4 + - - -
301A HIS* 3.4 27.9 - + + +
304A ILE* 3.5 16.6 - - + -
356A ARG 3.0 18.2 + - - +
357A GLY 3.5 4.7 - - - +
358A ILE 3.2 0.2 - - - -
359A ALA* 1.4 72.5 - - - +
361A LEU* 1.4 62.9 + - + +
362A HIS 3.4 0.3 + - - -
363A SER* 3.4 8.5 + - - -
365A HIS 5.6 0.8 + - - -
366A THR* 5.7 0.4 - - - -
367A PRO* 4.8 20.9 - - + +
372A LYS* 2.8 42.9 + - - -
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Residues in contact with LEU 361 (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 LEU* 3.5 31.4 - - + -
304A ILE* 3.8 10.8 - - + -
357A GLY 3.0 14.9 + - - +
358A ILE* 3.5 10.3 - - + +
360A HIS* 1.4 74.8 - - - +
362A HIS* 1.4 56.9 + - + +
372A LYS* 3.2 14.7 + - - +
374A PRO* 3.6 0.2 - - - +
375A ILE* 2.8 56.5 + - + +
377A HIS* 4.2 25.8 - - + +
395A LEU* 3.7 22.4 - - + -
398A PHE* 4.0 18.6 - - + -
446A ASP* 5.4 0.9 - - - +
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Residues in contact with HIS 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 2.9 38.8 + - + +
359A ALA* 3.7 6.1 - - - +
361A LEU* 1.4 76.3 - - + +
363A SER* 1.3 62.2 + - - +
374A PRO* 3.3 5.7 - - - +
375A ILE 3.3 18.2 - - - +
376A VAL* 4.3 1.5 - - + +
443A LYS* 2.9 84.3 + - + +
446A ASP* 2.8 28.3 + - + +
447A VAL* 4.5 6.5 - - + +
531A ALA* 4.4 8.9 + - + +
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA 3.0 16.6 + - - -
360A HIS* 3.7 11.9 - - - -
361A LEU 3.4 1.4 - - - -
362A HIS* 1.3 77.1 - - - +
364A ASP* 1.3 59.1 + - - +
365A HIS* 2.8 44.6 + - - -
372A LYS* 2.9 29.4 + - - +
374A PRO* 3.7 5.9 - - - +
443A LYS* 5.1 0.4 - - - +
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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
------------------------------------------------------------
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