Contacts of the helix formed by residues 414 - 432 (chain O) in PDB entry 5A31
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 414 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ARG* 4.5 17.0 - - - +
374O PRO* 4.3 5.8 - - + +
375O TYR* 3.7 36.1 - - + +
378O SER* 4.3 2.7 - - - +
408O LEU* 4.8 3.1 - - + -
409O HIS* 3.5 21.9 + - + +
412O HIS* 3.2 26.2 + - + +
413O SER* 1.3 71.2 - - - +
415O SER* 1.3 66.0 + - - +
416O GLU 3.2 2.7 - - - +
417O LEU* 3.1 46.7 + - + +
418O ILE* 3.7 11.1 + - - +
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Residues in contact with SER 415 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224O LYS* 5.7 4.7 - - - -
225O ASN* 5.3 5.0 + - - -
413O SER 3.0 8.0 + - - -
414O LEU* 1.3 72.5 - - - +
416O GLU* 1.3 67.9 + - - +
418O ILE* 3.4 3.9 + - - +
419O ASP* 2.7 32.4 + - - +
450O SER* 4.4 14.5 + - - -
451O LEU* 4.1 28.7 - - - -
461O ASN* 4.6 8.8 + - - -
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Residues in contact with GLU 416 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE 5.1 2.9 - - - +
11D ARG* 2.7 54.1 + - - +
224O LYS* 5.2 10.3 - - - -
375O TYR* 2.8 29.9 + - + -
379O LEU* 5.5 1.0 - - - +
414O LEU* 3.2 1.8 - - + +
415O SER* 1.3 85.2 + - - +
417O LEU* 1.3 62.3 + - + +
419O ASP* 3.4 4.8 + - - +
420O ILE* 3.0 29.9 + - + +
461O ASN* 5.4 5.2 - - - +
463O THR* 6.3 3.1 - - + -
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Residues in contact with LEU 417 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O TYR* 3.4 32.5 - - + +
378O SER* 3.2 20.4 - - - +
379O LEU* 3.7 20.4 - - + +
382O GLN* 3.2 37.2 - - + -
409O HIS* 3.8 7.4 - - - +
414O LEU* 3.1 30.9 + - + +
415O SER 3.3 0.6 - - - -
416O GLU* 1.3 86.8 - - - +
418O ILE* 1.3 57.3 + - - +
420O ILE* 3.0 13.0 - - + +
421O SER* 2.7 37.4 + - - -
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Residues in contact with ILE 418 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406O ASP* 5.5 1.3 - - - +
409O HIS* 3.6 37.2 - - + +
410O TRP* 3.7 46.9 - - + +
413O SER 4.9 0.4 - - - -
414O LEU 3.7 10.8 + - - +
415O SER* 3.4 6.7 + - - +
417O LEU* 1.3 78.5 - - - +
419O ASP* 1.3 75.3 + - - +
421O SER* 3.3 4.4 + - - -
422O ILE* 3.2 28.3 + - + +
448O MET* 3.6 31.9 - - + -
451O LEU* 4.4 13.7 - - + -
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Residues in contact with ASP 419 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415O SER* 2.7 24.9 + - - +
416O GLU* 3.8 7.0 - - - +
418O ILE* 1.3 87.9 - - - +
420O ILE* 1.3 64.1 + - - +
422O ILE 3.6 0.2 + - - -
423O ALA* 3.2 13.5 + - - +
445O LEU* 3.7 17.8 - - + +
448O MET* 4.2 8.3 - - - +
450O SER* 4.8 6.3 + - - -
451O LEU* 5.9 1.6 - - - +
461O ASN* 3.7 19.8 - - - +
463O THR* 5.2 2.2 - - - +
465O SER* 2.9 16.8 + - - +
466O PHE* 3.1 40.2 - - + -
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Residues in contact with ILE 420 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PRO* 3.7 23.1 - - + -
8D LEU* 3.3 49.8 - - + +
379O LEU* 4.9 4.3 - - + -
382O GLN* 4.8 4.0 - - + +
416O GLU* 3.0 20.5 + - + +
417O LEU* 3.0 36.6 - - + +
419O ASP* 1.3 76.9 - - - +
421O SER* 1.3 58.1 + - - +
423O ALA* 2.9 4.8 + - - +
424O GLN* 2.8 27.7 + - + -
465O SER* 3.6 13.3 + - - +
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Residues in contact with SER 421 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382O GLN* 3.0 34.5 + - - +
402O LEU* 4.7 4.6 - - - +
406O ASP* 2.8 29.9 + - - -
409O HIS* 3.8 2.9 - - - -
417O LEU 2.7 17.9 + - - -
418O ILE* 3.3 9.9 + - - -
420O ILE* 1.3 72.9 - - - +
422O ILE* 1.3 63.4 + - - +
424O GLN* 3.2 3.1 + - - +
425O LYS* 2.9 34.5 + - - +
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Residues in contact with ILE 422 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401I ASN* 4.6 10.3 - - - +
406O ASP* 5.6 3.4 - - - +
418O ILE* 3.2 20.0 + - + +
419O ASP 3.8 2.7 - - - +
420O ILE 3.2 0.4 - - - -
421O SER* 1.3 83.8 + - - +
423O ALA* 1.3 65.3 + - - +
425O LYS* 4.5 2.9 - - + +
426O THR* 3.1 23.7 + - + +
441O GLN* 3.4 46.2 - - + +
444O MET* 4.7 8.3 - - + -
445O LEU* 3.6 29.8 - - + +
448O MET* 4.0 26.5 - - + -
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Residues in contact with ALA 423 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PRO* 4.1 7.3 - - + +
419O ASP 3.2 3.2 + - - +
420O ILE 2.9 8.9 + - - +
422O ILE* 1.3 83.0 - - - +
424O GLN* 1.3 61.0 + - - +
426O THR* 3.1 13.2 + - - +
427O ALA* 3.1 21.0 + - - +
445O LEU* 4.2 4.5 - - + -
465O SER* 3.3 27.4 - - - +
468O VAL* 3.5 27.5 - - + +
469O ALA* 5.0 1.1 - - - +
472O HIS* 5.0 0.5 + - - -
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Residues in contact with GLN 424 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 3.8 6.7 - - + -
6D PRO* 3.7 16.7 - - + +
8D LEU* 3.7 13.3 - - - +
382O GLN* 3.0 42.8 + - - +
385O VAL* 4.4 3.9 - - - +
386O GLN* 2.7 41.3 + - - +
402O LEU* 4.4 4.4 - - + +
420O ILE* 2.8 16.0 + - - +
421O SER* 3.4 9.2 - - - +
423O ALA* 1.3 72.3 - - - +
425O LYS* 1.3 67.3 + - - +
427O ALA* 2.9 5.4 + - - +
428O ILE* 2.8 38.1 + - + +
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Residues in contact with LYS 425 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I GLU* 4.1 20.8 + - - +
399O MET* 4.0 19.2 + - + +
402O LEU* 3.7 37.9 - - + +
403O LYS* 5.0 9.5 - - - +
406O ASP* 2.9 30.2 + - - -
421O SER* 2.9 17.8 + - - +
422O ILE* 4.7 3.1 - - + +
424O GLN* 1.3 75.8 - - - +
426O THR* 1.3 67.1 + - - +
428O ILE* 3.1 8.3 + - - +
429O TRP* 2.8 34.9 + - + +
441O GLN* 3.1 36.4 + - + +
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Residues in contact with THR 426 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422O ILE* 3.1 18.1 + - + +
423O ALA* 3.1 17.9 - - - +
425O LYS* 1.3 77.7 - - - +
427O ALA* 1.3 56.8 + - - +
429O TRP* 3.5 2.4 + - - +
430O ARG* 3.0 28.4 + - - +
438O ALA* 3.8 19.4 + - - +
441O GLN* 4.0 14.5 - - + +
442O ALA* 4.1 22.3 - - + +
469O ALA* 4.8 9.4 - - + -
472O HIS* 3.1 27.1 + - - +
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Residues in contact with ALA 427 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 4.6 3.3 + - - -
4D LEU 3.5 24.2 - - - +
5D TYR* 3.8 23.3 - - + -
6D PRO* 4.7 0.2 - - + -
423O ALA 3.1 11.0 + - - +
424O GLN* 2.9 9.1 + - - +
426O THR* 1.3 79.1 + - - +
428O ILE* 1.3 50.9 + - - +
430O ARG* 3.1 4.3 + - - +
431O LEU* 2.7 35.3 + - - +
468O VAL* 6.0 0.2 - - + -
472O HIS* 3.6 16.4 - - + -
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Residues in contact with ILE 428 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.2 26.9 + - + +
385O VAL* 3.9 28.5 - - + +
386O GLN* 5.0 0.9 - - - -
389O ALA* 3.9 14.8 - - + -
398O LEU* 4.3 10.3 - - + -
399O MET* 4.0 18.6 - - + -
402O LEU* 4.6 7.2 - - + -
424O GLN* 2.8 29.4 + - + +
425O LYS* 3.5 6.7 - - - +
427O ALA* 1.3 70.6 - - - +
429O TRP* 1.3 62.6 + - - +
431O LEU* 3.0 4.2 + - + +
432O TYR* 2.8 53.4 + - + +
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Residues in contact with TRP 429 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I GLU* 6.2 2.3 - - + -
361I TYR* 4.0 22.0 - + - -
395O ALA* 3.8 30.7 - - + -
399O MET* 3.3 37.1 - - + +
425O LYS* 2.8 35.2 + - + +
426O THR* 3.7 4.5 - - - +
428O ILE* 1.3 74.4 - - - +
430O ARG* 1.3 63.1 + - - +
432O TYR* 3.2 8.4 + + + +
433O GLY 3.1 4.9 + - - -
434O ARG* 3.0 66.9 + - + +
437O MET* 3.3 48.5 - - + +
438O ALA 3.9 6.7 - - - +
441O GLN* 4.5 8.3 - - - +
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Residues in contact with ARG 430 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 4.3 15.9 - - + +
426O THR 3.0 18.1 + - - +
427O ALA* 3.4 7.4 - - - +
429O TRP* 1.3 75.6 - - - +
431O LEU* 1.3 61.3 + - - +
433O GLY* 3.3 13.6 + - - +
434O ARG 4.9 2.5 - - - +
435O SER* 5.3 3.4 - - - +
438O ALA* 4.2 8.9 - - + +
472O HIS* 3.5 37.1 - - + +
475O GLU* 4.0 31.7 + - - +
476O LEU* 3.5 36.5 - - + +
479O GLU* 3.6 25.8 + - - -
618O TYR* 4.2 18.9 + - - +
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Residues in contact with LEU 431 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 3.7 18.8 - - - +
5D TYR* 3.3 21.1 - - - +
389O ALA* 4.2 19.3 - - + +
390O PHE* 3.9 24.9 - - + -
427O ALA 2.7 13.4 + - - +
428O ILE 3.0 6.3 + - - +
430O ARG* 1.3 78.3 - - - +
432O TYR* 1.3 66.8 + - + +
433O GLY* 3.1 4.8 + - - -
578O GLU* 3.3 26.5 - - + +
616O LEU* 3.5 37.5 - - + +
617O GLN 4.6 0.5 + - - -
618O TYR* 5.1 4.9 + - - +
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Residues in contact with TYR 432 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389O ALA* 3.1 32.5 + - + -
393O LYS 3.5 25.9 + - - -
395O ALA* 4.3 20.4 - - + -
398O LEU* 3.3 31.6 - - + +
428O ILE* 2.8 27.4 + - + +
429O TRP* 3.2 10.3 + + + +
431O LEU* 1.3 87.6 - - + +
433O GLY* 1.3 60.3 + - - +
434O ARG* 3.2 19.8 + - - +
614O TYR 4.1 13.5 - - - -
615O ARG* 3.5 24.7 - - + +
617O GLN* 3.6 23.6 + - - +
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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