Contacts of the helix formed by residues 437 - 457 (chain F) in PDB entry 1Q57
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 ASP 437 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F SER* 1.3 82.2 - - - +
438F GLU* 1.3 63.8 + - - +
439F ARG* 2.9 64.1 + - + +
440F LYS* 3.0 21.6 + - + +
441F MET* 3.1 10.4 + - - +
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Residues in contact with GLU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F SER* 3.3 17.4 - - - +
429F VAL* 2.9 49.6 - - + +
436F SER 3.6 1.4 + - - -
437F ASP* 1.3 71.4 + - - +
439F ARG* 1.3 52.0 + - - +
440F LYS 3.3 0.2 - - - -
441F MET* 3.9 8.5 - - + +
442F ILE* 2.8 46.4 + - + +
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Residues in contact with ARG 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F ASP* 3.0 44.5 + - + +
438F GLU* 1.3 74.7 - - - +
440F LYS* 1.3 56.7 + - + +
442F ILE* 2.6 25.6 - - - +
443F ASP* 3.3 9.2 - - - +
488F GLY* 4.7 5.8 - - - +
489F SER* 3.1 32.7 - - - +
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Residues in contact with LYS 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436F SER 5.6 2.7 - - - +
437F ASP* 3.0 14.6 + - + +
439F ARG* 1.3 77.1 - - - +
441F MET* 1.3 96.3 + - + +
443F ASP* 2.9 29.8 + - - +
444F ASN* 3.0 36.2 + - - +
489F SER* 5.8 0.7 - - - -
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Residues in contact with MET 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402F THR* 4.1 24.7 - - + +
429F VAL* 4.1 25.4 - - + -
435F GLU* 4.0 21.1 - - + +
436F SER 4.9 2.0 - - - +
437F ASP 3.1 12.2 + - - +
438F GLU* 4.4 6.7 - - + +
440F LYS* 1.3 94.6 - - + +
442F ILE* 1.3 68.1 + - - +
443F ASP 2.9 0.9 + - - -
444F ASN* 3.0 31.9 + - + +
445F LEU* 3.1 30.5 + - + +
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Residues in contact with ILE 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426F ILE* 3.7 26.4 - - + +
427F SER* 6.4 0.9 - - - -
429F VAL* 4.8 6.8 - - - +
438F GLU* 2.8 24.8 + - - +
439F ARG* 2.6 33.4 - - - +
441F MET* 1.3 78.1 - - - +
443F ASP* 1.3 64.7 + - - +
445F LEU* 3.7 3.7 + - - +
446F MET* 3.0 26.5 + - - +
487F ARG* 6.5 1.1 - - - -
488F GLY* 3.2 17.3 - - - +
492F LEU* 3.1 49.1 - - + -
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Residues in contact with ASP 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439F ARG 3.3 9.0 - - - +
440F LYS* 2.9 15.0 + - - +
442F ILE* 1.3 90.2 - - - +
444F ASN* 1.3 64.3 + - - +
446F MET* 2.9 17.5 + - - +
447F THR* 3.1 14.7 + - + +
489F SER* 3.4 25.6 + - - +
490F GLY* 4.0 0.6 - - - -
491F ALA* 3.1 36.4 + - + +
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Residues in contact with ASN 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433E SER* 5.6 7.5 - - - -
440F LYS* 3.0 35.5 + - - +
441F MET* 3.0 11.9 + - + +
443F ASP* 1.3 76.5 - - - +
445F LEU* 1.3 60.2 + - - +
447F THR* 2.8 25.9 + - - -
448F LYS* 3.0 36.7 + - - +
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Residues in contact with LEU 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F THR* 4.2 11.9 - - - +
405F LEU* 5.7 6.1 - - + -
406F LEU* 3.3 23.8 - - + -
423F LEU* 5.3 6.3 - - + -
426F ILE* 3.9 32.5 - - + +
428F ILE 5.2 4.7 - - - +
429F VAL* 5.2 12.3 - - + +
441F MET* 3.1 25.3 + - + +
442F ILE* 3.9 6.5 - - - +
444F ASN* 1.3 73.4 - - - +
446F MET* 1.3 71.3 + - - +
448F LYS* 2.8 19.3 + - - +
449F LEU* 2.9 37.9 + - + -
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Residues in contact with MET 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F VAL* 4.6 8.7 - - + -
309F MET* 3.5 16.4 - - + -
426F ILE* 5.2 8.1 - - - -
442F ILE* 3.0 15.6 + - + +
443F ASP 2.9 15.5 - - - +
445F LEU* 1.3 74.0 - - - +
447F THR* 1.3 55.6 + - - +
449F LEU* 3.1 20.3 - - - +
450F LYS* 2.9 23.6 + - + +
462F VAL* 5.5 0.7 - - + -
491F ALA* 3.3 12.1 - - + +
492F LEU* 3.2 48.5 - - + +
495F LEU* 3.4 10.1 - - + +
496F SER* 3.1 33.9 - - - +
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Residues in contact with THR 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E VAL* 5.6 8.7 - - - +
438E GLU* 6.2 0.4 - - - +
443F ASP 3.2 14.6 - - - +
444F ASN* 2.8 20.5 + - - -
445F LEU 2.9 0.4 + - - -
446F MET* 1.3 71.7 - - - +
448F LYS* 1.3 71.4 + - - +
449F LEU 2.9 2.1 + - - -
450F LYS* 2.9 3.4 + - - +
451F GLY* 2.8 21.5 + - - -
491F ALA* 4.7 2.7 - - + -
495F LEU* 3.0 27.1 - - + -
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Residues in contact with LYS 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E SER* 5.4 10.9 - - - -
402F THR* 3.8 23.3 + - - +
403F ASP* 3.0 29.5 + - - +
406F LEU* 3.9 23.4 - - + +
441F MET* 4.8 0.2 - - - +
444F ASN* 3.0 38.5 + - - +
445F LEU* 2.8 12.2 + - - +
447F THR* 1.3 74.0 + - - +
449F LEU* 1.3 59.0 + - - +
451F GLY* 3.3 1.8 + - - -
452F PHE* 2.8 30.4 + - - +
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Residues in contact with LEU 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F VAL* 5.4 2.0 - - + -
405F LEU* 5.9 0.4 - - + -
406F LEU* 3.2 38.4 - - + -
409F LEU* 5.4 4.9 - - + -
423F LEU* 4.2 17.5 - - + -
426F ILE* 4.9 4.3 - - + -
445F LEU* 2.9 30.5 + - + +
446F MET* 3.1 21.8 - - - +
447F THR 2.9 0.2 + - - -
448F LYS* 1.3 73.4 - - - +
450F LYS* 1.3 67.3 + - - +
451F GLY 2.9 2.0 + - - -
452F PHE* 3.0 9.8 + - + +
453F ALA* 2.8 22.7 + - - +
460F LEU* 3.9 29.0 - - + +
462F VAL* 3.9 15.7 - - + -
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Residues in contact with LYS 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E GLU* 4.6 12.5 + - - +
305F GLY 3.7 3.8 - - - -
307F VAL* 3.6 20.6 - - + +
446F MET* 2.9 8.7 + - + +
447F THR* 2.9 10.0 + - - +
449F LEU* 1.3 76.6 - - - +
451F GLY* 1.3 57.4 + - - +
453F ALA* 3.2 2.9 - - - +
454F LYS* 2.8 60.0 + - - +
495F LEU* 3.4 39.7 + - + +
497F ASP* 2.9 16.6 + - - -
522F ARG* 2.9 31.7 - - - +
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Residues in contact with GLY 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E PHE* 6.3 0.7 - - - -
447F THR 2.8 12.8 + - - -
448F LYS* 3.5 4.5 - - - -
449F LEU 2.9 0.4 + - - -
450F LYS* 1.3 74.5 - - - +
452F PHE* 1.3 66.8 + - - -
453F ALA 2.9 0.7 + - - -
454F LYS* 5.3 1.1 - - - -
455F SER* 2.7 33.0 + - - -
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Residues in contact with PHE 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E PHE* 6.2 0.7 - - - -
406F LEU* 4.2 21.3 - - + -
409F LEU* 3.3 37.0 - - + -
410F ALA* 3.4 26.2 - - + -
413F ARG* 3.4 24.2 - - + -
414F SER* 5.9 0.4 - - - -
421F ILE* 4.4 3.8 - - + -
448F LYS 2.8 15.5 + - - +
449F LEU* 3.1 9.9 - - + +
451F GLY* 1.3 68.7 - - - +
453F ALA* 1.3 57.3 + - - +
455F SER* 4.1 5.8 - - - -
456F THR* 2.7 50.5 + - + +
458F VAL* 3.9 9.0 - - + -
460F LEU* 3.9 31.6 - - + -
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Residues in contact with ALA 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F GLY* 3.4 18.0 - - - +
306F GLU 3.7 5.4 - - - +
307F VAL* 3.4 28.5 - - + -
449F LEU 2.8 11.1 + - - +
450F LYS* 3.2 10.5 - - + +
451F GLY 2.9 0.6 + - - -
452F PHE* 1.3 74.4 - - - +
454F LYS* 1.3 55.8 + - - +
457F GLY* 2.6 37.8 + - - -
458F VAL* 3.7 14.7 + - - +
460F LEU* 4.5 5.2 - - + -
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Residues in contact with LYS 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E GLU 3.1 31.1 + - - +
344E GLU* 3.6 20.6 - - - +
345E SER* 5.1 8.3 - - - +
348E GLU* 4.0 14.2 + - - +
305F GLY* 3.1 21.0 + - - +
306F GLU* 4.9 1.3 - - - +
450F LYS* 2.8 45.5 + - - +
451F GLY* 4.3 1.3 - - - +
453F ALA* 1.3 75.5 - - - +
455F SER* 1.3 65.6 + - - +
456F THR 3.1 1.4 + - - -
457F GLY* 3.6 6.2 + - - -
497F ASP* 3.7 7.4 - - - -
522F ARG* 3.0 31.6 - - - +
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Residues in contact with SER 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E PHE* 3.1 57.1 - - - +
451F GLY* 2.7 26.2 + - - -
452F PHE* 3.6 3.3 + - - -
454F LYS* 1.3 73.0 - - - +
456F THR* 1.3 74.4 + - - +
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Residues in contact with THR 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E PHE* 4.6 7.9 - - + -
413F ARG* 2.9 39.9 + - + +
414F SER* 5.7 3.8 - - - +
452F PHE* 2.7 32.5 + - + +
453F ALA 3.1 1.8 + - - -
454F LYS 3.1 0.4 - - - -
455F SER* 1.3 97.9 - - - +
457F GLY* 1.3 57.4 + - - +
458F VAL* 3.1 17.0 - - - +
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Residues in contact with GLY 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F GLY* 3.2 11.9 - - - -
305F GLY* 3.0 22.5 + - - -
413F ARG* 3.0 13.2 + - - -
419F ASP* 5.9 0.3 - - - +
453F ALA 2.6 17.0 + - - -
454F LYS 3.6 6.1 + - - -
456F THR* 1.3 68.9 - - - +
458F VAL* 1.3 59.4 + - - -
459F VAL* 3.7 0.9 + - - +
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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
------------------------------------------------------------
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