Contacts of the helix formed by residues 441 - 456 (chain F) in PDB entry 5KRA
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 GLN 441 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393F TRP* 3.8 2.0 - - - -
439F ASN* 2.9 30.0 + - - +
440F LEU* 1.3 78.9 + - - +
442F GLY* 1.3 60.6 + - - +
443F GLU* 3.6 17.4 - - + +
444F GLU* 2.9 28.2 + - + +
445F PHE* 2.8 27.2 + - - +
503F ARG* 5.0 0.9 - - - +
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Residues in contact with GLY 442 (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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320F LEU* 4.5 7.0 - - - -
393F TRP* 3.5 27.7 - - - -
441F GLN* 1.3 73.2 + - - +
443F GLU* 1.3 66.0 + - - +
445F PHE* 3.7 3.9 - - - +
446F VAL* 3.0 33.0 + - - +
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Residues in contact with GLU 443 (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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316F VAL* 3.6 25.4 - - + +
320F LEU* 4.3 13.6 - - + +
441F GLN* 3.6 15.0 - - + +
442F GLY* 1.3 83.1 + - - +
444F GLU* 1.3 61.0 + - + +
446F VAL* 3.3 19.9 - - - +
447F CYS* 3.4 17.2 - - - -
489F LEU* 3.6 28.1 - - + +
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Residues in contact with GLU 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440F LEU* 3.5 13.0 - - + +
441F GLN* 2.9 32.8 + - + +
443F GLU* 1.3 78.9 - - + +
445F PHE* 1.3 59.2 + - - +
447F CYS* 3.3 3.5 + - - +
448F LEU* 3.0 32.1 + - - +
486F LEU* 4.0 22.6 - - + +
489F LEU* 4.5 11.7 - - + +
490F MET* 3.9 13.6 - - + +
503F ARG* 2.6 51.1 + - - -
507F LEU* 4.3 7.0 - - + -
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Residues in contact with PHE 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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323F GLU* 3.2 25.1 - - - -
389F ILE* 3.7 30.3 - - + -
390F GLY* 4.1 9.0 - - - -
393F TRP* 3.5 65.3 - + + -
440F LEU* 4.2 12.1 - - + +
441F GLN 2.8 11.7 + - - +
442F GLY* 3.3 8.0 + - - +
444F GLU* 1.3 77.4 - - - +
446F VAL* 1.3 71.3 + - + +
448F LEU* 3.2 6.5 + - - +
449F LYS* 3.0 52.0 + - + +
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Residues in contact with VAL 446 (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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316F VAL* 5.0 3.8 - - + +
319F LEU* 3.7 30.1 - - + +
320F LEU* 3.8 22.4 - - + -
323F GLU* 3.7 32.5 - - + +
360F TRP* 5.2 0.6 - - - +
442F GLY 3.0 14.3 + - - +
443F GLU* 3.3 20.2 - - - +
445F PHE* 1.3 83.6 - - + +
447F CYS* 1.3 64.6 + - - +
449F LYS* 3.9 8.7 - - - +
450F SER* 3.3 27.0 + - - -
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Residues in contact with CYS 447 (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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315F MET* 5.3 0.2 - - - -
316F VAL* 5.1 2.5 - - - -
319F LEU* 4.2 15.7 - - - -
443F GLU 3.4 16.4 - - - -
444F GLU 3.3 9.1 + - - +
445F PHE 3.1 0.8 - - - -
446F VAL* 1.3 80.6 - - - +
448F LEU* 1.3 64.8 + - - +
450F SER* 3.2 4.0 + - - -
451F ILE* 3.0 28.5 + - - +
482F ILE* 3.8 16.4 - - + +
485F THR* 3.8 28.7 - - - -
486F LEU* 3.7 26.5 - - + -
489F LEU* 4.2 2.2 - - - -
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Residues in contact with LEU 448 (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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389F ILE* 4.1 13.2 - - + -
435F PHE* 4.4 21.1 - - + -
440F LEU* 4.4 8.1 - - + -
444F GLU 3.0 17.0 + - - +
445F PHE* 3.2 7.6 + - - +
447F CYS* 1.3 75.8 - - - +
449F LYS* 1.3 58.5 + - - +
451F ILE* 3.2 7.2 + - + +
452F ILE* 2.9 34.7 + - - +
486F LEU* 4.4 11.0 - - + -
507F LEU* 4.0 51.4 - - + +
508F LEU* 4.1 20.9 - - + -
511F LEU* 4.3 12.2 - - + +
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Residues in contact with LYS 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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323F GLU* 2.4 40.7 + - - -
324F PRO* 3.8 15.6 - - - +
360F TRP* 3.6 24.2 - - + +
386F ILE* 3.7 35.4 - - + +
389F ILE* 4.3 12.5 - - + +
390F GLY* 5.4 1.1 - - - -
445F PHE* 3.0 39.6 + - + +
446F VAL* 3.9 6.7 - - - +
447F CYS 3.2 0.2 - - - -
448F LEU* 1.3 78.7 - - - +
450F SER* 1.3 60.3 + - - +
452F ILE* 3.5 12.2 + - - +
453F LEU* 3.2 20.6 + - - +
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Residues in contact with SER 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F LEU* 3.2 31.8 - - - +
360F TRP* 4.0 5.8 - - - -
364F VAL* 3.7 19.9 - - - +
446F VAL 3.3 11.2 + - - -
447F CYS 3.2 5.2 + - - -
449F LYS* 1.3 76.7 - - - +
451F ILE* 1.3 66.1 + - - +
453F LEU* 3.3 9.7 + - - +
454F LEU* 3.2 26.5 + - - +
482F ILE* 4.0 18.6 - - - -
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Residues in contact with ILE 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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509E LEU* 3.7 38.8 - - + -
447F CYS 3.0 20.7 + - - +
448F LEU* 3.2 10.1 + - - +
450F SER* 1.3 73.4 - - - +
452F ILE* 1.3 57.2 + - - +
454F LEU 3.2 1.6 + - - -
455F ASN* 2.8 40.0 + - + +
479F LEU* 3.9 15.1 - - + +
482F ILE* 3.7 22.7 - - + -
483F THR* 5.0 9.9 - - - +
486F LEU* 3.9 26.2 - - + -
508F LEU* 4.1 14.4 - - + -
511F LEU* 3.9 8.7 - - + -
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Residues in contact with ILE 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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382F ALA* 3.8 3.3 - - + +
385F GLU* 3.6 33.9 - - + +
386F ILE* 4.0 11.9 - - + -
389F ILE* 3.8 33.2 - - + -
448F LEU 2.9 18.3 + - - +
449F LYS* 3.6 8.1 - - - +
451F ILE* 1.3 77.2 - - - +
453F LEU* 1.3 63.6 + - - +
455F ASN* 4.8 2.2 - - - -
456F SER* 3.0 40.8 + - - +
511F LEU* 3.7 33.9 - - + -
514F ILE* 4.5 9.9 - - + -
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Residues in contact with LEU 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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360F TRP* 4.0 9.0 - - + -
361F ALA* 4.0 5.6 - - + -
364F VAL* 4.0 33.9 - - + -
367F PHE* 3.7 36.6 - - + -
378F LEU* 3.6 27.1 - - + +
379F LEU* 3.7 33.2 - - + +
382F ALA* 4.2 6.6 - - + +
386F ILE* 4.0 13.9 - - + -
449F LYS 3.2 11.2 + - - +
450F SER 3.4 8.5 - - - +
451F ILE 3.2 0.2 - - - -
452F ILE* 1.3 81.8 - - - +
454F LEU* 1.3 61.2 + - + +
456F SER 4.6 0.9 + - - -
457F GLY 4.9 0.3 + - - -
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Residues in contact with LEU 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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364F VAL* 5.0 5.2 - - + -
365F PRO 4.7 3.6 - - - +
366F GLY 5.5 1.8 - - - -
367F PHE* 4.2 32.1 - - + +
370F LEU* 4.8 6.5 - - + -
378F LEU* 4.0 17.4 - - + +
450F SER 3.2 7.8 + - - +
451F ILE 3.2 2.0 + - - -
453F LEU* 1.3 81.3 - - + +
455F ASN* 1.3 61.2 + - - +
458F VAL* 3.5 10.4 - - - +
475F ILE* 3.4 31.5 - - + +
478F VAL* 3.6 34.3 - - + -
479F LEU* 3.7 20.2 - - + -
482F ILE* 3.9 19.3 - - + -
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Residues in contact with ASN 455 (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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509E LEU* 3.3 45.4 + - - +
512E SER* 4.3 11.3 - - - -
451F ILE* 2.8 30.3 + - + +
452F ILE* 4.5 1.3 - - - +
454F LEU* 1.3 73.3 - - - +
456F SER* 1.3 71.1 + - - +
457F GLY 3.2 3.5 + - - -
458F VAL* 3.3 18.5 + - - +
459F TYR* 3.1 32.0 + - - -
479F LEU* 4.1 14.7 - - + +
511F LEU* 6.1 0.2 - - - +
515F ARG* 4.4 1.0 - - - +
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Residues in contact with SER 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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512E SER* 6.1 0.2 - - - -
513E HIS* 5.5 1.9 + - - -
381F CYS* 3.3 17.5 - - - -
382F ALA* 3.9 13.5 - - - -
385F GLU* 2.8 36.7 + - - -
452F ILE* 3.0 23.2 + - - +
454F LEU 3.7 0.2 - - - -
455F ASN* 1.3 78.4 + - - +
457F GLY* 1.3 58.6 + - - +
459F TYR* 4.9 3.6 + - - +
460F THR* 4.7 2.6 + - - +
515F ARG* 3.1 29.9 + - - +
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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