Contacts of the helix formed by residues 467 - 485 (chain F) in PDB entry 3IKM
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 HIS 467 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D LYS* 3.5 21.2 + - + -
556D THR* 2.8 48.2 - - + -
557D GLU* 3.4 29.1 + - - -
561D LYS* 4.6 15.7 - - - +
566D LEU* 6.3 1.3 - - + -
452F LEU* 5.2 2.5 - - + -
453F ILE* 4.4 9.2 + - - +
454F HIS* 3.6 1.5 - - - +
465F MET 4.2 0.8 - - - -
466F MET* 1.3 70.0 - - - +
468F ILE* 1.3 63.0 + - + +
469F SER* 3.5 13.3 + - - -
470F LYS* 3.5 29.4 - - + +
471F LEU* 2.2 40.9 - - + +
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Residues in contact with ILE 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LYS* 3.1 42.2 - - + +
398F VAL* 6.2 0.9 - - + -
402F LEU* 4.1 22.4 - - + -
441F VAL* 5.1 2.9 - - + -
443F VAL* 6.3 0.9 - - + -
452F LEU* 6.1 1.1 - - + +
453F ILE* 3.2 14.6 - - - +
454F HIS* 2.6 63.7 + - + +
455F LEU* 5.8 1.1 - - + -
466F MET 3.0 2.6 + - - -
467F HIS* 1.3 78.9 + - + +
469F SER* 1.3 52.5 + - - +
471F LEU* 2.7 6.9 - - - +
472F LYS* 2.5 47.0 - - + +
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Residues in contact with SER 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LYS* 4.3 18.4 - - - +
557D GLU* 3.5 15.5 + - - -
569D HIS* 5.2 6.8 + - - -
467F HIS* 3.3 19.4 + - - -
468F ILE* 1.3 74.3 - - - +
470F LYS* 1.3 63.6 + - - +
471F LEU* 3.1 2.9 - - - -
472F LYS* 2.5 31.2 + - - +
473F ASP* 2.7 15.9 + - - +
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Residues in contact with LYS 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D GLU* 5.7 1.3 - - - +
561D LYS* 4.0 17.3 - - - +
566D LEU* 6.2 4.0 - - + -
569D HIS* 4.6 17.8 + - + +
572D TRP* 3.2 39.4 - - + +
465F MET 5.6 0.6 + - - -
466F MET* 5.1 2.4 - - - +
467F HIS* 3.5 30.1 - - + +
469F SER* 1.3 79.4 - - - +
471F LEU* 1.3 76.1 + - + +
473F ASP* 2.9 11.7 + - - +
474F PHE* 2.5 32.3 + - - +
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Residues in contact with LEU 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D TRP* 5.8 0.2 - - - +
454F HIS* 3.5 14.6 - - + -
466F MET* 2.7 60.8 - - + -
467F HIS 2.2 36.6 - - - +
468F ILE* 2.7 22.4 - - - +
470F LYS* 1.3 90.7 - - + +
472F LYS* 1.3 56.7 + - - +
474F PHE* 2.4 39.2 + - + -
475F LEU* 2.6 18.5 + - - +
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Residues in contact with LYS 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LYS* 4.9 4.8 - - - +
385F LEU* 5.5 0.2 - - - -
402F LEU* 3.0 39.5 - - - +
405F GLU* 5.4 5.6 - - - +
406F LEU* 3.6 26.2 - - + +
441F VAL* 5.0 7.9 - - - -
454F HIS* 2.7 36.3 - - + +
468F ILE* 2.5 32.2 + - + +
469F SER* 2.5 19.0 + - - +
471F LEU* 1.3 73.3 - - - +
473F ASP* 1.3 65.6 + - - +
475F LEU* 2.7 41.3 + - + +
476F ILE* 3.2 7.3 + - - +
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Residues in contact with ASP 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D TRP* 6.0 2.5 - - + -
405F GLU* 4.3 12.3 - - - +
409F ASN* 6.1 1.0 - - - -
469F SER* 2.7 15.3 + - - +
470F LYS* 2.9 10.1 - - - +
472F LYS* 1.3 81.1 - - - +
474F PHE* 1.3 58.5 + - - +
476F ILE* 2.7 47.6 - - + +
477F LYS* 2.8 5.9 - - - +
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Residues in contact with PHE 474 (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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493D GLN* 5.4 8.7 - - - +
572D TRP* 4.4 11.0 - - + +
439F PHE* 3.8 21.5 - + - -
454F HIS* 5.0 2.2 - + - -
466F MET* 3.4 22.9 - - + -
470F LYS 2.5 6.2 + - - +
471F LEU* 2.4 52.2 + - + +
473F ASP* 1.3 68.4 - - - +
475F LEU* 1.3 72.7 + - + -
476F ILE 3.2 0.2 - - - -
477F LYS* 2.8 25.6 - - + +
478F TYR* 2.6 64.0 + + - -
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Residues in contact with LEU 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F LYS* 3.3 27.6 - - - +
383F VAL* 6.1 2.2 - - + -
406F LEU* 5.7 3.4 - - + -
411F ILE* 4.9 8.3 - - + -
439F PHE* 4.4 12.1 - - + -
454F HIS* 4.2 8.7 - - + -
471F LEU 2.6 29.9 + - - +
472F LYS* 2.7 37.7 - - + +
474F PHE* 1.3 109.2 - - + +
476F ILE* 1.3 66.0 + - - +
478F TYR* 2.8 27.4 + - + +
479F ILE* 3.1 11.1 + - - +
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Residues in contact with ILE 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F LYS* 4.0 1.1 - - - +
409F ASN* 5.8 11.7 - - + -
472F LYS 3.2 4.7 - - - +
473F ASP* 2.7 70.2 - - + +
475F LEU* 1.3 75.0 - - - +
477F LYS* 1.3 84.6 + - + +
479F ILE* 3.8 17.2 + - + +
480F SER* 3.5 14.4 + - - -
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Residues in contact with LYS 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D GLN* 5.8 2.0 - - - -
571D GLY 3.9 5.7 + - - -
572D TRP* 3.0 50.1 + - + +
573D TYR 5.9 1.1 - - - -
473F ASP 2.8 16.2 - - - +
474F PHE* 2.8 35.1 + - + +
476F ILE* 1.3 84.8 - - + +
478F TYR* 1.3 66.8 + - - +
480F SER* 2.3 34.2 + - - +
481F SER* 3.2 6.5 + - - +
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Residues in contact with TYR 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D LEU* 4.9 12.8 - - + -
577D CYS* 4.3 21.4 - - - +
578D PRO* 5.8 2.1 - - - +
376F PRO* 4.6 19.1 - - + -
382F LYS* 5.2 4.5 - - + -
438F LEU* 4.1 15.9 - - + +
439F PHE* 3.6 27.8 - + - -
458F ARG* 3.6 20.8 + - - -
474F PHE* 2.6 39.6 + + - -
475F LEU* 2.8 24.0 - - + +
477F LYS* 1.3 71.6 - - - +
479F ILE* 1.3 66.5 + - + +
481F SER* 2.9 19.9 + - - -
482F ALA* 2.9 12.6 + - + +
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Residues in contact with ILE 479 (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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376F PRO* 5.6 4.3 - - + -
377F CYS* 4.4 19.5 - - + +
382F LYS* 3.3 36.1 - - + +
410F GLY 4.7 14.8 - - - +
411F ILE* 5.1 1.3 - - + -
475F LEU 3.3 10.1 - - - +
476F ILE* 3.8 14.4 - - + +
477F LYS 2.9 2.4 + - - -
478F TYR* 1.3 75.6 - - + +
480F SER* 1.3 57.2 + - - +
482F ALA* 4.4 3.4 - - - -
483F LYS* 2.7 37.7 + - + +
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Residues in contact with SER 480 (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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476F ILE 3.5 5.9 + - - -
477F LYS* 2.3 39.9 + - - +
479F ILE* 1.3 78.0 - - - +
481F SER* 1.3 61.0 + - - -
483F LYS* 3.4 3.4 - - - +
484F ASN* 2.5 38.0 + - - +
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Residues in contact with SER 481 (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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574D ARG 5.5 3.6 - - - -
576D LEU* 3.3 40.3 - - - +
579D ARG* 5.3 0.5 + - - -
477F LYS* 3.2 5.3 + - - -
478F TYR* 2.9 13.5 + - - -
480F SER* 1.3 80.2 + - - +
482F ALA* 1.3 75.8 + - - +
484F ASN* 3.1 25.0 - - - +
485F VAL 3.5 3.5 + - - -
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Residues in contact with ALA 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D LEU* 4.0 13.7 - - + -
577D CYS* 5.8 2.7 - - - -
579D ARG* 5.1 5.0 + - - +
375F HIS* 3.3 12.5 - - - -
376F PRO* 3.2 32.8 - - + -
377F CYS* 4.9 0.2 - - - -
478F TYR* 3.1 21.5 - - + +
479F ILE 3.4 2.5 - - - +
481F SER* 1.3 85.2 + - - +
483F LYS* 1.3 68.5 + - - +
484F ASN 3.1 0.2 + - - -
485F VAL* 3.5 10.0 + - - +
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Residues in contact with LYS 483 (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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113F GLU* 3.8 28.0 + - - +
265F LYS* 4.1 21.1 - - - +
266F PHE* 4.8 3.2 - - + -
375F HIS* 3.7 3.9 + - - -
377F CYS* 3.4 25.2 - - - -
479F ILE* 2.7 24.4 + - + +
480F SER* 3.4 4.0 - - - +
482F ALA* 1.3 71.1 - - - +
484F ASN* 1.3 79.7 + - - +
485F VAL* 2.5 28.1 - - - +
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Residues in contact with ASN 484 (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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408E GLU* 5.6 5.0 + - - +
265F LYS* 3.7 13.0 + - - -
480F SER* 2.5 31.8 + - - +
481F SER* 3.1 13.2 - - - +
482F ALA 3.1 0.6 + - - -
483F LYS* 1.3 86.8 + - - +
485F VAL* 1.3 87.1 - - - +
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Residues in contact with VAL 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ARG* 2.6 47.2 + - - +
461D LYS* 5.3 9.0 - - - +
579D ARG* 5.7 7.6 - - - +
265F LYS* 3.3 49.7 + - + +
375F HIS* 5.0 3.4 - - + -
481F SER 3.5 6.9 + - - -
482F ALA 3.5 9.1 + - - +
483F LYS 2.5 31.4 - - - +
484F ASN* 1.3 91.5 - - - +
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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