Contacts of the helix formed by residues 544 - 571 (chain A) in PDB entry 2K1K
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 THR 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A PRO 4.2 9.4 - - - -
539A VAL* 4.8 4.9 - - + -
540A SER* 4.5 11.0 - - - +
542A GLY* 5.0 0.9 - - - -
543A LEU* 1.3 85.8 - - - +
545A GLY* 1.3 66.7 + - - +
546A GLY* 3.2 9.9 + - - -
547A GLU* 2.8 42.1 + - + +
548A ILE* 2.9 18.9 + - - +
544B THR* 5.4 2.8 + - - -
547B GLU* 5.8 0.3 - - - +
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Residues in contact with GLY 545 (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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537A PRO 5.1 0.8 + - - -
538A PRO 4.2 9.1 + - - -
544A THR* 1.3 73.2 - - - +
546A GLY* 1.3 63.3 + - - +
548A ILE* 3.2 10.9 + - - +
549A VAL* 3.1 32.6 + - - +
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Residues in contact with GLY 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A THR* 3.2 7.3 + - - -
545A GLY* 1.3 76.3 - - - +
547A GLU* 1.3 57.1 + - - +
549A VAL* 3.2 8.8 - - - +
550A ALA* 2.9 31.9 + - - +
547B GLU* 3.0 32.8 - - - +
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLY* 2.8 31.2 - - - +
543A LEU* 3.0 20.7 + - + -
544A THR* 2.8 34.3 + - + +
546A GLY* 1.3 75.2 - - - +
548A ILE* 1.3 64.2 + - - +
551A VAL* 3.1 13.1 + - + +
544B THR* 5.8 0.7 - - - +
546B GLY* 3.0 36.1 - - - +
547B GLU* 5.9 0.2 - - + -
549B VAL* 4.7 4.2 - - - +
550B ALA* 3.0 31.0 - - + +
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 4.7 11.0 - - - +
537A PRO 5.1 0.2 - - - +
543A LEU* 3.3 39.7 - - + -
544A THR 2.9 30.8 + - - +
545A GLY* 3.2 8.9 + - - +
547A GLU* 1.3 74.1 - - - +
549A VAL* 1.3 70.6 + - + +
550A ALA 3.1 0.3 + - - -
551A VAL* 3.2 7.7 + - - +
552A ILE* 3.1 25.7 + - + +
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Residues in contact with VAL 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLY* 3.1 17.4 + - - +
546A GLY* 3.2 18.2 - - - +
548A ILE* 1.3 80.1 - - + +
550A ALA* 1.3 63.0 + - + +
552A ILE* 2.9 26.4 - - + +
553A PHE* 3.0 20.6 + - + +
547B GLU* 4.7 4.0 - - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLY 2.9 21.6 + - - +
548A ILE 3.1 0.2 - - - -
549A VAL* 1.3 78.8 - - + +
551A VAL* 1.3 65.9 + - - +
553A PHE* 3.1 3.7 + - - +
554A GLY 3.1 19.1 + - - -
547B GLU* 3.0 33.7 - - + +
550B ALA* 3.2 11.2 - - + -
551B VAL* 3.2 22.0 - - + +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A GLU* 3.1 17.7 + - + +
548A ILE* 3.2 8.3 + - - +
550A ALA* 1.3 76.3 - - - +
552A ILE* 1.3 59.1 + - - +
554A GLY 3.4 0.2 + - - -
555A LEU* 2.8 41.5 + - + +
550B ALA* 3.2 29.6 - - + +
553B PHE* 4.7 10.5 - - + -
554B GLY* 3.7 19.7 - - - +
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Residues in contact with ILE 552 (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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548A ILE* 3.1 16.0 + - + +
549A VAL* 2.9 32.8 - - + +
551A VAL* 1.3 81.0 - - - +
553A PHE* 1.3 57.2 + - - +
555A LEU* 4.1 11.2 - - + -
556A LEU* 2.8 63.3 + - + +
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Residues in contact with PHE 553 (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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549A VAL* 3.0 22.2 + - + +
550A ALA* 3.1 8.9 + - - +
552A ILE* 1.3 77.6 - - - +
554A GLY* 1.3 60.7 + - - +
556A LEU* 4.2 2.1 - - - +
557A LEU* 3.2 53.8 + - + +
551B VAL* 4.6 9.4 - - + -
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Residues in contact with GLY 554 (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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550A ALA 3.1 7.3 + - - -
553A PHE* 1.3 79.5 - - - +
555A LEU* 1.3 57.0 + - - +
557A LEU* 4.9 2.0 - - - -
558A GLY* 2.7 32.7 + - - -
551B VAL* 3.8 26.4 - - - +
555B LEU* 3.2 21.4 - - - +
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Residues in contact with LEU 555 (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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551A VAL* 2.8 29.3 + - + +
552A ILE* 4.0 10.8 - - + +
554A GLY* 1.3 75.8 - - - +
556A LEU* 1.3 70.3 + - + +
559A ALA* 3.2 25.0 + - + +
554B GLY* 3.2 16.5 - - - +
558B GLY* 3.4 29.2 - - - +
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Residues in contact with LEU 556 (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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552A ILE* 2.8 53.6 + - + +
553A PHE* 4.2 2.2 - - - +
555A LEU* 1.3 83.2 - - + +
557A LEU* 1.3 59.4 + - + +
559A ALA* 4.5 0.5 - - - +
560A ALA* 2.9 34.2 + - - +
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Residues in contact with LEU 557 (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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553A PHE* 3.2 49.6 + - + +
554A GLY* 4.7 1.8 - - - +
556A LEU* 1.3 78.8 - - + +
558A GLY* 1.3 64.0 + - - +
560A ALA* 4.2 6.3 - - + -
561A LEU* 3.1 30.7 + - + +
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Residues in contact with GLY 558 (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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554A GLY 2.7 23.1 + - - -
555A LEU* 4.8 0.2 - - - -
556A LEU 3.1 0.4 - - - -
557A LEU* 1.3 79.2 - - - +
559A ALA* 1.3 61.8 + - - +
561A LEU* 4.1 1.6 - - - +
562A LEU* 3.1 23.1 + - - +
555B LEU* 3.5 23.7 - - - +
559B ALA* 4.3 8.2 - - - +
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Residues in contact with ALA 559 (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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555A LEU* 3.2 18.8 + - + +
556A LEU* 4.5 0.9 - - - +
558A GLY* 1.3 72.4 - - - +
560A ALA* 1.3 61.3 + - - +
562A LEU* 3.0 1.6 + - - +
563A LEU* 2.8 31.6 + - - +
558B GLY 4.3 10.8 - - - +
559B ALA* 4.6 4.8 - - - +
562B LEU* 3.6 34.9 - - + +
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Residues in contact with ALA 560 (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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556A LEU 2.9 23.3 + - - +
557A LEU* 4.2 8.1 - - + +
559A ALA* 1.3 80.0 - - - +
561A LEU* 1.3 63.9 + - - +
563A LEU* 3.3 5.7 + - - +
564A GLY* 3.1 17.8 + - - -
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Residues in contact with LEU 561 (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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557A LEU* 3.1 21.4 + - + +
558A GLY* 4.1 1.6 - - - +
560A ALA* 1.3 80.0 - - - +
562A LEU* 1.3 61.9 + - - +
564A GLY* 3.4 2.0 + - - -
565A ILE* 3.1 46.9 + - + +
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Residues in contact with LEU 562 (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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558A GLY 3.1 14.4 + - - +
559A ALA 3.0 9.3 + - - +
561A LEU* 1.3 75.9 - - - +
563A LEU* 1.3 67.4 + - - +
564A GLY 3.2 0.3 + - - -
565A ILE* 3.3 5.2 + - - +
566A LEU* 3.1 47.2 + - + +
559B ALA* 3.2 46.7 - - + +
562B LEU* 3.4 14.1 - - + -
563B LEU* 4.0 20.0 - - + -
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Residues in contact with LEU 563 (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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559A ALA 2.8 17.9 + - - +
560A ALA* 3.8 6.3 - - - +
562A LEU* 1.3 73.7 - - - +
564A GLY* 1.3 63.4 + - - +
566A LEU* 3.2 11.8 + - + +
567A VAL* 3.1 34.9 + - + +
571A ARG* 6.0 2.2 - - - +
562B LEU* 4.0 14.5 - - + +
566B LEU* 4.1 33.9 - - + -
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Residues in contact with GLY 564 (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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560A ALA 3.1 14.8 + - - -
561A LEU* 3.8 3.4 - - - -
562A LEU 3.1 0.4 - - - -
563A LEU* 1.3 76.5 - - - +
565A ILE* 1.3 63.4 + - - +
567A VAL* 2.8 18.0 + - - +
568A PHE* 2.8 32.6 + - - -
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Residues in contact with ILE 565 (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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561A LEU* 3.1 35.1 + - + +
562A LEU* 3.8 5.6 - - + +
564A GLY* 1.3 73.4 - - - +
566A LEU* 1.3 57.9 + - + +
568A PHE* 3.6 14.7 - - + -
569A ARG* 2.8 54.3 + - - +
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Residues in contact with LEU 566 (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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562A LEU* 3.1 39.8 + - + +
563A LEU* 3.3 14.1 - - + +
564A GLY 3.0 0.8 - - - -
565A ILE* 1.3 79.6 - - + +
567A VAL* 1.3 60.2 + - + +
569A ARG* 3.5 24.7 - - + +
571A ARG* 3.4 28.3 - - - +
563B LEU* 4.6 12.1 - - + -
566B LEU* 3.2 30.5 - - + -
571B ARG* 4.8 17.5 - - - +
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Residues in contact with VAL 567 (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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563A LEU* 3.3 25.1 - - + +
564A GLY* 2.8 9.2 + - - +
566A LEU* 1.3 78.1 - - + +
568A PHE* 1.3 64.6 + - + +
569A ARG 3.3 0.2 - - - -
571A ARG* 3.4 38.9 + - - +
572A ARG* 3.3 44.2 + - + +
573A ALA 4.8 2.5 - - - +
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Residues in contact with PHE 568 (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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564A GLY* 2.8 37.2 + - - +
565A ILE* 3.7 17.5 - - + +
567A VAL* 1.3 77.4 - - + +
569A ARG* 1.3 69.3 + - - +
570A SER* 3.4 0.9 - - - -
571A ARG 5.0 0.2 - - - -
572A ARG* 3.3 47.6 - - - +
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Residues in contact with ARG 569 (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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565A ILE* 2.8 34.7 + - - +
566A LEU* 3.5 25.6 - - + +
567A VAL 3.3 0.2 - - - -
568A PHE* 1.3 80.5 - - - +
570A SER* 1.3 67.5 + - - +
571A ARG* 5.2 1.1 - - + -
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Residues in contact with SER 570 (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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568A PHE 3.4 1.5 - - - -
569A ARG* 1.3 85.5 - - - +
571A ARG* 1.3 68.8 + - - +
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Residues in contact with ARG 571 (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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563A LEU* 6.0 2.2 - - - +
566A LEU* 3.4 34.6 + - - +
567A VAL* 3.4 28.2 + - - +
569A ARG* 5.7 0.4 - - - -
570A SER* 1.3 80.8 - - - +
572A ARG* 1.3 58.8 + - - +
573A ALA* 2.8 20.0 + - + +
566B LEU* 5.1 4.4 - - - +
571B ARG* 3.2 47.6 - - - +
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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