Contacts of the helix formed by residues 554 - 575 (chain A) in PDB entry 6R7X
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 VAL 554 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASN* 4.7 15.7 - - - +
401A ILE* 3.7 40.2 - - + -
552A ILE 3.8 1.2 + - - -
553A GLY* 1.3 69.7 - - - -
555A TRP* 1.3 70.5 + - + +
556A GLN 3.2 1.3 - - - -
557A LEU* 3.3 24.0 + - + +
558A ALA* 3.3 10.8 + - + +
704A PC1 3.3 37.3 - - + +
611B PHE* 6.0 0.7 - - + -
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Residues in contact with TRP 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 4.5 15.5 - - + +
405A LEU* 3.7 38.6 - - + -
494A THR 4.3 4.8 + - - -
495A PHE* 3.5 41.8 - + - -
498A TYR* 3.5 39.7 - + + +
499A LEU* 3.9 14.8 - - + -
502A PHE* 4.0 21.1 - + + -
552A ILE* 3.7 30.3 - - + -
553A GLY 3.2 1.0 - - - -
554A VAL* 1.3 82.0 - - + +
556A GLN* 1.3 60.0 + - - +
558A ALA* 3.3 13.1 + - + +
559A PHE* 2.9 42.5 + + + -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 2.7 44.7 + - - +
261A TRP* 3.3 24.5 + - - -
262A LYS* 3.5 26.7 - - + +
552A ILE* 3.4 19.4 - - + +
553A GLY 3.8 10.9 + - - +
554A VAL 3.2 0.8 - - - -
555A TRP* 1.3 78.3 - - - +
557A LEU* 1.3 56.2 + - - +
559A PHE* 3.5 4.0 + - - +
560A GLU* 3.0 51.6 + - - +
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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
----------------------------------------------------------
553A GLY 4.9 0.2 + - - -
554A VAL* 3.3 19.4 + - + +
556A GLN* 1.3 78.1 - - - +
558A ALA* 1.3 54.5 + - - +
560A GLU* 3.5 5.7 + - - +
561A THR* 2.6 46.7 + - - +
704A PC1 4.2 22.4 - - + -
711A UMQ 3.8 31.2 - - + -
611B PHE* 3.6 41.5 - - + -
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Residues in contact with ALA 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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405A LEU* 3.8 28.9 - - + -
502A PHE* 3.2 23.6 - - + -
554A VAL 3.3 9.0 + - - +
555A TRP* 3.3 21.6 + - + +
557A LEU* 1.3 79.2 - - - +
559A PHE* 1.3 56.7 + - - +
561A THR* 3.3 1.9 + - - -
562A MET 2.9 24.3 + - - -
704A PC1 3.8 13.4 - - + +
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Residues in contact with PHE 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 3.8 34.8 - + - -
218A PHE* 4.3 8.7 - + - -
258A LEU* 3.4 34.9 - - + +
498A TYR* 4.5 6.5 - + - -
501A LEU* 3.8 8.3 - - + -
502A PHE* 3.7 36.1 - + + -
505A PHE* 3.5 42.8 - + + -
552A ILE* 5.1 2.5 - - + -
555A TRP* 2.9 41.3 + + + +
556A GLN* 4.0 3.6 - - - +
558A ALA* 1.3 76.3 - - - +
560A GLU* 1.3 58.0 + - - +
562A MET* 3.4 6.0 + - - +
563A SER* 3.0 22.9 + - - -
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 4.0 23.2 - - + +
259A GLU* 4.9 2.9 - - - +
262A LYS* 4.5 12.5 + - - -
556A GLN* 3.0 41.4 + - - +
557A LEU* 3.9 6.0 - - - +
559A PHE* 1.3 72.6 - - - +
561A THR* 1.3 60.5 + - - +
563A SER* 3.3 4.5 + - - -
564A VAL* 2.9 33.9 + - + +
610A ALA* 5.4 8.2 - - - +
711A UMQ 3.4 35.4 - - + +
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 2.6 35.7 + - - +
558A ALA 3.7 4.0 - - - -
560A GLU* 1.3 73.4 - - - +
562A MET* 1.3 60.2 + - - +
564A VAL* 3.3 5.8 + - - +
565A ILE* 2.9 44.3 + - + +
704A PC1 4.2 26.7 - - + +
711A UMQ 4.0 38.0 - - + +
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Residues in contact with MET 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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409A PHE* 3.6 28.9 - - + -
413A PHE* 4.3 2.9 - - + -
502A PHE* 3.6 32.5 - - + +
505A PHE* 3.7 26.0 - - + +
506A GLY* 3.7 32.8 - - - +
509A SER* 5.3 2.0 - - - -
510A LEU* 3.8 21.8 - - - -
558A ALA 2.9 17.2 + - - +
559A PHE 3.6 5.6 - - - +
561A THR* 1.3 75.7 - - - +
563A SER* 1.3 56.5 + - - +
565A ILE* 3.4 5.0 + - - +
566A SER* 3.0 29.9 + - - -
704A PC1 5.7 0.8 - - - +
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Residues in contact with SER 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.4 0.5 - - - +
254A SER* 2.8 16.4 + - - -
255A THR* 4.5 1.2 + - - -
258A LEU* 4.2 12.8 - - - -
505A PHE* 4.2 8.9 - - - -
509A SER* 4.9 0.4 - - - -
559A PHE 3.0 16.5 + - - -
560A GLU* 3.3 5.8 + - - -
562A MET* 1.3 76.7 - - - +
564A VAL* 1.3 59.0 + - - +
566A SER* 3.3 18.3 + - - -
567A VAL* 3.5 13.9 - - - +
606A LYS* 2.6 37.4 + - - +
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Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 2.9 20.1 + - + +
561A THR* 3.8 6.1 - - - +
562A MET 3.2 0.2 - - - -
563A SER* 1.3 75.5 - - - +
565A ILE* 1.3 66.3 + - + +
566A SER 3.2 1.3 - - - -
567A VAL* 3.2 22.4 + - - +
568A VAL* 3.8 9.4 + - + +
603A LEU* 4.2 15.9 - - + +
606A LYS* 4.1 17.5 - - + -
607A PHE* 4.1 14.6 - - + -
711A UMQ 4.0 41.7 - - + -
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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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409A PHE* 4.2 26.2 - - + -
417A PHE* 5.1 1.3 - - + -
510A LEU* 3.8 17.7 - - + -
561A THR* 2.9 37.2 + - + +
562A MET* 3.9 5.8 - - + +
564A VAL* 1.3 76.9 - - + +
566A SER* 1.3 57.9 + - - +
568A VAL* 3.2 9.8 + - - +
569A THR* 3.0 33.8 + - - +
704A PC1 4.5 12.6 - - + -
710A UMQ 4.7 14.1 - - + -
711A UMQ 4.4 27.1 - - + -
901B UMQ 5.0 4.5 - - + -
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Residues in contact with SER 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.3 15.7 - - - +
254A SER* 5.5 0.3 + - - -
509A SER* 3.0 41.3 + - - -
510A LEU* 3.8 14.6 - - - +
562A MET* 3.0 15.4 + - - -
563A SER* 3.3 9.4 + - - -
565A ILE* 1.3 75.5 - - - +
567A VAL* 1.3 60.0 + - - +
569A THR* 3.8 2.9 - - - -
570A ASN* 2.9 33.8 + - - +
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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
----------------------------------------------------------
251A LEU* 3.7 25.1 - - + -
563A SER 3.5 16.8 - - - +
564A VAL 3.2 9.6 + - - +
565A ILE 3.2 0.6 - - - -
566A SER* 1.3 78.1 + - - +
568A VAL* 1.3 57.5 + - - +
570A ASN* 3.9 0.9 - - - +
571A CYS* 3.0 32.8 + - - +
599A GLU* 3.8 28.5 - - + +
602A LEU* 4.4 13.2 - - + -
603A LEU* 3.9 21.3 - - + +
606A LYS* 3.7 20.6 - - - -
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Residues in contact with VAL 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A VAL* 4.1 11.9 - - + +
565A ILE* 3.2 8.9 + - - +
567A VAL* 1.3 76.4 - - + +
569A THR* 1.3 58.5 + - - +
571A CYS* 4.0 0.7 - - - +
572A ALA* 2.9 29.1 + - - +
599A GLU* 3.4 26.7 - - - +
603A LEU* 5.0 4.3 - - + -
705A UMQ 3.8 24.3 - - + +
600B HIS* 4.6 14.6 - - + +
901B UMQ 4.5 25.4 - - + -
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Residues in contact with THR 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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417A PHE* 3.8 19.3 - - + -
421A PHE* 3.8 24.5 - - + -
510A LEU* 3.3 34.3 - - + +
511A PHE* 3.9 9.9 - - + -
565A ILE* 3.0 18.3 + - - +
566A SER 4.0 1.8 - - - -
568A VAL* 1.3 77.1 - - - +
570A ASN* 1.3 57.6 + - - +
572A ALA* 3.4 2.6 + - - +
573A LEU* 3.0 29.3 + - + +
901B UMQ 3.8 17.5 - - - +
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Residues in contact with ASN 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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247A ALA* 5.0 3.6 - - + +
250A ASN* 4.9 4.0 - - - +
251A LEU* 3.9 26.1 - - + +
509A SER 3.6 9.3 + - - -
510A LEU 2.9 21.9 - - - +
511A PHE* 4.1 0.9 - - - -
512A SER* 3.2 27.7 + - - -
513A CYS* 3.6 23.1 + - - +
566A SER 2.9 19.6 + - - +
567A VAL 3.9 2.7 - - - +
569A THR* 1.3 76.3 - - - +
571A CYS* 1.3 59.4 + - - +
573A LEU* 3.3 5.5 + - - +
574A ILE* 2.9 33.7 + - - +
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Residues in contact with CYS 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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247A ALA* 6.2 0.4 - - - -
251A LEU* 5.5 1.1 - - - -
567A VAL* 3.0 21.4 + - - +
568A VAL* 4.0 2.9 - - - +
570A ASN* 1.3 78.5 - - - +
572A ALA* 1.3 58.8 + - - +
574A ILE* 3.2 15.1 + - - +
575A GLY* 3.0 23.9 + - - -
595A VAL* 3.4 27.0 - - + +
598A VAL* 4.6 6.7 - - - -
599A GLU* 3.6 38.1 - - + -
602A LEU* 4.6 16.2 - - - -
705A UMQ 4.5 2.9 - - + -
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Residues in contact with ALA 572 (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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421A PHE* 3.7 23.3 - - + -
568A VAL 2.9 19.5 + - - +
569A THR 3.8 1.3 - - - +
571A CYS* 1.3 76.8 - - - +
573A LEU* 1.3 58.3 + - - +
574A ILE 3.4 0.2 - - - -
575A GLY 3.8 1.2 + - - -
576A MET* 3.3 31.0 + - + +
705A UMQ 3.8 17.4 - - + +
901B UMQ 3.7 27.4 - - + -
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Residues in contact with LEU 573 (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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243A TYR* 5.0 1.6 - - - -
420A ALA* 3.9 23.8 - - + +
421A PHE* 4.1 10.3 - - + -
426A MET* 3.8 26.5 - - + +
429A LEU* 4.4 2.0 - - + -
510A LEU 4.1 2.9 - - - +
511A PHE* 3.6 42.4 - - + -
513A CYS* 4.7 5.2 - - + -
514A VAL* 3.8 30.5 - - + +
569A THR* 3.0 20.8 + - + +
570A ASN* 3.3 7.6 + - - +
572A ALA* 1.3 76.8 - - - +
574A ILE* 1.3 63.6 + - - +
576A MET* 3.7 9.4 + - - +
577A SER* 3.7 13.2 + - - -
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Residues in contact with ILE 574 (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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242A LYS 4.9 1.6 - - - +
243A TYR* 3.3 40.4 - - + +
244A VAL* 5.4 4.3 - - + -
247A ALA* 3.7 17.9 - - + -
513A CYS* 4.0 7.9 - - - -
570A ASN 2.9 20.1 + - - +
571A CYS* 3.2 22.9 + - - +
573A LEU* 1.3 77.3 - - - +
575A GLY* 1.3 58.3 + - - +
576A MET 3.0 3.6 + - - -
577A SER* 2.8 24.6 + - - -
580A VAL* 3.5 31.7 - - + +
595A VAL* 4.5 10.3 - - + -
598A VAL* 6.0 4.3 - - + -
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Residues in contact with GLY 575 (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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571A CYS 3.0 11.8 + - - -
572A ALA 3.8 0.6 + - - -
573A LEU 3.4 0.4 - - - -
574A ILE* 1.3 74.5 - - - +
576A MET* 1.3 59.2 + - - -
581A ASN* 4.1 6.8 + - - -
591A LEU* 4.3 10.7 - - - +
595A VAL* 4.2 13.0 - - - +
705A UMQ 3.3 51.6 - - - +
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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
------------------------------------------------------------
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