Contacts of the helix formed by residues 546 - 568 (chain A) in PDB entry 1F7U
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 GLU 546 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.8 10.1 - - - -
466A LYS* 3.4 30.5 - - + +
467A ARG* 2.9 53.9 + - - +
468A ILE* 4.9 2.4 + - - +
541A ALA* 3.8 2.8 + - - +
544A THR* 3.0 28.6 + - - +
545A HIS* 1.3 78.0 - - - +
547A PRO* 1.3 71.1 - - - +
548A THR* 3.7 13.1 - - + +
549A THR* 3.1 24.3 + - - +
550A VAL 4.0 0.2 + - - -
915B A 5.2 2.0 - - - +
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Residues in contact with PRO 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 4.5 15.9 - - + -
171A PHE* 3.6 29.4 - - + -
463A MET* 3.6 45.5 - - + +
467A ARG* 3.9 18.6 - - + +
545A HIS 3.7 8.3 - - - +
546A GLU* 1.3 84.5 - - + +
548A THR* 1.3 57.7 + - - +
550A VAL* 2.9 10.2 + - - +
551A VAL* 2.8 26.5 + - - +
599A LEU* 4.0 3.8 - - + +
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Residues in contact with THR 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A MET 3.3 17.9 + - - -
464A GLN* 2.6 22.7 + - - -
465A GLY 3.8 9.4 + - - +
466A LYS* 4.1 22.2 - - + +
546A GLU* 3.7 17.3 - - + -
547A PRO* 1.3 80.7 - - - +
549A THR* 1.3 59.8 + - - +
551A VAL* 3.9 4.5 - - - -
552A THR* 2.7 46.8 + - - +
914B A 4.0 9.3 - - - +
915B A 4.3 9.6 - - - +
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Residues in contact with THR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A VAL* 3.6 20.7 - - + +
540A ASN* 3.6 26.2 + - + +
541A ALA* 3.9 20.4 - - - +
544A THR* 2.9 25.8 + - - +
546A GLU* 3.1 16.2 + - - +
547A PRO 3.1 0.8 - - - -
548A THR* 1.3 82.6 - - - +
550A VAL* 1.3 61.9 + - - +
552A THR* 4.2 3.6 - - - -
553A TYR* 3.7 10.7 + - - +
915B A 4.9 4.7 + - - -
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.9 22.0 - - + -
534A TYR* 5.0 5.8 - - + -
537A VAL* 4.0 13.7 - - + -
538A LEU* 4.5 3.8 - - + -
541A ALA* 3.9 20.0 - - + -
547A PRO 2.9 7.8 + - - +
549A THR* 1.3 76.6 - - - +
551A VAL* 1.3 65.8 + - - +
553A TYR* 3.1 4.9 + - - +
554A LEU* 3.0 40.6 + - + +
595A GLY* 4.3 12.6 - - - +
598A LEU* 4.1 13.2 - - + -
599A LEU* 4.1 17.3 - - + -
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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
----------------------------------------------------------
460A ILE* 4.1 10.3 - - + -
463A MET* 3.9 24.9 - - + +
464A GLN* 4.1 21.1 - - + +
489A LEU* 5.6 0.4 - - + -
547A PRO 2.8 19.0 + - - +
548A THR* 3.3 7.8 + - - +
550A VAL* 1.3 76.8 - - - +
552A THR* 1.3 62.9 + - - +
554A LEU* 3.1 8.8 + - + +
555A PHE* 3.1 47.6 + - + -
599A LEU* 3.6 24.5 - - + -
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Residues in contact with THR 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLN 4.8 1.2 + - - -
548A THR* 2.7 38.8 + - - -
549A THR* 4.2 4.5 - - - -
551A VAL* 1.3 73.4 - - - +
553A TYR* 1.3 62.3 + - - +
555A PHE* 3.3 7.6 + - - +
556A LYS* 3.2 44.3 + - + +
914B A 3.9 26.5 + - - +
922B C 5.0 9.0 - - - +
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Residues in contact with TYR 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 2.8 39.9 + - + -
531A LEU* 3.9 3.1 - - - -
533A GLN* 4.1 18.8 - - + -
534A TYR* 3.4 38.1 + + - +
537A VAL* 3.7 24.9 - - + -
549A THR 3.7 12.1 + - - +
550A VAL 3.1 8.3 + - - +
552A THR* 1.3 77.7 - - - +
554A LEU* 1.3 76.5 + - + +
556A LYS* 3.0 17.4 + - + +
557A LEU* 2.8 40.6 + - + +
591A VAL* 3.6 23.0 - - + +
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 4.2 16.4 - - + -
534A TYR* 4.9 1.1 - - + -
550A VAL* 3.0 16.8 + - + +
551A VAL* 3.1 9.4 + - - +
553A TYR* 1.3 98.2 - - + +
555A PHE* 1.3 58.6 + - - +
557A LEU* 3.6 12.6 - - + +
558A THR* 2.7 34.5 + - - +
591A VAL 4.6 1.6 - - - +
592A LEU* 4.0 20.4 - - + +
595A GLY* 3.8 31.2 - - - -
596A MET* 3.9 8.7 - - + +
599A LEU* 3.8 29.6 - - + -
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Residues in contact with PHE 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ILE* 4.0 7.0 - - + -
464A GLN* 3.7 15.0 - - - -
484A ASP* 3.4 61.2 - - - +
485A THR 3.4 21.5 - - - -
488A TYR* 3.9 15.5 - + - -
489A LEU* 3.8 24.7 - - + -
551A VAL* 3.1 44.4 + - + -
552A THR* 3.8 8.3 - - - +
553A TYR 3.1 0.4 - - - -
554A LEU* 1.3 75.0 - - - +
556A LYS* 1.3 66.7 + - + +
558A THR* 3.4 1.6 + - - -
559A HIS* 2.9 36.8 + + + +
923B G 5.2 0.9 - - - +
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Residues in contact with LYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN 4.8 11.7 + - - -
530A LEU* 3.7 22.5 - - + +
533A GLN* 5.5 3.9 + - - +
552A THR* 3.2 35.5 + - + +
553A TYR* 3.0 17.9 + - + +
555A PHE* 1.3 75.6 - - - +
557A LEU* 1.3 64.3 + - - +
559A HIS* 3.7 9.0 - - + +
560A GLN* 3.3 22.5 + - - +
922B C 4.3 21.5 - - - +
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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
----------------------------------------------------------
527A LEU* 3.8 22.0 - - + -
530A LEU* 4.3 13.6 - - + +
531A LEU* 3.9 18.4 - - + -
553A TYR* 2.8 34.1 + - + +
554A LEU* 3.6 9.6 - - + +
555A PHE 3.2 0.2 - - - -
556A LYS* 1.3 76.8 - - - +
558A THR* 1.3 60.3 + - + +
560A GLN* 3.2 5.7 + - - +
561A VAL* 3.0 36.2 + - + +
588A ALA* 4.0 7.4 - - + +
591A VAL* 3.8 25.6 - - + -
592A LEU* 3.9 24.7 - - + +
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Residues in contact with THR 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A TYR* 3.3 26.2 - - - -
489A LEU* 3.6 10.0 - - + +
492A ALA* 3.8 20.6 - - + -
496A LEU* 6.3 0.4 - - + -
554A LEU 2.7 25.1 + - - +
555A PHE* 3.4 8.0 + - - -
557A LEU* 1.3 75.6 - - + +
559A HIS* 1.3 57.6 + - - +
561A VAL* 3.7 8.7 - - + +
562A SER* 2.7 37.9 + - - -
592A LEU* 3.6 31.2 - - + -
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Residues in contact with HIS 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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484A ASP* 2.9 26.1 + - - -
488A TYR* 3.2 29.0 + + - -
555A PHE* 2.9 30.7 + + + +
556A LYS* 3.7 9.0 - - + +
557A LEU 3.3 0.2 - - - -
558A THR* 1.3 75.9 + - - +
560A GLN* 1.3 57.6 + - - +
562A SER* 3.4 3.3 + - - -
563A SER* 2.9 30.7 + - - -
923B G 3.2 37.8 + - - -
924B G 4.2 9.9 - - - -
940B C 4.4 5.5 + - - +
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Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 5.2 1.7 - - - +
523A ALA* 3.2 33.5 + - - +
526A LEU* 3.7 23.0 - - + +
527A LEU* 3.7 30.3 - - + +
530A LEU* 3.5 25.6 - - + +
556A LYS 3.3 2.8 + - - +
557A LEU 3.2 4.8 + - - +
558A THR 3.2 0.4 - - - -
559A HIS* 1.3 77.4 - - - +
561A VAL* 1.3 59.6 + - - +
563A SER* 3.2 14.2 + - - -
564A CYS* 2.8 36.1 + - - -
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Residues in contact with VAL 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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492A ALA* 5.4 6.1 - - + -
495A ARG* 6.3 1.8 - - + +
496A LEU* 3.6 38.4 - - + -
527A LEU* 3.8 13.0 - - + -
557A LEU* 3.0 25.5 + - + +
558A THR* 3.7 12.3 - - + +
559A HIS 3.4 0.2 - - - -
560A GLN* 1.3 74.1 - - - +
562A SER* 1.3 55.6 + - - +
564A CYS* 3.2 8.5 + - - +
565A TYR* 2.7 35.2 + - + +
585A TYR* 4.2 6.0 - - + -
588A ALA* 3.8 29.4 - - + +
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Residues in contact with SER 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A TYR* 3.2 12.0 + - - -
492A ALA* 5.0 6.1 - - - +
495A ARG* 3.8 18.8 + - - +
558A THR* 2.7 22.0 + - - -
559A HIS 3.6 1.6 - - - -
561A VAL* 1.3 77.6 - - - +
563A SER* 1.3 66.4 + - - +
565A TYR* 3.4 19.9 + - - +
566A ASP* 3.5 3.8 + - - +
939B C 3.9 2.0 + - - -
940B C 3.4 41.4 - - - +
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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
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523A ALA* 5.3 2.5 - - - -
559A HIS 2.9 18.8 + - - -
560A GLN* 3.5 25.0 + - - -
562A SER* 1.3 74.9 - - - +
564A CYS* 1.3 65.1 + - - +
566A ASP* 3.2 17.7 + - - +
567A VAL* 3.8 10.0 + - - +
940B C 3.8 12.4 + - - +
941B A 2.8 25.9 + - - +
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Residues in contact with CYS 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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523A ALA* 3.1 37.5 - - - -
527A LEU* 4.1 18.4 - - - -
560A GLN* 2.8 23.1 + - - +
561A VAL* 3.4 9.0 - - - +
563A SER* 1.3 77.9 - - - +
565A TYR* 1.3 58.1 + - - +
567A VAL* 2.9 9.8 + - - -
568A LEU* 2.7 42.6 + - + -
584A LEU* 6.3 0.2 - - + -
585A TYR* 3.0 20.3 + - + +
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Residues in contact with TYR 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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495A ARG* 3.3 50.8 - - + +
496A LEU* 5.4 6.3 - - + -
499A VAL* 3.6 26.0 - - + -
561A VAL* 2.7 19.2 + - + +
562A SER* 3.4 16.6 - - - +
563A SER 3.3 0.2 - - - -
564A CYS* 1.3 73.0 - - - +
566A ASP* 1.3 62.0 + - + +
569A TRP* 4.4 4.9 + + - -
585A TYR* 3.4 14.8 - + + -
935B C 2.9 51.4 + + - +
936B G 3.4 34.0 + - - +
937B A 3.5 13.7 - - - -
939B C 5.5 0.7 - - - -
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Residues in contact with ASP 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 SER 3.5 5.3 + - - +
563A SER 3.2 11.1 + - - +
564A CYS 3.0 1.0 + - - -
565A TYR* 1.3 83.6 - - + +
567A VAL* 1.3 66.2 + - + +
569A TRP* 3.9 13.5 + - - +
931B G 4.7 6.8 + - - -
940B C 3.1 37.1 + - - +
941B A 6.1 0.4 - - - -
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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
----------------------------------------------------------
523A ALA* 4.2 16.8 - - + -
563A SER 4.1 11.4 - - - +
564A CYS 2.9 7.8 + - - +
566A ASP* 1.3 92.0 - - + +
568A LEU* 1.3 81.4 + - + +
569A TRP* 3.7 10.8 + - - -
581A ARG* 4.7 3.1 + - - -
941B A 6.5 1.8 - - - -
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLU* 3.8 25.4 - - + +
523A ALA* 4.5 0.7 - - + -
524A ALA* 3.7 37.2 - - + +
564A CYS* 2.7 27.6 + - + +
567A VAL* 1.3 90.6 - - + +
569A TRP* 1.3 59.8 + - - +
581A ARG* 3.7 37.0 - - - +
584A LEU* 4.9 6.5 - - + -
585A TYR* 2.6 40.3 + - + +
935B C 2.9 9.8 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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