Contacts of the helix formed by residues 536 - 561 (chain A) in PDB entry 3L9X
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 GLY 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A LEU* 1.3 78.0 - - - +
537A PRO* 1.3 74.2 - - - +
538A TYR 3.2 3.3 + - - -
539A GLU* 3.4 4.4 + - - +
540A ALA* 3.0 21.7 + - - +
1011B PRO* 6.2 0.4 - - - -
1012B HIS* 3.4 23.1 + - - -
2402B ZN 3.9 17.9 - - - -
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Residues in contact with PRO 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 4.7 1.2 + - - -
531A GLU* 3.7 37.7 - - + +
535A LEU 3.6 3.6 - - - +
536A GLY* 1.3 82.4 - - - +
538A TYR* 1.3 63.1 + - - +
540A ALA* 3.4 2.4 + - - +
541A ARG* 3.0 23.6 + - - +
1012B HIS* 5.3 0.7 - - + -
1036B TYR 4.2 1.3 - - - +
1037B GLN* 3.2 54.5 - - + +
1040B PRO* 3.7 23.6 - - + +
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLY 3.2 0.8 - - - -
537A PRO* 1.3 76.7 - - - +
539A GLU* 1.3 68.0 + - - +
540A ALA 3.1 0.3 + - - -
541A ARG* 3.1 17.0 + - - +
542A GLU* 3.0 54.9 + - + +
1076A LEU* 3.9 23.0 - - - +
1080A LYS* 4.2 3.3 - - - -
1009B PRO* 3.3 28.3 - - + +
1010B TYR* 3.7 17.5 - + - -
1011B PRO* 6.3 0.2 - - + -
1036B TYR* 3.5 45.8 + + + +
1040B PRO* 3.7 24.0 - - + +
1042B PHE* 3.6 21.9 - + - -
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Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A LEU* 3.8 15.6 - - + +
536A GLY* 3.4 12.5 + - - +
538A TYR* 1.3 80.9 - - - +
540A ALA* 1.3 58.2 + - - +
542A GLU* 3.4 14.2 + - + +
543A ARG* 3.0 61.1 + - + +
1009B PRO 5.0 0.2 + - - -
1010B TYR* 4.1 21.6 - - + -
1013B HIS* 2.7 36.7 + - - -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 3.6 25.0 - - + +
530A LEU* 4.1 20.8 - - + +
531A GLU* 4.4 4.0 - - + +
535A LEU* 3.7 20.1 - - + +
536A GLY 3.0 17.0 + - - +
537A PRO* 3.5 8.7 - - + +
538A TYR 3.1 0.2 - - - -
539A GLU* 1.3 73.9 - - - +
541A ARG* 1.3 63.9 + - - +
543A ARG* 3.3 6.2 + - - +
544A ALA 3.1 17.3 + - - -
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Residues in contact with ARG 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 3.4 28.6 - - - +
537A PRO 3.0 17.0 + - - +
538A TYR* 3.1 19.7 + - - +
540A ALA* 1.3 71.8 - - - +
542A GLU* 1.3 65.6 + - - +
544A ALA* 3.2 4.3 + - - +
545A ASP* 2.7 68.8 + - - +
1041A ASP 3.7 14.3 + - - -
1042A PHE* 3.2 25.5 + - - +
1076A LEU* 6.1 0.2 - - - +
1040B PRO* 2.8 29.8 + - + +
1041B ASP* 3.4 29.2 - - - +
1042B PHE* 3.5 22.4 - - - -
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Residues in contact with GLU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TYR* 3.0 42.0 + - + +
539A GLU* 3.5 11.6 - - + +
541A ARG* 1.3 83.7 - - - +
543A ARG* 1.3 57.4 + - + +
545A ASP* 3.1 12.2 + - - +
546A VAL* 3.0 32.6 + - + +
1080A LYS* 2.7 35.4 + - - -
1010B TYR* 2.6 31.7 + - - -
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Residues in contact with ARG 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 4.5 8.4 - - + +
535A LEU* 3.7 35.4 - - - +
539A GLU* 3.0 43.2 + - + +
540A ALA* 3.5 8.5 - - - +
541A ARG 3.3 0.6 - - - -
542A GLU* 1.3 77.1 - - + +
544A ALA* 1.3 55.7 + - - +
546A VAL* 3.5 8.1 + - - +
547A PHE* 3.1 27.2 + - - +
417B LEU* 3.7 6.7 - - + +
420B SER 5.8 0.9 - - - -
421B SER* 3.0 43.9 + - - +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LEU* 4.2 19.2 - - + +
527A ARG* 3.8 24.9 - - + -
540A ALA 3.1 13.1 + - - +
541A ARG 3.4 8.5 - - - +
543A ARG* 1.3 72.1 - - - +
545A ASP* 1.3 57.5 + - - +
547A PHE* 3.4 0.9 + - - +
548A ARG* 2.7 40.3 + - - +
417B LEU* 3.9 18.7 - - + +
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Residues in contact with ASP 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ARG* 2.7 59.6 + - - +
542A GLU* 3.3 12.9 - - - +
544A ALA* 1.3 73.1 - - - +
546A VAL* 1.3 63.7 + - + +
548A ARG* 2.9 29.2 + - - +
549A ARG* 3.1 32.5 + - - +
1041A ASP* 5.6 1.2 - - - +
1043A ASN* 3.5 26.5 + - + +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLU* 3.0 18.3 + - + +
543A ARG* 3.7 10.5 - - - +
545A ASP* 1.3 74.3 - - + +
547A PHE* 1.3 68.6 + - - +
549A ARG* 3.5 15.9 + - - +
550A PHE* 3.1 23.8 + - + +
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Residues in contact with PHE 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A PHE* 4.2 5.6 - + - -
523A LEU* 3.3 31.6 - - + -
543A ARG 3.1 17.8 + - - +
544A ALA 3.8 1.3 - - - +
546A VAL* 1.3 76.0 - - - +
548A ARG* 1.3 61.1 + - - +
550A PHE* 3.3 20.6 + + - +
551A ASN* 2.8 54.8 + - + +
413B ILE* 4.1 21.8 - - + -
416B ARG* 3.4 52.3 - - + -
417B LEU* 3.7 22.4 - - + -
420B SER* 4.8 7.0 - - - +
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A PHE* 3.9 20.6 - - + -
520A GLU* 2.8 39.4 + - - -
523A LEU* 3.8 15.7 - - + +
527A ARG* 6.0 2.0 - - - +
544A ALA* 2.7 26.0 + - - +
545A ASP* 2.9 36.3 + - - +
546A VAL 3.4 0.2 - - - -
547A PHE* 1.3 73.8 - - - +
549A ARG* 1.3 54.7 + - - +
551A ASN* 3.1 2.3 + - - +
552A ILE* 2.8 57.9 + - + +
1041A ASP* 6.0 2.0 - - - +
1043A ASN* 4.2 15.4 - - - +
524B LYS* 3.6 17.4 - - - +
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Residues in contact with ARG 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ASP* 3.1 19.6 + - - +
546A VAL* 3.8 16.6 - - - +
547A PHE 3.3 0.2 - - - -
548A ARG* 1.3 78.4 - - - +
550A PHE* 1.3 63.6 + - - +
552A ILE* 3.5 7.2 + - - +
553A GLN* 3.1 28.6 + - + +
1039A TYR* 5.0 1.6 - - - -
1043A ASN* 2.9 43.0 + - - +
1044A ILE 3.7 14.1 + - - -
1045A ASP* 3.7 39.1 + - - +
1046A ILE 5.5 0.2 - - - +
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Residues in contact with PHE 550 (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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546A VAL* 3.1 17.4 + - + +
547A PHE* 3.6 19.7 - + - +
549A ARG* 1.3 80.2 - - - +
551A ASN* 1.3 72.1 + - - +
553A GLN* 3.4 10.0 + - + +
554A MET* 3.1 46.8 + - + +
416B ARG* 3.3 32.3 - - - -
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Residues in contact with ASN 551 (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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516A ARG* 2.7 41.6 + - - +
519A PHE* 3.4 12.2 - - + -
547A PHE* 2.8 46.6 + - + +
548A ARG 3.6 3.6 - - - +
550A PHE* 1.3 81.6 - - + +
552A ILE* 1.3 62.2 + - - +
554A MET* 3.1 25.6 + - - +
555A VAL* 3.0 22.7 + - - +
413B ILE* 4.2 8.9 - - - +
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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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503A TYR* 4.8 7.9 + - + +
516A ARG* 4.0 20.2 - - - +
519A PHE* 5.2 1.3 - - + -
548A ARG* 2.8 49.0 + - + +
549A ARG* 3.9 6.7 - - - +
551A ASN* 1.3 73.3 - - - +
553A GLN* 1.3 57.3 + - - +
555A VAL* 3.4 3.2 + - - +
556A GLU* 2.9 47.0 + - + +
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Residues in contact with GLN 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 ARG* 3.1 21.7 + - + +
550A PHE* 3.7 9.5 - - + +
552A ILE* 1.3 77.5 - - - +
554A MET* 1.3 61.8 + - - +
556A GLU* 3.7 5.9 + - - +
557A GLU* 3.2 21.5 + - + +
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Residues in contact with MET 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 PHE* 3.1 38.9 + - + +
551A ASN* 3.1 30.5 + - - +
553A GLN* 1.3 77.5 - - - +
555A VAL* 1.3 68.9 + - + +
557A GLU* 3.3 12.3 + - - +
558A MET* 3.1 39.9 + - + +
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Residues in contact with VAL 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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500A VAL* 3.9 26.5 - - + -
503A TYR* 3.2 39.7 - - + -
504A ILE* 4.6 1.5 - - + +
516A ARG* 3.9 23.3 - - - +
551A ASN* 3.0 19.3 + - - +
552A ILE* 4.2 3.4 - - - +
554A MET* 1.3 85.2 - - + +
556A GLU* 1.3 59.8 + - - +
558A MET* 3.3 19.3 + - - +
559A ALA* 2.9 26.9 + - - +
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Residues in contact with GLU 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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503A TYR* 2.3 34.6 + - - +
507A ARG* 2.8 41.8 + - - +
512A GLU 4.9 0.8 - - - +
552A ILE* 2.9 31.6 + - + +
553A GLN* 3.9 6.5 - - - +
555A VAL* 1.3 74.3 - - - +
557A GLU* 1.3 61.9 + - - +
559A ALA* 3.3 1.8 + - - +
560A MET* 3.0 39.9 + - + +
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Residues in contact with GLU 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 GLN* 3.2 13.8 + - + +
554A MET* 3.5 12.7 - - - +
555A VAL 3.3 0.2 - - - -
556A GLU* 1.3 73.0 - - - +
558A MET* 1.3 67.7 + - - +
560A MET* 3.3 7.6 + - + +
561A VAL* 3.0 39.7 + - + +
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Residues in contact with MET 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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500A VAL* 4.4 13.9 - - + -
504A ILE* 3.9 23.0 - - + +
508A GLN* 5.0 0.2 + - - -
554A MET* 3.1 35.9 + - + +
555A VAL* 3.3 26.9 + - - +
557A GLU* 1.3 77.6 - - + +
559A ALA* 1.3 62.1 + - - +
561A VAL* 3.5 25.2 - - - +
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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
----------------------------------------------------------
503A TYR* 4.6 0.9 - - + -
504A ILE* 4.0 20.8 - - + +
507A ARG* 4.1 30.3 - - + -
508A GLN* 2.9 28.6 + - + +
555A VAL 2.9 17.2 + - - +
556A GLU* 3.5 9.4 - - - +
557A GLU 3.2 0.2 - - - -
558A MET* 1.3 75.3 - - - +
560A MET* 1.3 73.6 + - - +
561A VAL 4.0 0.2 - - - -
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Residues in contact with MET 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ARG* 4.4 23.6 - - + +
508A GLN* 5.1 2.7 + - + -
556A GLU* 3.0 26.5 + - + +
557A GLU* 3.8 6.5 - - + +
559A ALA* 1.3 84.9 - - + +
561A VAL* 1.3 67.3 + - + +
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLN* 4.9 6.7 - - - -
557A GLU* 3.0 40.0 + - + +
558A MET* 3.5 20.2 - - - +
559A ALA 4.0 3.4 - - - -
560A MET* 1.3 81.6 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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