Contacts of the helix formed by residues 549 - 570 (chain A) in PDB entry 3PRF
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A LYS 5.4 1.3 - - - +
548A PHE* 1.3 79.5 - - - +
550A MET* 1.3 53.1 + - - +
551A ILE* 4.4 16.6 - - + +
552A LYS* 2.7 16.8 + - + +
553A LEU* 2.7 34.6 + - - +
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Residues in contact with MET 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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549A GLU* 1.3 72.7 - - - +
551A ILE* 1.3 63.7 + - + +
553A LEU* 3.7 18.3 - - + +
554A ILE* 2.8 54.0 + - + +
650A MET* 3.5 33.0 - - - +
682A ARG* 3.9 14.4 - - + -
684A ASN* 3.4 51.6 + - - +
685A CYS* 3.7 20.6 - - + +
686A PRO* 4.2 4.9 - - + -
721A LEU* 4.8 5.2 - - + -
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Residues in contact with ILE 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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549A GLU* 3.2 15.7 - - + +
550A MET* 1.3 88.0 - - + +
552A LYS* 1.3 56.7 + - - +
554A ILE* 3.9 3.1 - - - +
555A ASP* 3.2 24.9 + - - +
721A LEU* 3.7 34.3 - - + +
722A PRO* 5.4 10.5 - - + +
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Residues in contact with LYS 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 PHE* 3.8 33.3 - - + -
549A GLU* 2.7 24.0 + - + +
551A ILE* 1.3 78.9 - - - +
553A LEU* 1.3 58.3 + - - +
555A ASP* 3.1 14.3 + - + +
556A ILE* 2.9 44.6 + - + +
584A LEU* 5.1 1.6 - - - -
587A ASP* 3.1 30.4 + - - +
588A LEU* 4.6 11.4 - - - +
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Residues in contact with LEU 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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541A LEU* 4.7 5.4 - - + -
548A PHE* 3.5 38.1 - - + +
549A GLU 2.7 30.5 + - - +
550A MET* 3.7 22.2 - - + +
552A LYS* 1.3 70.5 - - - +
554A ILE* 1.3 58.3 + - - +
556A ILE* 3.4 8.6 + - + +
557A ALA* 3.0 26.3 + - - +
649A LEU* 3.5 48.2 - - + +
650A MET* 3.6 14.5 - - + +
682A ARG* 4.9 10.3 - - - +
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Residues in contact with ILE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A MET* 2.8 46.8 + - + +
551A ILE* 3.9 5.2 - - - +
553A LEU* 1.3 70.3 - - - +
555A ASP* 1.3 61.7 + - - +
557A ALA* 3.2 9.0 + - - +
558A ARG* 2.8 27.7 + - + +
650A MET* 4.8 2.0 - - + -
686A PRO* 4.1 14.6 - - + -
689A MET* 4.0 17.5 - - + -
714A ILE* 4.0 11.3 - - + +
717A LEU* 4.1 6.5 - - + -
718A ALA* 3.8 29.8 - - + -
721A LEU* 3.7 28.3 - - + -
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Residues in contact with ASP 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 ILE 3.2 15.5 + - - +
552A LYS* 3.1 20.5 + - + +
554A ILE* 1.3 75.6 - - - +
556A ILE* 1.3 59.4 + - + +
558A ARG* 2.5 37.4 + - - +
559A GLN* 2.9 53.2 + - - +
588A LEU 4.8 2.3 - - - +
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Residues in contact with ILE 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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537A LEU* 3.8 31.4 - - + -
548A PHE* 4.6 14.8 - - + -
552A LYS* 2.9 40.7 + - + +
553A LEU* 3.6 11.2 - - - +
555A ASP* 1.3 75.2 - - - +
557A ALA* 1.3 58.2 + - - +
559A GLN* 3.5 5.2 + - - +
560A THR* 2.7 36.3 + - - +
582A ILE* 5.2 0.2 - - + -
584A LEU* 4.3 23.6 - - + -
590A VAL* 3.8 26.0 - - + +
649A LEU* 4.0 14.8 - - + -
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Residues in contact with ALA 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 LEU 3.0 14.3 + - - +
554A ILE* 3.3 12.8 - - - +
556A ILE* 1.3 76.9 - - - +
558A ARG* 1.3 56.6 + - - +
560A THR* 3.4 4.8 + - - -
561A ALA* 2.9 30.0 + - - +
642A PHE* 3.7 4.2 - - - -
645A VAL* 6.1 0.4 - - - -
646A LEU* 3.7 28.9 - - + -
649A LEU* 4.0 10.3 - - + +
650A MET* 5.3 1.3 - - + -
689A MET* 4.6 6.5 - - + -
714A ILE* 3.9 9.6 - - + -
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Residues in contact with ARG 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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512A ASN* 5.5 2.2 + - - -
554A ILE* 2.8 16.5 + - + +
555A ASP* 2.5 40.5 + - - +
557A ALA* 1.3 73.1 - - - +
559A GLN* 1.3 75.7 + - - +
561A ALA* 3.1 4.4 + - - +
562A GLN* 2.7 44.5 + - - +
711A LEU* 3.8 14.8 - - + +
714A ILE* 3.7 23.2 - - + +
715A GLU* 3.9 28.3 + - + +
718A ALA* 5.6 5.6 - - + -
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Residues in contact with GLN 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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512A ASN* 3.0 34.7 + - - +
555A ASP* 2.9 41.1 + - - +
556A ILE* 4.0 3.3 - - - +
558A ARG* 1.3 96.6 - - - +
560A THR* 1.3 62.1 + - - +
562A GLN* 3.0 19.5 + - - +
563A GLY 3.0 11.3 + - - -
584A LEU* 5.6 1.0 - - - +
588A LEU 3.3 23.2 + - - -
589A THR* 3.5 12.6 - - - +
590A VAL* 3.2 27.2 + - + +
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Residues in contact with THR 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 ILE* 2.7 28.2 + - - +
557A ALA* 3.6 5.1 - - - -
559A GLN* 1.3 71.4 - - - +
561A ALA* 1.3 66.7 + - - +
563A GLY 3.3 1.9 + - - -
564A MET* 3.2 27.9 + - + +
577A LEU* 4.5 6.5 - - + -
582A ILE* 3.9 28.2 - - + +
590A VAL* 3.7 20.0 - - - +
592A ILE* 3.5 16.9 - - + +
642A PHE* 3.9 21.3 - - + -
645A VAL* 4.8 5.5 - - + +
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Residues in contact with ALA 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 ALA 2.9 14.7 + - - +
558A ARG 3.3 9.0 - - - +
560A THR* 1.3 75.7 - - - +
562A GLN* 1.3 61.4 - - - +
564A MET* 3.3 2.1 + - - +
565A ASP* 3.1 24.3 + - - +
642A PHE* 3.6 14.2 - - + -
707A PHE* 3.9 11.8 - - + -
710A ILE* 4.4 9.9 - - + -
711A LEU* 3.9 14.7 - - + +
714A ILE* 3.8 20.0 - - + -
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Residues in contact with GLN 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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510A HIS* 3.8 9.8 - - + +
512A ASN* 3.3 17.7 - - - +
558A ARG* 2.7 26.2 + - - +
559A GLN* 3.1 15.7 - - - +
561A ALA* 1.3 74.4 - - - +
563A GLY* 1.3 59.8 + - - +
565A ASP* 3.5 3.9 + - - +
566A TYR* 3.4 16.3 + - - +
711A LEU* 3.4 32.1 - - + +
715A GLU* 4.0 6.6 - - - +
477B HIS* 3.3 26.1 + - - +
478B GLY* 3.3 26.9 + - - +
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Residues in contact with GLY 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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510A HIS* 4.4 1.8 - - - -
512A ASN* 3.8 19.9 - - - +
513A ILE* 3.5 12.6 - - - +
559A GLN 3.0 10.9 + - - -
560A THR 3.3 3.3 + - - -
562A GLN* 1.3 73.7 - - - +
564A MET* 1.3 59.2 + - - +
566A TYR* 3.5 6.9 - - - +
567A LEU* 3.0 31.5 + - - +
592A ILE* 4.0 10.1 - - - -
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Residues in contact with MET 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 THR* 3.2 18.4 + - + +
561A ALA 3.7 0.9 - - - +
562A GLN 3.2 0.2 - - - -
563A GLY* 1.3 76.4 - - - +
565A ASP* 1.3 60.1 + - - +
567A LEU* 3.2 27.3 + - + +
568A HIS* 2.8 50.4 + - + +
574A HIS* 4.4 3.1 - - + -
577A LEU* 3.9 26.7 - - + -
592A ILE* 3.9 13.5 - - + -
638A ASP* 3.4 35.2 - - + +
642A PHE* 4.8 0.2 - - + -
707A PHE* 3.6 35.2 - - + -
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Residues in contact with ASP 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 ALA 3.1 13.9 + - - +
562A GLN* 3.7 10.5 - - - +
564A MET* 1.3 74.1 - - - +
566A TYR* 1.3 53.2 + - - +
568A HIS* 3.2 3.8 + - - +
569A ALA* 2.6 38.4 + - - +
707A PHE* 3.9 11.1 - - + +
708A PRO* 3.4 41.9 - - - +
711A LEU* 3.7 21.9 - - + +
477B HIS* 4.1 17.0 + - - +
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Residues in contact with TYR 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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507A LYS 4.0 0.5 + - - -
508A THR* 3.9 15.0 - - + -
509A ARG* 2.9 45.6 + - - +
510A HIS* 3.5 37.7 - + + -
513A ILE* 4.0 9.6 - - + -
562A GLN 3.4 10.9 + - - +
563A GLY 3.5 8.1 - - - +
565A ASP* 1.3 80.2 - - - +
567A LEU* 1.3 66.3 + - - +
569A ALA* 3.3 6.9 + - - +
570A LYS* 3.0 59.5 + - + +
450B TRP* 4.1 1.9 - - - -
476B TRP* 4.1 21.3 - + - -
477B HIS* 3.6 22.3 + + + -
517B MET 5.0 1.4 + - - -
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Residues in contact with LEU 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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508A THR* 4.0 18.4 - - + -
513A ILE* 3.8 19.5 - - + -
563A GLY 3.0 22.3 + - - +
564A MET* 3.2 35.0 + - + +
566A TYR* 1.3 78.5 - - + +
568A HIS* 1.3 58.3 + - + +
570A LYS 3.4 1.7 + - - -
571A SER 3.2 3.6 + - - -
572A ILE* 2.7 57.4 + - + +
574A HIS* 4.3 15.0 - - + +
592A ILE* 4.5 3.1 - - + -
595A PHE* 3.8 32.1 - - + -
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Residues in contact with HIS 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 MET* 2.8 24.2 + - + +
565A ASP* 3.7 7.4 - - - +
567A LEU* 1.3 74.9 - - - +
569A ALA* 1.3 58.3 + - - +
570A LYS 3.1 0.2 - - - -
571A SER* 2.7 22.9 + - - +
572A ILE 3.2 20.4 - - - -
635A PHE* 3.5 64.1 - + + +
638A ASP* 3.1 24.4 + - + +
639A VAL* 4.7 0.4 - - + -
706A LEU* 5.6 1.6 - - - +
707A PHE* 3.4 37.6 + + + +
708A PRO* 6.2 1.6 - - + -
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Residues in contact with ALA 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 ASP* 2.6 24.6 + - - +
566A TYR 3.5 4.3 - - - +
568A HIS* 1.3 72.7 - - - +
570A LYS* 1.3 60.4 + - + +
571A SER* 3.2 5.2 + - - -
477B HIS* 3.4 32.3 - - + +
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Residues in contact with LYS 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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507A LYS* 3.3 46.5 + - - +
566A TYR* 3.0 55.1 + - + +
568A HIS 3.1 0.2 - - - -
569A ALA* 1.3 77.7 - - + +
571A SER* 1.3 68.6 + - - +
572A ILE* 3.3 23.3 + - + +
599A THR* 4.4 3.5 + - - -
449B ASP 4.3 8.7 + - - -
450B TRP* 4.1 19.4 - - - +
476B TRP* 4.4 18.7 - - + -
477B HIS* 5.8 0.9 - - - +
517B MET 5.2 0.2 + - - -
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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
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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