Contacts of the helix formed by residues 541 - 564 (chain A) in PDB entry 2PFV
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 ASP 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A SER* 3.1 13.1 + - - +
540A LYS* 1.3 74.1 - - - +
542A LYS* 1.3 64.0 + - - +
543A GLU* 3.6 8.1 + - - +
544A GLN* 3.1 37.7 + - + +
545A ILE* 3.1 25.9 + - - +
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Residues in contact with LYS 542 (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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540A LYS 3.1 12.3 + - - +
541A ASP* 1.3 70.7 + - - +
543A GLU* 1.3 57.9 + - - +
545A ILE* 3.2 7.4 + - - +
546A LYS* 2.8 52.8 + - - +
599A SER* 3.4 27.3 + - - +
600A PHE* 3.9 13.7 - - + +
601A LYS* 5.1 11.1 - - - +
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASP* 3.2 8.0 + - - +
542A LYS* 1.3 76.4 - - - +
544A GLN* 1.3 65.3 + - - +
546A LYS* 3.8 29.9 + - - +
547A GLU* 3.0 29.6 + - + +
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ASP* 5.0 10.4 - - - +
541A ASP* 3.1 34.6 + - + +
543A GLU* 1.3 79.3 - - - +
545A ILE* 1.3 64.9 + - + +
547A GLU* 3.4 17.6 + - - +
548A LYS* 3.2 46.0 + - - +
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Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ASP* 5.5 1.8 - - - +
539A SER* 3.8 29.4 - - - +
540A LYS 4.8 0.4 - - - -
541A ASP 3.1 20.2 + - - +
542A LYS 3.6 7.4 - - - +
544A GLN* 1.3 76.3 - - + +
546A LYS* 1.3 65.8 + - - +
548A LYS* 3.0 20.3 + - + +
549A PHE* 3.3 18.9 + - + -
596A TYR* 3.9 42.4 - - + -
599A SER* 3.1 34.1 - - - +
600A PHE* 3.8 18.8 - - + -
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Residues in contact with LYS 546 (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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542A LYS* 2.8 39.2 + - - +
543A GLU* 3.7 28.9 + - - +
545A ILE* 1.3 76.0 - - - +
547A GLU* 1.3 57.8 + - - +
549A PHE* 3.3 8.0 + - - +
550A ARG* 2.9 28.1 + - - +
600A PHE* 3.5 34.1 - - + -
606A HIS* 3.6 37.7 + - + +
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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
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543A GLU* 3.0 23.8 + - + +
544A GLN* 3.4 22.2 - - - +
546A LYS* 1.3 75.1 - - - +
548A LYS* 1.3 65.2 + - + +
550A ARG* 3.3 41.9 + - - -
551A LYS* 3.1 27.1 + - + +
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Residues in contact with LYS 548 (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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526A LEU* 4.7 3.5 - - + +
529A SER* 2.9 53.5 + - - +
530A VAL 5.0 0.2 - - - +
532A ILE* 6.0 0.6 - - - +
533A ASP* 3.5 27.8 - - - +
544A GLN* 3.2 29.5 + - - +
545A ILE* 3.0 15.0 + - + +
547A GLU* 1.3 78.8 - - + +
549A PHE* 1.3 63.4 + - - +
551A LYS* 3.6 5.6 + - - +
552A PHE* 3.3 20.6 + - - +
592A PHE* 4.1 16.8 - - + -
596A TYR* 4.7 18.4 - - + -
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Residues in contact with PHE 549 (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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545A ILE* 3.3 29.8 + - + -
546A LYS* 3.6 9.4 - - - +
548A LYS* 1.3 77.5 - - - +
550A ARG* 1.3 66.2 - - - +
552A PHE* 3.1 5.0 + + - +
553A ASN* 2.8 36.5 + - - +
589A TYR* 3.7 15.7 - + - -
592A PHE* 3.2 36.8 - + - -
593A TYR* 4.4 12.1 - + - -
596A TYR* 3.8 28.5 - - + -
600A PHE* 4.6 2.5 - + - -
606A HIS 4.8 8.5 - - - +
607A ILE* 3.5 53.8 - - + -
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Residues in contact with ARG 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 LYS 2.9 17.6 + - - +
547A GLU* 3.3 38.9 + - - +
548A LYS 3.3 0.2 - - - -
549A PHE* 1.3 77.6 - - - +
551A LYS* 1.3 67.2 + - - +
553A ASN* 3.2 10.8 + - + +
554A GLU* 2.9 62.3 + - + +
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Residues in contact with LYS 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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522A LEU* 5.4 0.3 - - - +
547A GLU* 3.1 22.1 + - + +
548A LYS* 3.9 6.3 - - - +
550A ARG* 1.3 86.5 - - - +
552A PHE* 1.3 64.0 + - - +
554A GLU* 3.3 9.3 + - - +
555A GLY* 3.0 20.3 + - - -
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Residues in contact with PHE 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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522A LEU* 4.1 31.3 - - + +
523A THR* 5.4 4.5 - - + -
526A LEU* 3.8 41.3 - - + -
548A LYS 3.3 10.8 + - - +
549A PHE* 3.1 10.8 + - - +
551A LYS* 1.3 77.3 - - - +
553A ASN* 1.3 65.0 + - - +
555A GLY 3.1 2.6 + - - +
556A PHE* 2.6 62.7 + + + +
585A VAL* 4.4 10.1 - - + -
589A TYR* 3.4 39.0 - + + -
592A PHE* 4.9 0.7 - - + -
614A LEU* 4.0 16.6 - - + -
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Residues in contact with ASN 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 PHE* 2.8 38.3 + - - +
550A ARG* 3.5 10.4 - - + +
552A PHE* 1.3 82.5 - - - +
554A GLU* 1.3 58.3 + - + +
556A PHE* 3.2 6.5 + - - +
557A GLU* 2.9 40.8 + - - +
589A TYR* 4.8 5.7 + - - -
606A HIS 5.7 1.0 + - - -
608A LYS* 3.8 37.1 - - + +
609A TYR* 3.7 19.4 + - + -
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Residues in contact with GLU 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 ARG* 2.9 64.5 + - + +
551A LYS* 3.7 7.8 - - - +
553A ASN* 1.3 75.5 - - + +
555A GLY* 1.3 64.1 + - - +
557A GLU* 3.9 7.3 - - - +
558A ASP* 3.0 27.8 + - - +
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Residues in contact with GLY 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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522A LEU* 3.6 20.6 - - - +
551A LYS 3.0 12.5 + - - -
552A PHE 3.5 2.2 - - - -
554A GLU* 1.3 76.9 - - - +
556A PHE* 1.3 62.3 + - - +
558A ASP* 3.8 5.9 - - - +
559A LEU* 3.1 24.8 + - - +
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Residues in contact with PHE 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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519A TRP* 4.2 12.8 - + - -
522A LEU* 3.7 11.1 - - + +
552A PHE* 2.6 43.2 + + + +
553A ASN* 3.5 5.4 - - - +
554A GLU 3.2 0.2 - - - -
555A GLY* 1.3 72.3 - - - +
557A GLU* 1.3 63.3 + - + +
559A LEU* 3.0 5.4 + - - +
560A VAL* 2.8 46.7 + - + +
585A VAL* 4.4 4.3 - - + -
609A TYR* 4.1 19.3 - + - -
614A LEU* 3.3 39.7 - - + -
617A VAL* 3.7 20.9 - - + -
618A LEU* 3.5 34.1 - - + -
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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 ASN* 2.9 25.9 + - - +
554A GLU* 4.0 5.5 - - - +
556A PHE* 1.3 82.1 - - + +
558A ASP* 1.3 62.1 + - - +
560A VAL* 3.9 5.8 - - + +
561A SER* 3.0 25.1 + - - -
608A LYS* 2.7 33.3 + - - +
609A TYR* 2.5 33.4 + - - +
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Residues in contact with ASP 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 GLU 3.0 18.7 + - - +
555A GLY* 3.8 5.6 - - - +
557A GLU* 1.3 78.3 - - - +
559A LEU* 1.3 57.4 + - - +
561A SER* 3.5 6.3 + - - -
562A LYS* 3.0 61.2 + - - +
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Residues in contact with LEU 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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470A GLN* 4.2 10.5 - - - +
518A ASP* 3.5 45.8 - - + +
519A TRP* 3.5 50.3 - - + +
522A LEU* 3.9 13.9 - - + -
555A GLY 3.1 11.1 + - - +
556A PHE* 3.0 8.6 + - - +
558A ASP* 1.3 75.0 - - - +
560A VAL* 1.3 61.0 + - - +
562A LYS* 4.6 8.1 - - + -
563A THR* 2.7 38.1 + - - +
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Residues in contact with VAL 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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519A TRP* 4.0 9.0 - - + -
556A PHE* 2.8 55.2 + - + +
557A GLU* 3.9 7.0 - - - +
559A LEU* 1.3 76.0 - - - +
561A SER* 1.3 64.2 + - - +
563A THR* 3.3 2.4 + - - -
564A LYS* 3.2 49.3 + - - +
617A VAL* 4.1 16.6 - - + -
618A LEU* 4.5 0.9 - - + -
621A LEU* 3.7 21.4 - - + +
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Residues in contact with SER 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 GLU 3.0 19.1 + - - -
558A ASP* 3.5 8.1 - - - -
560A VAL* 1.3 78.4 - - - +
562A LYS* 1.3 63.9 + - - +
564A LYS* 3.3 23.5 + - - +
565A GLN* 3.8 12.9 + - - +
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Residues in contact with LYS 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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470A GLN* 3.4 18.4 - - - +
518A ASP* 5.8 3.1 - - - +
558A ASP* 3.0 47.0 + - - +
559A LEU* 3.9 10.3 - - + +
561A SER* 1.3 77.2 - - - +
563A THR* 1.3 63.8 + - - +
565A GLN* 2.9 39.1 + - - +
566A TYR* 3.3 10.4 - - + +
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Residues in contact with THR 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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470A GLN* 3.0 26.5 + - - +
519A TRP* 3.3 16.6 + - + -
559A LEU 2.7 21.7 + - - -
560A VAL 3.3 5.1 + - - -
562A LYS* 1.3 76.9 - - - +
564A LYS* 1.3 61.2 + - - +
565A GLN 3.2 0.9 + - - -
566A TYR* 3.2 22.7 + - + +
577A LEU* 4.9 10.3 - - + -
581A ILE* 4.5 13.7 - - + -
621A LEU* 3.8 26.1 - - + +
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Residues in contact with LYS 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 VAL* 3.2 39.2 + - - +
561A SER* 3.6 13.3 - - - +
562A LYS 3.1 1.0 - - - -
563A THR* 1.3 76.4 - - - +
565A GLN* 1.3 60.8 + - + +
566A TYR 3.1 2.6 + - - -
567A LYS* 2.9 36.6 + - - +
617A VAL* 6.1 0.4 - - - +
620A GLN* 6.2 0.2 - - - +
621A LEU* 3.3 22.7 - - + +
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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