Contacts of the helix formed by residues 540 - 560 (chain A) in PDB entry 4EMX
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 THR 540 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LYS* 5.1 0.2 - - - +
538A LYS 3.6 5.6 + - - +
539A ALA* 1.3 76.3 - - - +
541A LYS* 1.3 59.0 + - - +
542A GLU* 3.8 11.4 - - - +
543A GLN* 2.6 44.8 + - - +
544A LEU* 2.8 14.0 + - - +
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Residues in contact with LYS 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 5.9 4.0 - - + -
413A LYS* 4.9 4.7 - - - +
539A ALA 3.9 1.4 + - - -
540A THR* 1.3 71.2 - - - +
542A GLU* 1.3 66.4 + - + +
544A LEU* 4.2 8.1 - - - +
545A LYS* 3.3 37.7 + - + +
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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
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540A THR* 2.9 9.1 - - - +
541A LYS* 1.3 81.6 - - + +
543A GLN* 1.3 61.7 + - - +
544A LEU 3.2 2.9 + - - -
545A LYS* 3.7 28.3 + - - +
546A ALA* 3.7 19.2 + - - +
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Residues in contact with GLN 543 (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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536A LYS* 5.1 10.9 - - - +
539A ALA* 3.2 34.0 - - - +
540A THR* 2.6 30.1 + - - +
542A GLU* 1.3 72.1 - - - +
544A LEU* 1.3 59.6 + - + +
546A ALA* 4.0 5.5 - - - +
547A VAL* 3.5 25.0 + - + +
579A SER 4.9 2.2 + - - -
580A GLN 5.9 0.2 + - - -
581A ALA 5.3 0.4 + - - -
582A ALA 2.5 34.0 + - - +
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 4.0 23.3 - - + -
413A LYS* 4.1 5.2 - - - +
529A LEU* 4.4 13.5 - - + +
532A LEU* 3.9 31.4 - - + +
533A VAL* 3.9 28.3 - - + -
536A LYS* 5.0 2.0 - - + +
539A ALA* 3.7 39.5 - - + +
540A THR 2.8 12.6 + - - +
541A LYS* 4.2 4.9 - - - +
543A GLN* 1.3 78.4 - - + +
545A LYS* 1.3 58.1 + - + +
546A ALA 2.9 9.3 + - - -
547A VAL* 3.3 3.4 + - + +
548A MET* 3.2 24.4 + - - +
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Residues in contact with LYS 545 (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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398A LEU* 4.6 23.3 - - + +
402A LYS* 6.4 2.2 - - + -
405A ASN* 6.3 3.1 - - + -
406A ALA* 6.4 2.7 - - + -
409A VAL* 6.6 0.2 - - + -
541A LYS* 3.3 26.7 + - + +
542A GLU* 3.7 24.3 + - - +
544A LEU* 1.3 76.0 - - + +
546A ALA* 1.3 57.4 + - - +
548A MET* 4.3 9.9 - - - +
549A ASP* 3.7 22.5 + - - +
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Residues in contact with ALA 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 GLU 3.7 16.0 + - - +
543A GLN* 4.0 8.1 - - - +
544A LEU 2.9 1.2 - - - -
545A LYS* 1.3 79.2 - - - +
547A VAL* 1.3 63.5 + - + +
548A MET 3.4 1.6 - - - -
549A ASP* 3.4 7.9 + - - +
550A ASP* 3.2 22.9 + - - +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 3.8 32.8 - - + -
543A GLN* 3.5 19.3 + - + +
544A LEU* 3.3 3.1 + - + +
546A ALA* 1.3 76.6 - - + +
548A MET* 1.3 60.2 + - - +
549A ASP 3.3 0.4 - - - -
550A ASP* 3.8 7.0 - - + +
551A PHE* 3.1 28.4 + - + +
575A LEU 5.5 0.2 - - - +
579A SER* 3.3 44.0 - - - +
582A ALA* 5.2 7.6 - - + -
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Residues in contact with MET 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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401A TYR* 3.3 27.1 - - + +
405A ASN* 3.5 36.6 - - + +
525A LYS* 4.0 22.7 - - + +
526A GLN* 4.0 13.9 - - + -
529A LEU* 3.9 31.1 - - + +
532A LEU* 5.4 1.0 - - - +
544A LEU 3.2 17.1 + - - +
545A LYS* 4.3 9.6 - - - +
547A VAL* 1.3 76.9 - - - +
549A ASP* 1.3 59.9 + - - +
551A PHE* 3.4 7.7 + - - +
552A ALA* 3.0 28.5 + - - +
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Residues in contact with ASP 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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402A LYS* 4.6 18.2 + - - -
545A LYS 3.7 16.2 + - - +
546A ALA* 3.4 11.6 + - - +
547A VAL 3.3 0.4 - - - -
548A MET* 1.3 80.0 - - - +
550A ASP* 1.3 61.1 + - - +
552A ALA* 3.6 7.7 - - - +
553A ALA* 3.1 30.3 + - - +
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Residues in contact with ASP 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 ALA 3.2 15.5 + - - +
547A VAL* 3.9 10.4 - - + +
548A MET 3.3 0.4 - - - -
549A ASP* 1.3 73.9 - - - +
551A PHE* 1.3 64.1 + - - +
553A ALA* 4.3 2.1 - - - +
554A PHE* 3.1 30.2 + - - +
575A LEU* 3.2 38.0 - - - +
579A SER* 4.4 8.8 + - - +
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Residues in contact with PHE 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PHE* 4.5 22.2 - - + -
525A LYS* 4.8 11.0 - - + +
528A ALA* 5.9 3.4 - - + -
547A VAL* 3.1 17.9 + - + +
548A MET* 3.4 9.4 + - - +
550A ASP* 1.3 74.5 + - - +
552A ALA* 1.3 56.5 + - - +
554A PHE* 3.5 10.5 - - + -
555A VAL* 3.0 37.3 + - - +
575A LEU* 5.9 0.2 - - - -
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Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 5.9 1.3 - - + +
525A LYS* 4.2 29.2 + - + +
548A MET* 3.0 18.5 + - + +
549A ASP* 3.6 12.6 - - - +
551A PHE* 1.3 76.4 - - - +
553A ALA* 1.3 62.7 + - + +
555A VAL* 3.4 3.1 + - - +
556A GLU* 3.1 21.9 + - - +
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Residues in contact with ALA 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 ASP 3.1 14.8 + - - +
550A ASP* 4.4 2.5 - - - +
552A ALA* 1.3 79.7 - - + +
554A PHE* 1.3 59.4 + - - +
556A GLU* 3.6 8.3 + - - +
557A LYS* 2.9 36.9 + - - +
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Residues in contact with PHE 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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507A PHE 5.6 1.6 - - - -
508A THR* 6.6 0.2 - - + -
509A PHE* 3.5 39.9 - + + -
550A ASP* 3.1 22.1 + - - +
551A PHE* 3.5 21.1 - - - -
553A ALA* 1.3 77.4 - - - +
555A VAL* 1.3 59.2 + - + +
557A LYS* 3.6 13.0 - - + +
558A CYS* 2.9 36.8 + - - +
568A PHE* 3.7 28.3 - + - -
571A GLU* 3.7 16.4 - - + +
572A GLY* 3.6 26.7 - - - -
575A LEU* 4.2 17.0 - - + -
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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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509A PHE* 4.3 28.5 - - + -
513A ILE* 4.4 8.7 - - + -
521A ARG* 4.1 26.9 - - + -
525A LYS* 5.2 11.0 - - + +
551A PHE 3.0 23.4 + - - +
552A ALA* 3.8 5.2 - - - +
554A PHE* 1.3 72.6 - - + +
556A GLU* 1.3 61.6 + - - +
559A CYS* 2.9 36.5 + - + +
568A PHE* 3.9 28.2 - - + -
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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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552A ALA 3.1 13.5 + - - +
553A ALA* 3.7 9.9 - - - +
555A VAL* 1.3 76.5 - - - +
557A LYS* 1.3 59.0 + - - +
559A CYS* 3.9 2.6 - - - -
560A LYS* 2.9 64.2 + - + +
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Residues in contact with LYS 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 ALA* 2.9 30.4 + - - +
554A PHE* 3.6 11.4 - - + +
555A VAL 3.4 0.2 - - - -
556A GLU* 1.3 76.5 - - - +
558A CYS* 1.3 61.7 + - - +
560A LYS* 3.0 27.6 - - - +
561A ALA* 3.6 5.3 - - + +
567A CYS* 4.6 9.9 - - - -
571A GLU* 5.4 9.0 - - + -
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Residues in contact with CYS 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 PHE* 2.9 29.5 + - - +
557A LYS* 1.3 79.3 - - - +
559A CYS* 1.3 60.2 + - - +
561A ALA* 3.5 13.7 + - - +
564A LYS* 3.7 18.9 - - - +
567A CYS* 2.0 64.2 - - + -
568A PHE* 3.2 32.1 - - + -
571A GLU* 4.9 1.1 - - - -
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Residues in contact with CYS 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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513A ILE* 4.0 4.9 - - - -
514A CYS* 2.0 64.2 - - + +
521A ARG* 5.2 2.9 - - - -
555A VAL* 2.9 26.2 + - + +
556A GLU* 4.1 3.6 - - - +
558A CYS* 1.3 75.3 - - - +
560A LYS* 1.3 60.0 + - + +
561A ALA 3.3 6.8 + - - +
564A LYS* 5.2 2.8 - - - +
568A PHE* 3.9 13.2 - - - -
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Residues in contact with LYS 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 GLU* 2.9 50.2 + - + +
557A LYS* 3.0 12.2 - - - +
559A CYS* 1.3 75.0 - - + +
561A ALA* 1.3 56.8 + - - +
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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
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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