Contacts of the helix formed by residues 540 - 560 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LYS* 5.1 0.4 - - - +
538B LYS 3.5 6.2 + - - +
539B ALA* 1.3 73.5 - - - +
541B LYS* 1.3 56.8 + - - +
542B GLU* 3.9 10.1 - - - +
543B GLN* 2.5 46.0 + - - +
544B LEU* 2.8 14.2 + - - +
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 6.4 2.0 - - - -
409B VAL* 5.9 3.8 - - + -
413B LYS* 4.9 4.0 - - - +
539B ALA 3.9 1.6 + - - -
540B THR* 1.3 70.4 - - - +
542B GLU* 1.3 86.9 + - - +
544B LEU* 4.2 8.4 - - - +
545B LYS* 3.2 56.0 + - + +
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B THR* 2.9 8.4 - - - +
541B LYS* 1.3 109.6 + - - +
543B GLN* 1.3 62.9 + - - +
544B LEU 3.1 2.5 + - - -
545B LYS* 3.6 19.2 + - - +
546B ALA* 3.7 18.9 + - - +
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Residues in contact with GLN 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ALA* 4.7 7.4 - - + -
540B THR* 2.5 38.0 + - - +
542B GLU* 1.3 72.6 - - - +
544B LEU* 1.3 57.7 + - - +
546B ALA* 3.9 5.3 + - - +
547B VAL* 3.5 26.7 + - - +
582B ALA 4.7 14.1 - - - +
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 3.8 32.8 - - + -
413B LYS* 4.3 4.5 - - - +
529B LEU* 4.3 14.6 - - + +
532B LEU* 4.1 32.4 - - + +
533B VAL* 4.0 20.2 - - + -
536B LYS 5.1 0.4 - - - +
539B ALA* 3.7 39.7 - - + +
540B THR 2.8 11.9 + - - +
541B LYS* 4.2 5.6 - - - +
543B GLN* 1.3 79.5 - - - +
545B LYS* 1.3 58.9 + - + +
546B ALA 3.0 8.6 + - - -
547B VAL* 3.4 3.2 + - + +
548B MET* 3.2 24.4 + - - +
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Residues in contact with LYS 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 4.5 23.2 - - + +
402B LYS* 6.5 1.1 - - + -
405B ASN* 6.3 2.9 - - + -
406B ALA* 6.6 0.2 - - + -
409B VAL* 6.5 0.7 - - + -
541B LYS* 3.2 43.9 + - + +
542B GLU* 3.6 23.9 + - - +
544B LEU* 1.3 75.3 - - + +
546B ALA* 1.3 55.9 + - - +
548B MET* 4.3 9.8 - - - +
549B ASP* 3.7 24.1 + - - +
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Residues in contact with ALA 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B GLU 3.7 16.2 + - - +
543B GLN* 4.0 7.4 - - - +
544B LEU 3.0 1.4 - - - -
545B LYS* 1.3 77.8 - - - +
547B VAL* 1.3 62.5 + - + +
548B MET 3.3 1.8 - - - -
549B ASP* 3.4 7.3 + - - +
550B ASP* 3.1 24.1 + - - +
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 3.7 34.1 - - + -
543B GLN 3.5 17.7 + - - +
544B LEU* 3.4 3.4 + - + +
546B ALA* 1.3 76.9 - - + +
548B MET* 1.3 63.4 + - - +
550B ASP* 3.9 7.9 - - + +
551B PHE* 3.2 23.6 + - + +
575B LEU 5.5 0.2 - - - +
579B SER* 3.3 44.0 - - - +
582B ALA* 5.1 8.3 - - + +
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Residues in contact with MET 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 3.5 20.6 - - + +
405B ASN* 3.4 43.5 - - + +
525B LYS* 3.8 30.9 - - + +
526B GLN* 4.0 4.3 - - + -
529B LEU* 3.9 30.7 - - + +
532B LEU* 5.5 0.8 - - - +
544B LEU 3.2 17.1 + - - +
545B LYS* 4.3 9.9 - - - +
547B VAL* 1.3 77.5 - - - +
549B ASP* 1.3 61.7 + - - +
551B PHE* 3.4 8.1 + - - +
552B ALA* 3.0 27.4 + - - +
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Residues in contact with ASP 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS* 4.6 18.9 + - - -
545B LYS 3.7 15.0 - - - +
546B ALA* 3.4 12.2 + - - +
547B VAL 3.4 0.2 - - - -
548B MET* 1.3 78.6 - - - +
550B ASP* 1.3 60.2 + - - +
552B ALA* 3.7 7.8 - - - +
553B ALA* 3.0 32.6 + - - +
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Residues in contact with ASP 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B ALA 3.1 16.1 + - - +
547B VAL* 4.0 10.8 - - + +
548B MET 3.3 0.2 - - - -
549B ASP* 1.3 77.8 - - - +
551B PHE* 1.3 57.2 + - - +
553B ALA* 4.4 2.5 - - - +
554B PHE* 3.1 35.7 + - - +
575B LEU* 3.3 37.0 - - - +
579B SER* 4.3 9.0 + - - +
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Residues in contact with PHE 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B PHE* 4.4 23.3 - - + -
525B LYS* 4.8 9.0 - - + +
528B ALA* 5.9 3.8 - - + -
547B VAL* 3.2 19.1 + - + +
548B MET* 3.8 8.7 - - - +
550B ASP* 1.3 75.9 + - - +
552B ALA* 1.3 56.8 + - - +
554B PHE* 3.6 10.6 - - + -
555B VAL* 3.0 36.9 + - - +
575B LEU* 5.9 0.2 - - - -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 5.7 2.5 - - + +
525B LYS* 4.1 29.2 + - + +
548B MET 3.0 17.9 + - - +
549B ASP* 3.7 10.8 - - - +
550B ASP 3.3 0.2 - - - -
551B PHE* 1.3 73.3 - - - +
553B ALA* 1.3 66.3 + - - +
555B VAL* 3.3 5.2 + - - +
556B GLU* 3.1 22.2 + - - +
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Residues in contact with ALA 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP 3.0 14.5 + - - +
550B ASP* 4.4 2.7 - - - +
552B ALA* 1.3 78.1 - - - +
554B PHE* 1.3 57.3 + - - +
556B GLU* 3.5 8.5 + - - +
557B LYS* 2.9 36.3 + - - +
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Residues in contact with PHE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B PHE 5.5 2.0 - - - -
508B THR* 6.2 0.2 - - - -
509B PHE* 3.5 43.3 - + + -
550B ASP* 3.1 17.1 + - - +
551B PHE* 3.6 24.5 - - + -
553B ALA* 1.3 76.0 - - - +
555B VAL* 1.3 61.1 + - + +
557B LYS* 3.4 13.3 + - + +
558B CYS* 3.0 45.8 + - + +
568B PHE* 4.6 9.2 - - + -
571B GLU* 3.8 15.3 - - + +
572B GLY* 3.6 26.5 - - - -
575B LEU* 4.1 19.5 - - + -
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Residues in contact with VAL 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B PHE* 4.3 37.5 - - + -
513B ILE* 4.3 20.4 - - + -
521B ARG* 4.1 27.6 - - + -
525B LYS* 5.2 11.7 - - + +
551B PHE 3.0 23.4 + - - +
552B ALA* 3.8 4.5 - - - +
554B PHE* 1.3 78.2 - - + +
556B GLU* 1.3 61.3 + - - +
558B CYS* 3.6 3.0 + - - +
559B CYS* 2.9 33.8 + - + +
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Residues in contact with GLU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B ALA 3.1 13.1 + - - +
553B ALA* 3.6 11.9 - - - +
555B VAL* 1.3 76.0 - - - +
557B LYS* 1.3 63.5 + - - +
559B CYS* 3.9 3.3 - - - +
560B LYS* 2.9 36.7 + - + +
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Residues in contact with LYS 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B ALA* 2.9 26.9 + - - +
554B PHE* 3.7 13.0 - - + +
555B VAL 3.4 0.2 - - - -
556B GLU* 1.3 77.7 - - - +
558B CYS* 1.3 59.2 + - - +
560B LYS* 3.1 30.4 + - - +
561B ALA* 3.6 5.5 - - + +
567B CYS* 5.1 10.5 - - - -
571B GLU* 5.4 9.2 - - + -
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Residues in contact with CYS 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B CYS* 5.0 0.2 - - - -
554B PHE* 3.0 31.8 + - + +
555B VAL* 4.2 3.6 - - - +
557B LYS* 1.3 75.4 - - - +
559B CYS* 1.3 64.7 + - - +
561B ALA* 3.6 12.9 - - - +
564B LYS* 3.6 21.1 - - - +
567B CYS* 2.1 66.0 - - + -
568B PHE* 3.2 14.8 - - + +
571B GLU* 4.9 2.0 - - - -
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Residues in contact with CYS 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ILE* 4.0 12.6 - - - -
514B CYS* 2.0 62.2 - - + +
521B ARG* 5.3 2.9 - - - -
555B VAL* 2.9 26.2 + - - +
556B GLU* 4.2 4.0 - - - +
558B CYS* 1.3 77.5 - - - +
560B LYS* 1.3 58.0 + - - +
561B ALA 3.2 7.1 + - - +
564B LYS* 5.3 2.0 - - - +
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Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLU* 2.9 28.0 + - + +
557B LYS* 3.1 11.2 + - - +
559B CYS* 1.3 73.8 - - - +
561B ALA* 1.3 55.3 + - - +
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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
------------------------------------------------------------
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