Contacts of the helix formed by residues 539 - 554 (chain B) in PDB entry 2VXO
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 539 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 4.3 4.7 - - - +
58A GLU* 3.2 54.0 - - - +
504B LEU* 5.8 0.3 - - - +
505B HIS* 3.5 27.1 + - + +
537B GLU 3.4 4.2 + - - -
538B PRO* 1.3 70.1 - - - +
540B TRP* 1.3 62.1 + - - +
541B GLU* 3.6 9.9 + - - +
542B SER* 2.6 28.6 + - - +
543B LEU* 3.0 32.7 + - - +
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Residues in contact with TRP 540 (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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538B PRO* 3.6 36.7 + - + +
539B ASP* 1.3 76.1 + - - +
541B GLU* 1.3 58.7 + - + +
543B LEU* 3.4 15.0 + - + +
544B ILE* 2.9 33.0 + - + +
562B TYR* 3.8 14.1 - + + -
564B PHE* 3.7 33.9 - + - -
652B THR* 3.8 12.1 - - + -
653B PRO* 3.5 56.4 - - + +
659B VAL* 4.1 20.9 - - + +
662B VAL* 5.0 2.5 - - + -
663B LEU* 5.8 2.9 - - + -
680B TYR* 3.8 22.0 - + - -
682B LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 541 (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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32A ASP 2.7 19.4 - - - +
33A ALA* 3.0 29.6 - - - +
34A GLY* 3.1 11.4 + - - -
56A PRO* 4.3 11.8 - - + +
57A LEU* 3.5 23.3 + - + +
497B LYS* 5.5 1.2 + - - -
539B ASP* 3.5 6.7 + - - +
540B TRP* 1.3 75.3 - - - +
542B SER* 1.3 60.6 + - - +
544B ILE* 3.9 8.1 - - + +
545B PHE* 3.0 26.5 + - - +
652B THR* 4.6 13.0 - - + -
655B ASN* 4.6 5.2 + - - +
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Residues in contact with SER 542 (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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56A PRO* 3.6 10.2 - - - +
501B ILE* 3.4 40.7 - - - +
505B HIS* 4.6 4.8 - - - -
507B LEU* 6.2 0.7 - - - -
539B ASP* 2.6 36.6 + - - +
541B GLU* 1.3 76.4 - - - +
543B LEU* 1.3 61.5 + - - +
545B PHE* 3.3 3.9 + - - +
546B LEU* 2.9 33.9 + - - +
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Residues in contact with LEU 543 (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 LEU* 4.5 12.8 - - + -
532B ILE* 3.9 27.8 - - + -
538B PRO* 3.6 29.8 - - + -
539B ASP 3.0 25.5 + - - +
540B TRP* 3.7 16.6 - - + +
541B GLU 3.4 0.2 - - - -
542B SER* 1.3 77.3 - - - +
544B ILE* 1.3 50.5 + - - +
546B LEU* 3.0 11.3 + - + +
547B ALA* 2.7 34.3 + - - +
562B TYR* 3.7 31.0 - - + -
682B LEU* 3.9 20.0 - - + +
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Residues in contact with ILE 544 (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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540B TRP* 2.9 21.4 + - + +
541B GLU* 3.9 8.5 - - + +
542B SER 3.3 0.2 - - - -
543B LEU* 1.3 73.2 - - - +
545B PHE* 1.3 63.6 + - - +
547B ALA* 3.3 9.0 + - - +
548B ARG* 3.2 53.3 + - + +
650B PRO* 4.2 24.5 - - + +
651B ALA 4.9 0.9 - - - +
652B THR* 2.9 38.1 - - + +
653B PRO* 5.6 0.4 - - + -
680B TYR* 6.2 0.4 - - + -
682B LEU* 4.0 21.1 - - + +
684B SER* 6.1 0.2 - - - +
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Residues in contact with PHE 545 (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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494B ASP* 3.5 44.9 - - + -
497B LYS* 3.5 46.9 - - + +
498B LEU* 4.3 10.8 - - + -
501B ILE* 3.5 24.5 - - + -
541B GLU 3.0 14.4 + - - +
542B SER* 3.4 8.7 - - - +
544B ILE* 1.3 73.4 - - - +
546B LEU* 1.3 72.1 + - + +
548B ARG* 3.0 12.2 + - + +
549B LEU* 2.9 44.4 + - + +
552B ARG* 4.4 11.7 - - - -
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Residues in contact with LEU 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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469B VAL* 4.3 17.0 - - + +
470B ALA* 6.0 2.7 - - - -
498B LEU* 3.6 30.1 - - + -
501B ILE* 4.5 9.2 - - + -
502B THR* 5.4 0.9 - - + -
507B LEU* 3.7 29.8 - - + -
532B ILE* 3.9 26.9 - - + -
542B SER 2.9 17.4 + - - +
543B LEU* 3.0 16.4 + - + +
545B PHE* 1.3 81.8 - - + +
547B ALA* 1.3 57.7 + - - +
549B LEU* 4.3 4.5 - - + -
550B ILE* 3.0 41.5 + - + +
560B VAL* 4.8 0.4 - - - -
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Residues in contact with ALA 547 (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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543B LEU 2.7 9.2 + - - +
544B ILE 3.4 9.9 - - - +
546B LEU* 1.3 78.4 - - - +
548B ARG* 1.3 57.9 + - + +
551B PRO* 2.9 25.3 - - - +
560B VAL* 3.8 20.6 - - + +
682B LEU* 3.4 47.1 - - + +
683B THR* 4.5 7.0 - - - +
687B PRO* 5.5 1.0 - - - +
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Residues in contact with ARG 548 (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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34A GLY 6.3 1.0 - - - -
497B LYS* 6.1 0.8 - - - +
544B ILE* 3.2 36.3 + - + +
545B PHE* 3.0 12.8 + - + +
547B ALA* 1.3 78.4 - - + +
549B LEU* 1.3 66.2 + - - +
551B PRO* 3.6 3.8 - - - +
552B ARG* 3.3 40.6 + - - +
649B ILE* 5.0 7.7 - - - +
650B PRO* 6.1 0.4 - - - +
682B LEU 5.7 2.0 - - - +
684B SER* 4.1 25.3 + - - +
687B PRO* 6.3 2.2 - - - -
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Residues in contact with LEU 549 (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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469B VAL* 4.4 7.9 - - + -
490B THR* 4.4 8.3 - - + -
494B ASP* 3.6 35.9 - - + +
498B LEU* 3.8 39.3 - - + -
545B PHE* 2.9 30.1 + - + +
546B LEU* 3.8 7.2 - - + +
548B ARG* 1.3 76.3 - - - +
550B ILE* 1.3 61.8 + - - +
552B ARG* 2.9 35.8 + - + +
553B MET* 3.0 35.0 + - + +
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Residues in contact with ILE 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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466B LEU* 3.6 29.4 - - + -
469B VAL* 4.3 26.2 - - + -
509B ALA* 4.8 6.1 - - + -
530B CYS* 4.0 20.9 - - - -
532B ILE* 4.3 19.1 - - + -
546B LEU* 3.0 22.1 + - + +
549B LEU* 1.3 79.7 - - + +
551B PRO* 1.4 66.1 - - + +
553B MET* 3.2 8.2 + - - +
554B CYS* 2.8 29.4 + - + +
557B VAL* 4.2 15.3 - - + -
560B VAL* 4.1 12.8 - - + -
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Residues in contact with PRO 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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520B GLN* 4.2 5.4 + - - +
547B ALA 2.9 29.2 - - - +
548B ARG* 3.6 6.5 - - - +
550B ILE* 1.4 93.9 - - + +
552B ARG* 1.3 55.2 + - + +
554B CYS 3.4 13.7 - - - +
555B HIS* 3.0 24.8 - - - -
557B VAL* 3.8 16.6 - - + +
559B ARG 5.2 3.1 - - - +
560B VAL* 3.9 12.1 - - + -
683B THR* 5.2 2.0 - - + -
687B PRO* 3.7 31.2 - - + -
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Residues in contact with ARG 552 (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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370A ARG* 3.9 25.0 - - - +
371A PRO 4.0 5.6 - - - +
372A ASP* 3.5 9.7 - - - +
491B THR* 6.0 1.4 - - - +
494B ASP* 2.8 32.5 + - - -
545B PHE* 4.4 10.1 - - - -
548B ARG* 3.3 26.3 + - - +
549B LEU* 2.9 37.1 + - + +
551B PRO* 1.3 77.0 - - + +
553B MET* 1.3 62.5 + - + +
555B HIS* 3.2 22.0 + - - -
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Residues in contact with MET 553 (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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371A PRO 5.1 0.7 - - - -
372A ASP* 3.5 4.4 - - - +
373A LEU* 2.8 54.0 + - + +
374A ILE 3.3 6.2 + - - -
465B ILE* 4.1 3.6 - - + -
469B VAL* 3.6 31.6 - - + -
486B VAL* 3.7 25.8 - - + +
489B CYS* 5.0 8.7 - - + +
490B THR* 3.8 26.2 - - + -
498B LEU* 5.8 0.4 - - - -
549B LEU* 3.0 34.6 + - + +
550B ILE* 3.7 8.5 - - - +
552B ARG* 1.3 77.1 - - + +
554B CYS* 1.3 66.5 + - - +
555B HIS 3.9 0.7 - - - -
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Residues in contact with CYS 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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373A LEU* 5.0 1.1 - - - -
374A ILE* 3.9 19.5 - - - -
462B THR* 4.5 9.2 - - - -
465B ILE* 3.8 30.5 - - - -
466B LEU* 4.7 7.4 - - - -
550B ILE* 2.8 13.4 + - + +
551B PRO* 3.4 13.0 - - - +
553B MET* 1.3 84.9 - - - +
555B HIS* 1.3 56.2 + - - +
556B ASN* 3.1 19.7 - - - +
557B VAL* 3.1 31.4 + - + +
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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