Contacts of the helix formed by residues 543 - 554 (chain B) in PDB entry 3V42
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 543 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B VAL 5.3 4.2 - - - +
481B THR* 4.2 6.8 + - - -
484B ASN* 5.8 1.4 + - - -
540B GLY* 4.1 10.4 - - - +
541B ALA 3.4 2.0 - - - -
542B SER* 1.3 88.1 + - - +
544B GLU* 1.3 66.6 + - - +
545B ASP* 3.4 5.4 - - + +
546B ASN* 3.2 26.4 + - - +
547B VAL* 2.9 21.0 + - - +
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Residues in contact with GLU 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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542B SER 3.9 0.4 + - - -
543B GLU* 1.3 76.1 - - + +
545B ASP* 1.3 72.4 + - - +
547B VAL* 3.4 5.9 + - - +
548B LYS* 3.1 47.6 + - - +
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Residues in contact with ASP 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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366B TRP* 3.2 37.0 + - - -
370B MET* 3.5 13.4 - - + +
475B ALA 4.3 9.0 - - - +
478B VAL* 4.4 6.4 - - - +
479B GLY* 3.1 24.0 + - - +
480B PRO* 3.6 22.2 - - + -
543B GLU* 3.4 2.9 - - + +
544B GLU* 1.3 86.3 - - - +
546B ASN* 1.3 57.1 + - - +
548B LYS* 3.2 4.4 + - - +
549B LEU* 2.9 25.3 + - - +
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Residues in contact with ASN 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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480B PRO* 3.3 7.4 - - - +
481B THR* 2.8 44.9 + - - +
511B TRP* 3.5 19.5 - - + -
540B GLY 3.5 16.2 + - - -
541B ALA* 3.7 16.8 - - - +
543B GLU* 3.2 29.9 + - - +
545B ASP* 1.3 78.0 - - - +
547B VAL* 1.3 63.1 + - - +
549B LEU* 3.2 6.8 + - - +
550B LEU* 2.9 27.2 + - - +
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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
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536B LEU* 3.7 19.3 - - + -
541B ALA 3.5 15.7 - - - +
542B SER 3.8 8.5 - - - +
543B GLU 2.9 17.2 + - - +
544B GLU* 3.8 6.1 - - - +
546B ASN* 1.3 77.4 - - - +
548B LYS* 1.3 66.7 + - + +
550B LEU* 3.2 9.3 + - - +
551B LYS* 3.0 23.5 + - + +
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Residues in contact with LYS 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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370B MET* 4.1 15.1 - - - +
544B GLU* 3.1 41.7 + - - +
545B ASP* 3.7 5.8 - - - +
547B VAL* 1.3 79.5 - - + +
549B LEU* 1.3 63.1 + - - +
551B LYS* 3.3 11.9 + - + +
552B PHE* 3.1 22.9 + - - +
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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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369B LEU* 4.1 12.8 - - + +
370B MET* 3.9 11.6 - - + -
480B PRO* 3.8 25.6 - - + -
482B ILE* 3.9 18.4 - - + -
511B TRP* 4.1 26.0 - - + -
545B ASP 2.9 16.5 + - - +
546B ASN* 3.6 6.3 - - - +
548B LYS* 1.3 78.0 - - - +
550B LEU* 1.3 67.1 + - + +
552B PHE* 3.2 3.5 + - - +
553B TRP* 2.9 66.0 + - + +
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Residues in contact with LEU 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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511B TRP* 3.9 18.4 - - + +
514B LYS* 3.9 15.3 - - + -
515B VAL* 3.5 41.7 - - + +
518B LEU* 4.3 19.5 - - + -
536B LEU* 4.3 17.0 - - + -
541B ALA* 3.8 30.7 - - + +
546B ASN 2.9 18.5 + - - +
547B VAL* 3.7 6.7 - - - +
549B LEU* 1.3 77.7 - - + +
551B LYS* 1.3 65.3 + - - +
553B TRP* 3.9 0.5 - - - +
554B MET* 3.2 24.2 + - - +
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Residues in contact with LYS 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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547B VAL* 3.0 15.4 + - + +
548B LYS* 3.6 14.6 - - + +
549B LEU 3.2 0.2 - - - -
550B LEU* 1.3 77.2 - - - +
552B PHE* 1.3 64.6 + - - +
554B MET* 3.4 18.0 + - - +
555B THR* 4.3 4.7 + - - +
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Residues in contact with PHE 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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369B LEU 3.4 12.6 - - - -
370B MET* 3.4 18.2 - - - +
371B GLY* 3.1 41.5 - - - -
395B LEU* 4.0 17.3 - - + -
399B CYS* 3.9 29.4 - - + -
401B ARG* 6.2 3.6 - - - -
416B ASN* 4.7 3.1 - - - -
548B LYS 3.1 16.8 + - - +
549B LEU 3.9 2.2 - - - +
551B LYS* 1.3 78.1 - - - +
553B TRP* 1.3 66.2 + + - +
554B MET 3.0 1.7 + - - -
555B THR* 3.0 47.9 + - + +
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Residues in contact with TRP 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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369B LEU* 3.2 32.8 + - + -
394B MET 3.6 24.7 - - - -
395B LEU* 4.0 6.6 - - - +
396B PRO* 3.6 29.8 - - + -
399B CYS* 4.3 5.2 - - - -
482B ILE* 4.1 18.8 - - + -
508B LYS* 3.9 19.5 - - + -
511B TRP* 3.8 21.5 - - + -
512B MET* 3.9 26.7 - - + +
515B VAL* 3.8 17.2 - - + +
549B LEU* 2.9 42.7 + - + +
552B PHE* 1.3 89.2 - + - +
554B MET* 1.3 56.5 + - - +
555B THR 3.1 0.2 - - - -
556B GLY* 2.8 23.1 + - - -
557B LEU 4.1 0.2 + - - -
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Residues in contact with MET 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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515B VAL* 3.4 25.8 - - + +
518B LEU* 4.1 21.1 - - + -
519B PHE* 3.8 46.0 - - + +
522B THR* 5.6 1.6 - - - +
550B LEU 3.2 10.6 + - - +
551B LYS* 3.5 16.4 - - - +
552B PHE 3.0 1.8 + - - -
553B TRP* 1.3 77.1 - - - +
555B THR* 1.3 55.1 + - + +
556B GLY 3.1 0.7 - - - -
557B LEU* 3.2 19.5 - - + +
558B SER* 2.9 35.2 + - - +
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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