Contacts of the helix formed by residues 542 - 550 (chain B) in PDB entry 2BVA
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 SER 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B GLU* 2.9 30.2 + - - -
540B LYS 4.0 1.2 + - - -
541B VAL* 1.3 74.5 - - - +
543B PRO* 1.3 76.1 - - - +
544B SER* 3.6 3.8 + - - -
545B LEU* 2.9 21.3 + - - +
546B LYS* 3.0 7.3 + - - +
574B LYS* 3.3 19.5 + - - -
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Residues in contact with PRO 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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541B VAL 3.5 0.4 - - - -
542B SER* 1.3 85.7 - - - +
544B SER* 1.3 57.1 + - - +
546B LYS* 3.4 26.8 - - + +
547B GLY* 3.0 23.0 + - - -
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Residues in contact with SER 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* 2.9 7.8 + - - -
543B PRO* 1.3 76.3 - - - +
545B LEU* 1.3 61.1 + - - +
547B GLY* 3.9 2.0 - - - +
548B PHE* 2.9 26.1 + - - +
569B HIS* 3.4 7.5 - - - -
570B PRO* 5.5 1.6 - - - -
571B PHE* 3.3 35.8 - - - +
574B LYS* 3.8 10.4 + - - -
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Residues in contact with LEU 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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414B GLU* 3.7 20.2 - - + +
417B ILE* 4.0 19.1 - - + -
505B VAL* 4.2 19.7 - - + -
509B VAL* 5.6 5.8 - - + -
535B LEU* 6.3 1.8 - - + -
541B VAL* 3.6 17.9 - - + -
542B SER* 2.9 12.5 + - - +
544B SER* 1.3 78.6 + - - +
546B LYS* 1.3 57.3 + - - +
548B PHE* 2.7 40.0 + - + +
549B LEU* 2.8 24.5 + - + +
571B PHE* 3.3 33.0 - - + -
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Residues in contact with LYS 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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535B LEU* 6.0 2.7 - - - -
538B LEU* 4.1 31.2 + - + +
541B VAL* 2.8 32.0 + - + +
542B SER 3.0 11.7 - - - +
543B PRO* 3.4 28.5 - - + +
545B LEU* 1.3 79.9 - - - +
547B GLY* 1.3 63.3 + - - +
548B PHE 3.1 0.2 + - - -
549B LEU* 3.3 3.7 + - - +
550B ASP* 3.2 29.4 + - - +
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Residues in contact with GLY 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 PRO 3.0 12.8 + - - -
544B SER* 3.9 2.0 - - - -
546B LYS* 1.3 78.5 - - - +
548B PHE* 1.3 62.8 + - - +
550B ASP* 3.5 10.6 + - - +
551B ARG* 3.4 24.8 + - - +
569B HIS* 4.5 7.4 - - - -
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Residues in contact with PHE 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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421B CYS* 3.2 39.5 - - + -
425B LEU* 4.4 8.7 - - + -
505B VAL* 4.5 11.4 - - + -
544B SER 2.9 17.6 + - - +
545B LEU* 2.7 34.4 + - + +
547B GLY* 1.3 77.8 - - - +
549B LEU* 1.3 60.1 + - + -
551B ARG* 3.2 9.7 + - - +
552B LEU* 2.9 40.2 - - + +
566B LEU* 5.7 3.8 - - + -
569B HIS* 3.9 24.7 - + + -
571B PHE* 3.5 25.4 - + + -
572B LEU* 3.7 25.1 - - + -
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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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502B GLY* 3.6 14.4 - - - +
505B VAL* 3.5 41.7 - - + -
506B ILE* 4.2 17.7 - - + -
533B PRO 5.3 0.9 - - - +
535B LEU* 5.1 13.7 - - + +
545B LEU* 2.8 22.1 + - + +
546B LYS* 4.1 4.0 - - - +
548B PHE* 1.3 70.8 - - + +
550B ASP* 1.3 61.0 + - - +
551B ARG 3.0 5.4 - - - -
552B LEU* 2.9 25.0 + - + -
553B LEU* 2.9 46.5 + - + +
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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 LYS* 3.2 21.1 + - - +
547B GLY* 3.8 9.5 - - - +
548B PHE 3.3 0.2 - - - -
549B LEU* 1.3 78.5 - - - +
551B ARG* 1.3 60.5 + - - +
552B LEU 3.3 0.4 - - - -
553B LEU* 4.7 5.2 - - - +
554B VAL* 3.2 25.6 - - - +
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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