Contacts of the helix formed by residues 542 - 553 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A GLU* 2.9 29.5 + - - -
540A LYS 4.0 2.2 + - - -
541A VAL* 1.3 81.2 - - - +
543A PRO* 1.3 68.0 - - - +
544A SER* 2.9 28.6 + - - -
545A LEU 2.9 11.1 + - - -
546A LYS 3.5 0.3 + - - -
574A LYS* 4.0 14.1 + - - -
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Residues in contact with PRO 543 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A VAL 3.7 4.9 - - - +
542A SER* 1.3 83.5 - - - +
544A SER* 1.3 55.9 - - - +
545A LEU 3.5 0.2 - - - -
546A LYS* 3.5 33.8 - - - +
547A GLY* 3.1 20.4 + - - -
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Residues in contact with SER 544 (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 SER* 2.9 19.9 + - - -
543A PRO* 1.3 76.4 - - - +
545A LEU* 1.3 60.0 + - - +
546A LYS 3.2 0.2 - - - -
547A GLY* 3.1 2.3 + - - +
548A PHE* 2.9 29.5 + - - +
569A HIS* 4.2 3.4 - - - -
570A PRO* 5.3 4.0 - - - -
571A PHE* 4.0 26.8 - - - +
574A LYS* 4.5 10.1 + - - +
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Residues in contact with LEU 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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414A GLU* 2.8 41.1 - - - +
417A ILE* 4.3 19.3 - - + -
505A VAL* 5.0 3.1 - - + -
509A VAL* 3.5 22.7 - - + -
535A LEU* 4.4 1.6 - - + -
541A VAL* 4.0 17.5 - - + -
542A SER 2.9 7.6 + - - +
544A SER* 1.3 76.6 + - - +
546A LYS* 1.3 55.8 + - - +
548A PHE* 3.9 3.1 - - + +
549A LEU* 2.7 66.9 + - + +
571A PHE* 3.4 27.1 - - + -
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Residues in contact with LYS 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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535A LEU* 6.2 1.3 - - + -
538A LEU* 3.9 25.4 - - + -
541A VAL* 3.8 24.6 - - + +
542A SER 3.5 1.2 + - - -
543A PRO* 3.5 37.6 + - + +
544A SER 3.2 0.2 - - - -
545A LEU* 1.3 77.8 - - - +
547A GLY* 1.3 51.9 + - - +
549A LEU* 3.1 6.3 + - - -
550A ASP* 2.5 55.9 + - - +
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Residues in contact with GLY 547 (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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543A PRO 3.1 11.6 + - - -
544A SER* 3.1 5.2 + - - -
546A LYS* 1.3 81.7 - - - +
548A PHE* 1.3 64.2 + - - +
550A ASP* 3.2 19.7 + - - +
551A ARG* 3.4 14.9 + - - +
569A HIS* 3.9 8.1 - - - -
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Residues in contact with PHE 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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421A CYS* 4.8 11.4 - - + -
425A LEU* 4.5 11.0 - - + -
501A LEU* 4.6 7.2 - - + -
505A VAL* 5.0 8.3 - - + -
544A SER 2.9 12.8 + - - +
545A LEU* 3.9 3.8 - - + +
547A GLY* 1.3 75.5 - - - +
549A LEU* 1.3 66.8 + - + +
551A ARG* 2.9 15.4 + - - +
552A LEU* 3.3 33.0 + - + +
566A LEU* 3.3 44.8 - - + +
569A HIS* 3.2 41.9 - + + +
571A PHE* 3.8 34.5 - + + -
572A LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A GLY* 4.7 1.8 - - - +
505A VAL* 3.3 32.1 - - + -
506A ILE* 4.6 14.4 - - + +
509A VAL* 4.9 0.2 - - + -
533A PRO 5.5 0.9 - - - +
535A LEU* 4.3 20.6 - - + -
545A LEU* 2.7 53.9 + - + +
546A LYS* 3.4 7.0 - - - +
548A PHE* 1.3 76.9 - - + +
550A ASP* 1.3 60.2 + - - +
551A ARG 3.0 5.5 + - - -
552A LEU* 3.3 14.0 + - - +
553A LEU* 3.4 47.7 + - + +
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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 LYS* 2.5 43.4 + - - +
547A GLY* 3.3 12.2 - - - +
548A PHE 3.1 0.2 - - - -
549A LEU* 1.3 73.2 - - - +
551A ARG* 1.3 64.7 + - + +
553A LEU* 4.7 6.1 - - - +
554A VAL* 4.7 6.8 - - - +
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Residues in contact with ARG 551 (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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547A GLY 3.4 15.7 - - - +
548A PHE* 2.9 8.9 + - - +
550A ASP* 1.3 84.5 + - + +
552A LEU* 1.3 63.0 + - + +
553A LEU 3.5 0.7 - - - -
554A VAL* 3.1 23.1 - - - +
559A GLN* 3.1 26.3 + - - +
560A ARG 4.5 0.8 - - - -
561A ALA* 3.3 50.8 + - + +
565A GLU* 3.7 8.3 + - - -
566A LEU* 5.4 3.4 - - + -
569A HIS* 4.7 12.8 - - + +
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Residues in contact with LEU 552 (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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498A ILE* 3.3 35.6 - - + +
499A TRP* 3.9 13.0 - - - -
501A LEU* 3.6 24.0 - - + -
502A GLY* 4.6 14.8 - - - +
505A VAL* 5.1 2.0 - - + -
548A PHE* 3.3 37.7 - - + +
549A LEU* 3.3 8.6 + - - +
551A ARG* 1.3 77.5 - - - +
553A LEU* 1.3 58.8 + - - +
554A VAL 3.1 9.6 + - - -
560A ARG* 3.4 18.6 + - - +
561A ALA* 4.4 4.0 - - + +
566A LEU* 3.4 31.4 - - + -
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Residues in contact with LEU 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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499A TRP* 3.8 17.7 - - + +
502A GLY* 4.4 14.1 - - - +
503A ILE* 3.7 28.5 - - + -
506A ILE* 4.4 5.6 - - + -
532A PRO* 3.6 28.2 - - + +
533A PRO* 3.5 36.8 - - + +
549A LEU* 3.4 40.1 + - + +
550A ASP* 5.1 4.8 - - - +
551A ARG 3.5 0.4 - - - -
552A LEU* 1.3 79.4 - - - +
554A VAL* 1.3 61.6 + - - +
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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