Contacts of the helix formed by residues 550 - 567 (chain A) in PDB entry 4BDT
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 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A LEU* 2.9 33.2 + - + +
547A ASP* 4.0 17.6 - - - +
549A ALA* 1.3 76.9 - - - +
551A ARG* 1.3 60.1 + - - +
552A GLN 3.5 0.2 - - - -
553A TRP* 3.8 26.6 - - + +
554A LYS* 3.6 20.6 + - - +
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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 ASP* 3.4 42.5 + - - +
548A GLU* 3.7 28.4 + - - +
549A ALA 3.2 0.2 - - - -
550A GLU* 1.3 77.0 - - - +
552A GLN* 1.3 63.0 + - - +
553A TRP 3.2 1.1 - - - -
554A LYS* 3.3 26.2 - - + +
555A ALA* 3.3 10.7 + - - +
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Residues in contact with GLN 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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548A GLU* 3.3 23.2 + - - +
549A ALA* 3.8 8.9 + - - +
551A ARG* 1.3 77.8 - - - +
553A TRP* 1.3 61.4 + - + +
555A ALA* 4.0 7.2 - - + +
556A GLU* 3.2 34.3 + - - +
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Residues in contact with TRP 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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546A LEU* 5.5 6.1 - - + -
549A ALA* 3.0 33.6 + - + +
550A GLU* 3.9 28.3 - - + +
551A ARG 3.2 1.0 - - - -
552A GLN* 1.3 82.5 - - + +
554A LYS* 1.3 58.9 + - - +
556A GLU* 3.8 16.1 - - - +
557A PHE* 3.1 26.7 + - - +
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Residues in contact with LYS 554 (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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550A GLU 3.6 12.3 + - - +
551A ARG* 3.3 20.2 - - + +
553A TRP* 1.3 76.4 - - - +
555A ALA* 1.3 67.5 + - + +
556A GLU 3.3 0.2 - - - -
557A PHE* 3.8 6.8 - - - +
558A HIS* 2.9 30.5 + - + +
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Residues in contact with ALA 555 (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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551A ARG 3.3 12.5 + - - +
552A GLN* 4.0 8.1 - - + +
554A LYS* 1.3 87.3 - - + +
556A GLU* 1.3 60.3 + - - +
558A HIS* 3.5 6.3 + - - +
559A ARG* 3.5 22.9 + - - +
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Residues in contact with GLU 556 (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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552A GLN* 3.2 23.5 + - - +
553A TRP* 3.8 17.5 + - - +
555A ALA* 1.3 76.9 - - - +
557A PHE* 1.3 57.6 - - - +
559A ARG* 3.6 34.0 + - - +
560A TRP* 3.3 21.3 + - - +
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Residues in contact with PHE 557 (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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553A TRP 3.1 18.7 + - - +
554A LYS* 3.5 6.3 + - - +
555A ALA 3.3 0.4 - - - -
556A GLU* 1.3 78.9 - - - +
558A HIS* 1.3 60.7 + - - +
559A ARG 3.4 0.4 - - - -
560A TRP* 3.7 33.9 - + + -
561A SER* 2.9 40.6 + - - -
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Residues in contact with HIS 558 (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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554A LYS* 2.9 20.1 + - + +
555A ALA* 3.8 8.3 - - - +
556A GLU 3.5 0.2 - - - -
557A PHE* 1.3 78.1 - - - +
559A ARG* 1.3 60.8 + - - +
561A SER* 2.7 23.1 + - - -
562A SER* 3.3 14.4 + - - -
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Residues in contact with ARG 559 (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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555A ALA 3.5 16.2 + - - +
556A GLU* 3.6 40.4 + - - +
558A HIS* 1.3 77.9 + - - +
560A TRP* 1.3 86.6 + - - +
562A SER* 2.9 20.1 + - - +
563A TYR* 3.1 58.5 - - + +
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Residues in contact with TRP 560 (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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556A GLU 3.3 17.9 + - - +
557A PHE* 3.5 28.9 + + + +
558A HIS 3.3 0.4 - - - -
559A ARG* 1.3 103.9 - - - +
561A SER* 1.3 71.6 + - - +
563A TYR* 3.2 16.1 + + + +
564A MET* 3.4 42.7 + - + +
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Residues in contact with SER 561 (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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557A PHE* 2.9 33.1 + - - -
558A HIS* 2.7 28.9 + - - -
560A TRP* 1.3 86.7 - - - +
562A SER* 1.3 56.0 + - - +
564A MET* 3.1 8.2 + - - +
565A VAL* 3.1 31.1 + - - +
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Residues in contact with SER 562 (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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558A HIS* 3.3 10.9 + - - -
559A ARG* 2.9 24.1 + - - -
561A SER* 1.3 76.8 + - - +
563A TYR* 1.3 66.4 + - - +
564A MET 3.1 4.9 - - - -
565A VAL* 3.2 17.5 - - - +
566A HIS* 3.2 26.2 + - - +
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Residues in contact with TYR 563 (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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559A ARG* 3.1 57.5 + - + +
560A TRP* 3.2 11.2 + + + +
562A SER* 1.3 83.6 + - - +
564A MET* 1.3 59.0 + - - +
566A HIS* 4.1 9.7 - - + +
567A TRP* 3.7 19.6 + - - +
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Residues in contact with MET 564 (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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560A TRP* 3.4 41.2 + - + +
561A SER* 3.1 11.6 + - - +
562A SER 3.1 0.4 - - - -
563A TYR* 1.3 79.3 - - - +
565A VAL* 1.3 65.3 + - + +
566A HIS 3.1 1.3 - - - -
567A TRP* 3.1 53.6 + - + +
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Residues in contact with VAL 565 (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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561A SER* 3.1 19.2 + - - +
562A SER* 3.2 20.2 - - - +
564A MET* 1.3 76.2 - - + +
566A HIS* 1.3 67.4 + - - +
567A TRP 4.2 3.5 - - - +
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Residues in contact with HIS 566 (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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562A SER 3.2 15.5 + - - +
563A TYR* 4.1 11.2 - - + +
565A VAL* 1.3 78.8 - - + +
567A TRP* 1.3 70.1 + - - +
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Residues in contact with TRP 567 (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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563A TYR 3.7 13.4 + - - +
564A MET* 3.1 46.9 + - + +
565A VAL 4.2 3.6 - - - +
566A HIS* 1.3 88.2 + - - +
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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