Contacts of the helix formed by residues 539 - 552 (chain A) in PDB entry 2DX0
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 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A VAL* 3.4 6.0 + - - +
538A GLU* 1.3 80.7 - - - +
540A ARG* 1.3 67.9 + - - +
541A THR* 3.3 15.2 + - - -
542A SER* 3.2 18.9 + - - -
543A ALA* 2.9 23.7 + - - +
564A ARG* 3.8 6.8 + - - +
567A GLU* 3.5 17.0 + - - -
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Residues in contact with ARG 540 (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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539A SER* 1.3 73.0 + - - +
541A THR* 1.3 65.1 + - - +
543A ALA* 3.3 3.6 + - - +
544A GLU* 3.2 29.7 + - - +
564A ARG* 3.1 21.7 - - - +
567A GLU* 3.3 15.1 + - - +
585A HIS* 3.2 51.6 + - + +
626A GLU* 5.8 1.2 + - - -
1001A SO4 2.7 31.2 + - - +
582B ARG* 3.1 55.3 - - - +
584B GLN* 5.0 7.1 + - - -
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Residues in contact with THR 541 (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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539A SER* 3.2 9.3 + - - -
540A ARG* 1.3 82.5 - - - +
542A SER* 1.3 61.7 + - - +
544A GLU* 3.3 10.8 + - + +
545A LYS* 3.2 49.3 + - + +
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Residues in contact with SER 542 (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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537A VAL* 3.9 18.8 - - - +
538A GLU 4.9 1.7 + - - -
539A SER* 3.2 25.0 + - - -
541A THR* 1.3 80.0 - - - +
543A ALA* 1.3 61.2 + - - +
545A LYS* 3.3 13.2 + - - +
546A LEU* 3.1 24.8 + - - +
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Residues in contact with ALA 543 (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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537A VAL* 3.7 10.0 - - + +
539A SER 2.9 12.6 + - - +
540A ARG 3.5 9.4 - - - +
541A THR 3.2 0.2 - - - -
542A SER* 1.3 77.2 - - - +
544A GLU* 1.3 56.9 + - - +
546A LEU* 3.4 6.0 + - - +
547A LEU* 3.0 34.4 + - - +
562A LEU* 4.4 5.6 - - + +
564A ARG* 3.7 31.9 - - - +
576A SER* 4.1 11.2 - - - +
585A HIS* 4.4 2.5 - - + -
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Residues in contact with GLU 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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540A ARG* 3.2 23.9 + - - +
541A THR* 3.3 10.2 + - + +
543A ALA* 1.3 74.3 - - - +
545A LYS* 1.3 61.4 + - + +
547A LEU* 3.5 1.4 + - - +
548A GLN* 2.9 28.6 + - - +
583A VAL* 3.8 29.0 - - + +
585A HIS* 2.6 35.3 + - + +
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Residues in contact with LYS 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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541A THR* 3.2 38.2 + - + +
542A SER* 3.6 11.7 - - - +
543A ALA 3.3 0.2 - - - -
544A GLU* 1.3 73.2 - - + +
546A LEU* 1.3 57.6 + - - +
548A GLN* 3.1 11.8 + - - +
549A GLU* 2.8 48.5 + - + +
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Residues in contact with LEU 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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534A HIS* 4.6 2.2 - - + -
537A VAL* 4.2 9.0 - - + -
542A SER* 3.1 13.6 + - - +
543A ALA* 3.6 6.7 - - - +
545A LYS* 1.3 80.0 - - - +
547A LEU* 1.3 61.7 + - - +
549A GLU* 3.9 14.4 + - + +
550A TYR* 3.0 26.5 + - + +
562A LEU* 3.9 17.7 - - + -
635B VAL* 3.8 22.4 - - + -
636B PRO* 6.4 0.2 - - + -
637B ASN* 3.5 28.3 - - - +
638B PRO* 4.0 21.1 - - + +
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Residues in contact with LEU 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 ALA 3.0 20.1 + - - +
544A GLU 3.8 3.6 - - - +
546A LEU* 1.3 76.0 - - - +
548A GLN* 1.3 59.9 + - - +
550A TYR* 4.8 1.1 - - - -
551A CYS* 2.7 47.5 + - - +
560A THR 4.0 15.9 - - - +
561A PHE 4.7 0.2 - - - -
562A LEU* 4.5 6.1 - - + -
576A SER* 3.7 29.6 - - - +
577A PHE 4.1 3.1 - - - -
578A TRP* 4.4 6.3 - - + -
583A VAL* 3.6 39.9 - - + -
635B VAL* 3.3 31.6 - - + -
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Residues in contact with GLN 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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544A GLU 2.9 18.8 + - - +
545A LYS* 3.6 11.2 - - - +
547A LEU* 1.3 77.2 - - - +
549A GLU* 1.3 67.3 + - + +
552A ALA* 2.8 46.4 + - + +
578A TRP* 4.1 17.4 - - + -
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Residues in contact with GLU 549 (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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545A LYS* 2.8 35.8 + - + +
546A LEU* 3.9 14.5 + - + +
548A GLN* 1.3 79.0 - - + +
550A TYR* 1.3 61.6 + - - +
552A ALA* 4.6 1.4 + - - +
553A GLU 5.1 1.9 + - - -
554A THR* 4.2 9.5 - - - +
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Residues in contact with TYR 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 LEU* 3.0 21.0 + - + +
547A LEU 4.1 1.6 - - - +
549A GLU* 1.3 79.0 - - - +
551A CYS* 1.3 54.6 + - - +
554A THR* 2.4 38.5 + - + +
556A ALA* 4.2 6.2 - - + +
560A THR* 4.2 19.1 - - + -
633B ASP* 5.8 3.5 - - + +
634B PRO 4.0 12.6 + - - -
635B VAL* 4.1 14.4 - - + -
636B PRO* 3.2 45.5 - - + +
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Residues in contact with CYS 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 LEU* 2.7 29.7 + - - +
550A TYR* 1.3 79.3 - - - +
552A ALA* 1.3 64.2 + - - +
553A GLU 3.1 4.6 + - - -
554A THR* 3.5 11.7 + - - -
555A GLY 3.9 5.9 + - - -
556A ALA* 3.7 16.8 + - + +
560A THR* 3.7 31.9 - - - -
578A TRP* 3.4 46.5 + - + +
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Residues in contact with ALA 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 GLN* 2.8 40.2 + - + +
549A GLU* 5.3 0.4 - - - +
551A CYS* 1.3 73.9 - - - +
553A GLU* 1.3 71.1 + - + +
555A GLY 5.2 0.3 + - - -
578A TRP* 3.9 18.5 - - + -
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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