Contacts of the helix formed by residues 533 - 545 (chain A) in PDB entry 3ODX
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 ASP 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A PHE* 4.5 1.4 - - - -
529A LYS* 2.7 42.7 + - - +
530A GLN 3.8 4.0 - - - +
531A ARG 3.8 0.4 - - - -
532A LYS* 1.3 82.8 - - - +
534A PRO* 1.3 66.8 - - - +
535A ARG* 3.0 27.8 + - - +
536A PHE* 3.1 18.2 + - - +
537A CYS 3.0 22.3 + - - -
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Residues in contact with PRO 534 (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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530A GLN 4.6 0.9 - - - +
532A LYS 3.7 8.5 - - - +
533A ASP* 1.3 86.6 - - - +
535A ARG* 1.3 66.4 + - - +
537A CYS* 3.8 9.1 - - + +
538A ALA* 2.9 26.9 + - - +
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Residues in contact with ARG 535 (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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449A CYS* 3.5 36.3 + - - +
450A LEU 5.7 0.8 + - - -
451A PHE* 2.7 43.6 - - - +
533A ASP* 3.0 18.2 + - - +
534A PRO* 1.3 78.4 - - - +
536A PHE* 1.3 60.9 + - - +
538A ALA* 3.6 5.0 + - - +
539A PHE* 3.2 21.1 + - - +
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Residues in contact with PHE 536 (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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446A MET* 3.9 27.6 - - + -
451A PHE* 3.5 42.0 - + + -
452A PHE* 4.3 10.1 - + - -
526A LEU* 3.6 27.4 - - + -
529A LYS* 3.4 35.0 - - + -
530A GLN* 3.3 34.5 - - + -
533A ASP* 3.1 16.6 + - - +
535A ARG* 1.3 76.7 - - - +
537A CYS* 1.3 66.4 + - - +
539A PHE* 2.9 15.0 + + - +
540A VAL* 3.1 26.0 + - + +
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Residues in contact with CYS 537 (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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530A GLN* 3.5 43.1 - - - +
533A ASP 3.0 8.3 + - - +
534A PRO* 3.8 10.3 - - + +
536A PHE* 1.3 76.2 - - - +
538A ALA* 1.3 56.7 + - - +
540A VAL* 3.2 4.6 + - - +
541A GLN* 2.9 51.8 + - - +
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Residues in contact with ALA 538 (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 PRO 2.9 20.9 + - - +
535A ARG* 3.9 5.6 - - - +
537A CYS* 1.3 72.6 - - - +
539A PHE* 1.3 61.6 + - - +
541A GLN* 3.9 15.1 - - - +
542A GLU* 3.1 24.6 + - - +
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Residues in contact with PHE 539 (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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441A LEU 4.3 12.8 - - - -
442A PHE* 5.3 0.4 - + - -
445A PRO* 3.4 30.1 - - + -
446A MET* 3.8 31.6 - - + -
449A CYS* 3.9 20.2 - - - -
451A PHE* 3.7 24.5 - + + -
535A ARG 3.2 14.8 + - - +
536A PHE* 2.9 11.8 + + - +
538A ALA* 1.3 76.4 - - - +
540A VAL* 1.3 71.0 + - + +
542A GLU* 3.3 15.6 + - - +
543A ALA* 2.9 33.0 + - + +
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Residues in contact with VAL 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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442A PHE* 4.5 8.1 - - + -
446A MET* 4.6 7.0 - - + -
530A GLN* 3.4 32.8 - - + +
536A PHE* 3.1 36.0 + - + +
537A CYS* 3.7 6.1 - - - +
539A PHE* 1.3 79.6 - - + +
541A GLN* 1.3 69.3 + - + +
543A ALA* 3.7 4.9 - - - +
544A GLU* 2.8 49.6 + - + +
554A LEU* 4.8 4.7 - - + -
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Residues in contact with GLN 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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537A CYS* 2.9 38.0 + - - +
538A ALA* 3.9 14.3 - - - +
540A VAL* 1.3 76.1 - - + +
542A GLU* 1.3 54.9 + - - +
544A GLU* 2.8 32.9 + - - +
545A SER* 3.0 13.0 + - - -
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Residues in contact with GLU 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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538A ALA 3.1 16.7 + - - +
539A PHE* 3.6 14.9 - - - +
541A GLN* 1.3 77.3 - - - +
543A ALA* 1.3 67.0 + - - +
545A SER* 2.9 25.1 + - - +
546A ARG* 2.6 46.4 + - - +
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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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441A LEU* 3.8 21.8 - - + +
442A PHE* 3.8 24.0 - - + -
539A PHE* 2.9 24.0 + - + +
540A VAL* 3.7 4.5 - - - +
542A GLU* 1.3 81.8 + - - +
544A GLU* 1.3 57.9 + - - +
546A ARG* 3.0 34.0 + - - +
549A CYS* 3.4 8.1 - - - -
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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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442A PHE* 3.9 15.7 - - + -
530A GLN* 5.3 0.7 + - - -
540A VAL* 2.8 34.9 + - + +
541A GLN* 2.8 14.9 + - - +
543A ALA* 1.3 73.2 - - - +
545A SER* 1.3 57.4 + - - +
546A ARG 3.4 0.6 + - - +
549A CYS* 3.8 21.0 - - - +
551A ARG* 5.6 3.3 - - - -
552A LEU 4.6 3.5 - - - +
553A GLN* 3.3 34.4 + - + +
554A LEU* 2.7 33.7 + - - +
555A LYS* 4.2 1.6 + - - +
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Residues in contact with SER 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 GLN 3.0 9.3 + - - -
542A GLU* 2.9 20.0 + - - +
543A ALA 3.1 0.2 - - - -
544A GLU* 1.3 78.0 - - - +
546A ARG* 1.3 62.8 + - - +
547A PRO* 3.6 4.7 - - - +
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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