Contacts of the helix formed by residues 584 - 599 (chain A) in PDB entry 1D0N
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 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A GLY 4.0 3.8 + - - -
583A ALA* 1.3 83.3 + - - +
585A GLU* 1.3 71.4 + - - +
586A ALA* 3.5 2.2 - - - -
587A GLU* 3.0 19.1 - - - +
588A LYS* 3.2 33.7 + - - +
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Residues in contact with GLU 585 (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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584A SER* 1.3 78.3 - - - +
586A ALA* 1.3 68.4 + - + +
588A LYS* 3.2 12.5 + - - +
589A THR* 2.9 36.2 + - + +
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Residues in contact with ALA 586 (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* 3.8 13.2 - - + -
547A GLY* 3.9 24.9 - - - +
549A THR* 3.3 14.1 - - + +
584A SER* 3.5 1.2 - - - -
585A GLU* 1.3 80.7 - - + +
587A GLU* 1.3 72.3 + - - +
589A THR* 2.9 24.2 - - - +
590A GLY 3.1 6.4 + - - -
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Residues in contact with GLU 587 (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 VAL* 3.6 14.9 - - - +
543A ALA* 3.1 38.0 + - - +
549A THR* 4.7 2.2 - - - -
564A ASN 5.0 0.3 - - - -
565A ASP* 4.0 13.2 + - - +
566A ALA* 4.0 24.0 - - + +
582A GLY 5.5 0.4 - - - -
583A ALA* 3.8 9.0 - - + -
584A SER* 3.0 40.7 - - - +
586A ALA* 1.3 78.3 - - - +
588A LYS* 1.3 52.2 + - - +
590A GLY 3.6 0.5 - - - -
591A ALA* 2.7 37.2 + - - +
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Residues in contact with LYS 588 (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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566A ALA* 4.7 2.2 - - + +
577A LEU* 4.9 10.5 - - + +
579A VAL* 3.8 37.3 - - + +
583A ALA* 5.0 2.4 - - + -
584A SER* 3.2 29.8 + - - +
585A GLU* 3.2 10.1 + - - +
587A GLU* 1.3 74.9 - - - +
589A THR* 1.3 68.5 + - - +
591A ALA* 2.7 20.4 + - - +
592A GLN* 3.0 20.4 + - - +
604A GLN* 6.5 0.9 - - + -
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Residues in contact with THR 589 (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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549A THR* 5.5 0.7 - - + -
585A GLU* 2.9 36.8 + - + +
586A ALA* 2.9 25.6 - - - +
588A LYS* 1.3 76.3 - - - +
590A GLY* 1.3 61.0 + - - +
592A GLN* 3.1 31.3 + - - +
593A GLU* 3.2 10.9 + - - +
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Residues in contact with GLY 590 (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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514A GLY 5.6 2.2 - - - -
516A PRO* 3.3 28.7 - - - +
541A VAL* 4.1 8.4 - - - +
549A THR* 4.1 16.2 - - - -
586A ALA 3.1 10.8 + - - -
587A GLU 3.6 0.7 - - - -
589A THR* 1.3 84.1 - - - +
591A ALA* 1.3 65.2 + - - +
593A GLU* 3.4 7.3 + - - -
594A LEU* 3.5 4.5 + - - +
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Residues in contact with ALA 591 (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 VAL* 3.7 24.7 - - + +
566A ALA* 4.6 9.6 - - + -
567A PHE 5.0 0.2 - - - +
568A VAL* 3.4 5.6 - - + +
577A LEU* 3.6 18.2 - - + -
587A GLU 2.7 22.4 + - - +
588A LYS* 2.7 13.2 + - - +
590A GLY* 1.3 70.8 - - - -
592A GLN* 1.3 58.6 + - - +
594A LEU* 3.3 13.2 - - - +
595A LEU* 2.8 20.8 - - - +
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Residues in contact with GLN 592 (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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577A LEU* 3.9 19.6 - - + +
588A LYS* 3.0 16.4 + - - +
589A THR* 3.1 26.6 + - - +
591A ALA* 1.3 73.6 - - - +
593A GLU* 1.3 55.4 + - - +
594A LEU 2.8 6.1 - - - -
595A LEU* 2.7 35.4 + - + +
596A ARG* 3.1 10.0 + - - +
602A PRO* 5.6 4.7 - - + -
604A GLN* 5.7 2.1 + - - -
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Residues in contact with GLU 593 (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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514A GLY 5.4 1.3 - - - +
515A LYS* 3.7 33.1 - - + +
516A PRO* 3.8 22.2 - - + -
518A ILE* 5.5 0.3 - - - +
589A THR 3.2 13.8 + - - +
590A GLY* 3.8 6.7 - - - +
591A ALA 3.4 0.2 - - - -
592A GLN* 1.3 82.0 + - - +
594A LEU* 1.3 59.9 + - - +
596A ARG* 3.7 42.7 + - - +
597A VAL* 3.4 23.0 + - + +
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Residues in contact with LEU 594 (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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518A ILE* 3.5 41.7 - - + -
520A TYR* 5.5 0.2 - - + -
539A PHE* 3.4 43.3 - - + -
541A VAL* 5.0 1.8 - - + -
551A ALA* 3.7 13.7 - - + -
568A VAL* 4.4 8.3 - - + -
590A GLY 3.5 8.5 + - - +
591A ALA 3.3 14.3 + - - +
592A GLN 2.8 0.2 - - - -
593A GLU* 1.3 78.9 - - - +
595A LEU* 1.3 60.3 + - + +
596A ARG 3.2 0.2 - - - -
597A VAL* 3.0 14.3 + - + +
598A LEU* 2.8 47.0 + - + +
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Residues in contact with LEU 595 (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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568A VAL* 3.4 38.4 - - + -
570A LYS* 6.4 0.7 - - - -
575A ALA* 3.5 27.8 - - + -
577A LEU* 3.6 7.6 - - + -
591A ALA 2.8 29.2 - - - +
592A GLN* 2.7 24.7 + - + +
594A LEU* 1.3 74.6 - - - +
596A ARG* 1.3 60.2 - - - +
598A LEU* 3.2 11.8 + - + +
599A ARG 2.9 18.5 + - - -
600A ALA* 3.2 26.2 + - + +
602A PRO* 4.0 20.0 - - + -
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Residues in contact with ARG 596 (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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515A LYS* 5.7 2.4 - - - +
592A GLN 3.1 8.7 + - - +
593A GLU* 3.7 40.8 + - - +
594A LEU 3.2 0.2 - - - -
595A LEU* 1.3 76.0 - - - +
597A VAL* 1.3 66.1 + - - +
599A ARG* 3.1 19.9 + - - +
600A ALA 5.2 1.8 - - - +
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Residues in contact with VAL 597 (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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440A GLN* 4.0 16.4 - - + +
515A LYS* 6.5 0.7 - - + -
518A ILE* 5.1 10.5 - - + -
520A TYR* 3.8 21.5 - - - +
593A GLU* 3.4 20.9 - - + +
594A LEU* 3.0 16.5 + - + +
596A ARG* 1.3 76.5 - - + +
598A LEU* 1.3 60.8 + - + +
599A ARG* 3.0 18.5 + - - +
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Residues in contact with LEU 598 (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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520A TYR* 4.7 9.2 - - + +
537A ARG* 4.4 20.2 - - - +
539A PHE* 4.5 22.7 - - + -
568A VAL* 4.4 7.2 - - + -
570A LYS* 4.8 25.8 - - + -
594A LEU* 2.8 48.2 + - + +
595A LEU* 3.2 21.3 + - + +
597A VAL* 1.3 71.5 - - + +
599A ARG* 1.3 72.0 + - - +
600A ALA* 4.5 8.0 - - + +
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Residues in contact with ARG 599 (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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595A LEU 2.9 6.5 + - - -
596A ARG* 3.1 10.9 + - - +
597A VAL 3.0 14.3 - - - +
598A LEU* 1.3 82.4 - - - +
600A ALA* 1.3 58.0 + - - +
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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