Contacts of the helix formed by residues 579 - 588 (chain A) in PDB entry 2ODP
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 THR 579 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A GLY 4.1 8.5 - - - +
578A SER* 1.3 78.1 - - - +
580A CYS* 1.3 64.0 + - - +
581A ARG* 3.4 11.7 + - - +
582A ASP* 2.9 39.2 + - - +
583A HIS* 3.1 10.7 + - - -
730A LEU* 3.8 12.3 - - - +
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Residues in contact with CYS 580 (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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564A CYS* 2.0 55.1 - - + +
579A THR* 1.3 70.4 - - - +
581A ARG* 1.3 65.6 + - - +
583A HIS* 3.1 4.0 + - - +
584A GLU* 3.0 23.7 + - - +
713A PHE* 4.1 11.2 - - - -
716A GLN* 3.8 22.7 - - - -
720A ARG* 4.4 9.6 - - - +
730A LEU* 4.1 5.2 - - + +
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Residues in contact with ARG 581 (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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579A THR* 3.2 10.2 + - - +
580A CYS* 1.3 76.9 - - - +
582A ASP* 1.3 64.5 + - - +
584A GLU* 3.2 50.9 + - - +
585A ASN* 2.9 55.8 + - - +
714A ARG* 5.2 2.4 - - - +
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Residues in contact with ASP 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A ARG* 5.7 5.1 - - - -
577A GLY 4.6 0.7 - - - +
578A SER* 3.3 19.3 + - - +
579A THR* 2.9 39.7 + - - +
581A ARG* 1.3 79.3 - - - +
583A HIS* 1.3 57.5 + - - +
585A ASN* 3.4 15.0 + - - +
586A GLU* 2.8 28.2 + - - +
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Residues in contact with HIS 583 (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 PRO* 3.9 9.0 - - + -
564A CYS* 2.8 40.6 - - - +
565A THR 3.7 2.5 + - - -
568A ALA* 4.1 4.9 - - + -
569A ASN* 2.7 56.3 + - + +
572A LEU* 4.4 14.9 - - + +
574A ARG* 4.8 6.0 - - + +
578A SER* 4.2 4.2 - - - -
579A THR 3.1 10.9 + - - +
580A CYS 3.1 8.9 + - - +
582A ASP* 1.3 78.3 - - - +
584A GLU* 1.3 58.3 + - - +
586A GLU* 3.4 5.8 - - - +
587A LEU* 2.9 35.0 + - + +
713A PHE* 4.0 4.9 - - + -
730A LEU* 3.6 14.4 - - + +
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Residues in contact with GLU 584 (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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580A CYS* 3.0 10.2 + - - +
581A ARG* 3.2 41.3 + - - +
583A HIS* 1.3 76.5 - - - +
585A ASN* 1.3 56.7 + - - +
588A LEU* 2.9 45.8 + - + +
711A ASN* 5.0 0.3 - - - +
713A PHE* 3.5 41.5 - - + +
714A ARG* 2.4 44.8 + - - -
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Residues in contact with ASN 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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581A ARG* 2.9 53.9 + - - +
582A ASP* 3.4 17.0 + - - +
584A GLU* 1.3 72.3 - - - +
586A GLU* 1.3 55.3 + - - +
588A LEU 5.1 0.2 - - - -
589A ASN* 2.6 43.8 + - - +
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Residues in contact with GLU 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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572A LEU* 4.1 30.8 - - + +
574A ARG* 3.2 42.6 + - + -
582A ASP 2.8 17.3 + - - +
583A HIS* 3.3 11.6 + - - +
585A ASN* 1.3 77.9 - - - +
587A LEU* 1.3 56.4 + - + +
589A ASN* 2.6 18.7 + - - +
667A ARG* 4.1 16.3 + - - -
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Residues in contact with LEU 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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563A PRO* 4.2 18.8 - - + -
572A LEU* 3.8 31.9 - - + -
583A HIS* 2.9 18.2 + - + +
584A GLU 4.5 0.2 - - - +
586A GLU* 1.3 80.8 - - + +
588A LEU* 1.3 66.7 + - + +
589A ASN* 3.7 2.0 + - - -
593A VAL* 3.9 4.2 - - - +
665A LEU* 3.6 29.4 - - + +
667A ARG* 3.8 36.4 + - + +
672A PHE* 4.1 31.6 - - + -
674A VAL* 4.2 13.9 - - + -
713A PHE* 4.2 2.9 - - + -
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Residues in contact with LEU 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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584A GLU* 2.9 32.2 + - + +
585A ASN* 5.1 0.4 - - - -
587A LEU* 1.3 79.3 - - + +
589A ASN* 1.3 62.5 + - - +
590A LYS 3.5 8.6 + - - +
593A VAL* 4.2 8.3 - - + -
609A LEU* 4.1 11.7 - - + -
611A MET* 3.5 36.8 - - + +
644A LEU* 4.2 20.0 - - + -
665A LEU* 4.1 15.7 - - + -
674A VAL* 4.4 7.0 - - + -
711A ASN* 5.0 2.5 - - - +
713A PHE* 3.8 32.3 - - + -
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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