Contacts of the helix formed by residues 576 - 584 (chain F) in PDB entry 2A07
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 576 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560F LYS 5.0 0.9 - - - +
561F CYS* 2.8 22.2 + - - +
563F VAL* 4.5 16.1 - - + +
574F THR* 4.1 0.8 + - - +
575F VAL* 1.3 70.9 - - - +
577F GLU* 1.3 64.0 + - - +
578F VAL* 3.1 13.2 + - - +
579F GLU* 2.7 51.5 + - + +
580F TYR* 2.9 11.4 + - - +
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Residues in contact with GLU 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F VAL* 3.2 21.5 + - - +
576F ASP* 1.3 72.3 + - - +
578F VAL* 1.3 64.2 + - + +
580F TYR* 3.4 10.0 + - - +
581F GLN* 3.1 15.8 + - - +
584F ARG* 2.5 47.6 + - - +
514G ARG* 3.6 29.6 + - - -
518G MET* 4.5 11.2 - - - +
523G ARG* 6.3 1.8 - - - +
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Residues in contact with VAL 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576F ASP* 3.0 8.6 + - - +
577F GLU* 1.3 76.4 - - + +
579F GLU* 1.3 63.4 + - - +
581F GLN* 2.8 43.1 + - - +
582F LYS 3.9 1.7 + - - -
584F ARG* 5.4 0.2 - - - +
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Residues in contact with GLU 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560F LYS* 3.2 36.5 - - + +
561F CYS* 3.3 31.1 - - + +
576F ASP* 2.7 33.1 + - - +
578F VAL* 1.3 75.2 - - - +
580F TYR* 1.3 60.0 + - - +
581F GLN 3.3 0.5 + - - -
582F LYS* 3.5 20.9 + - - +
583F ARG* 4.5 3.3 + - - +
560J LYS* 5.5 2.9 + - - -
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Residues in contact with TYR 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561F CYS* 3.6 30.0 - - + +
562F PHE* 4.4 2.7 - + - -
575F VAL* 4.5 5.4 - - + -
576F ASP 2.9 11.1 + - - +
577F GLU* 3.5 18.6 - - - +
578F VAL 3.1 0.2 - - - -
579F GLU* 1.3 74.4 - - - +
581F GLN* 1.3 63.7 + - - +
582F LYS 3.3 0.4 - - - -
583F ARG* 3.3 28.6 + - + +
584F ARG* 3.4 18.2 + - + +
510G ALA* 3.5 13.6 - - + +
511G THR* 2.9 43.7 + - + +
514G ARG* 3.8 45.2 - - + +
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Residues in contact with GLN 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F GLU 3.1 7.4 + - - +
578F VAL* 2.8 37.0 + - - +
580F TYR* 1.3 75.4 - - - +
582F LYS* 1.3 65.6 + - - +
584F ARG* 3.0 53.5 + - + +
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Residues in contact with LYS 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B T 6.1 1.0 - - - -
11B T 4.0 27.4 + - - +
578F VAL 3.9 1.4 + - - +
579F GLU* 3.5 14.7 + - - +
581F GLN* 1.3 80.1 - - - +
583F ARG* 1.3 82.6 + - - +
584F ARG 3.2 5.2 + - - +
560J LYS* 5.7 6.5 - - - +
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Residues in contact with ARG 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B T 3.6 38.6 + - - +
12B T 3.9 25.6 + - - +
559F HIS* 3.8 26.1 + - - -
561F CYS* 5.7 5.2 - - - -
579F GLU 5.0 1.8 - - - +
580F TYR* 3.3 32.2 + - + +
581F GLN 3.2 0.4 - - - -
582F LYS* 1.3 95.9 - - + +
584F ARG* 1.3 64.9 + - - +
510G ALA* 6.4 2.2 - - + -
560J LYS* 4.7 13.3 - - - +
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Residues in contact with ARG 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F GLU* 2.5 57.5 + - - +
580F TYR* 3.4 16.9 + - + +
581F GLN* 3.0 52.2 + - + +
582F LYS 4.2 3.2 - - - +
583F ARG* 1.3 84.0 - - - +
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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