Contacts of the helix formed by residues 573 - 581 (chain A) in PDB entry 3Q8A
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 ASN 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A LEU* 5.1 0.9 - - - +
571A ALA* 3.6 2.1 - - - +
572A THR* 1.3 87.9 + - - +
574A ILE* 1.3 61.6 + - - +
575A TYR* 3.3 38.7 + - - +
576A THR* 2.9 39.2 + - + +
577A VAL* 3.5 12.0 - - - +
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Residues in contact with ILE 574 (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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523A LEU* 4.1 15.5 - - + -
552A PHE* 4.2 22.9 - - + -
554A PHE* 4.4 12.3 - - + -
562A ILE* 4.4 20.9 - - + -
566A LEU* 4.4 16.1 - - + +
572A THR 4.3 0.2 - - - -
573A ASN* 1.3 68.8 - - - +
575A TYR* 1.3 74.1 + - + +
576A THR 2.7 16.8 + - - -
577A VAL* 2.9 19.1 + - - +
578A LEU* 2.9 30.0 + - + +
581A ILE* 4.2 16.6 - - + -
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Residues in contact with TYR 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 3.2 30.9 - - + +
548A THR* 3.4 36.8 - - + +
550A PHE 2.9 15.4 + - - -
551A ASP* 3.5 7.6 - - - +
552A PHE* 3.8 22.9 + + - -
573A ASN* 3.3 26.6 + - - +
574A ILE* 1.3 89.3 - - + +
576A THR* 1.3 61.0 + - + +
577A VAL 3.5 1.1 - - - -
578A LEU* 3.8 20.9 - - - +
594A LYS* 2.7 33.6 + - - -
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Residues in contact with THR 576 (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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573A ASN* 2.9 32.7 + - + +
574A ILE 2.7 0.2 + - - -
575A TYR* 1.3 82.4 - - + +
577A VAL* 1.3 70.8 - - - +
578A LEU 3.9 0.2 - - - -
579A ASP* 4.6 3.5 - - - +
580A LYS* 5.7 0.9 + - - -
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Residues in contact with VAL 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LEU* 3.7 21.5 - - + -
569A LEU* 5.0 4.7 - - + +
571A ALA* 3.9 19.7 - - + -
573A ASN 3.5 11.9 - - - +
574A ILE* 2.9 19.1 + - - +
576A THR* 1.3 95.2 - - - +
578A LEU* 1.3 63.9 + - - +
579A ASP* 3.4 11.4 - - - -
580A LYS* 3.2 27.8 + - + +
581A ILE* 2.9 22.9 + - + +
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Residues in contact with LEU 578 (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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523A LEU* 3.6 24.3 + - + -
524A LYS* 3.8 23.8 - - + +
527A LEU* 4.7 3.8 - - + -
540A LEU* 4.5 12.3 - - + -
547A ILE* 4.0 31.2 - - + -
552A PHE* 4.3 9.2 - - + -
574A ILE* 2.9 45.3 - - + +
575A TYR* 3.8 19.5 - - - +
576A THR 3.9 0.4 - - - -
577A VAL* 1.3 72.9 - - - +
579A ASP* 1.3 57.0 + - - +
580A LYS 2.7 16.2 + - - -
581A ILE* 2.8 24.0 + - - +
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Residues in contact with ASP 579 (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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522A THR* 3.5 26.9 + - - +
524A LYS* 3.5 34.6 + - + +
576A THR 4.6 2.4 - - - +
577A VAL* 3.7 9.0 + - - -
578A LEU* 1.3 85.9 + - - +
580A LYS* 1.3 90.0 + - - +
581A ILE 3.6 0.2 - - - -
582A LYS* 5.4 1.2 + - - -
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Residues in contact with LYS 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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565A GLN* 4.1 3.8 - - - +
569A LEU* 4.0 37.5 - - + +
576A THR 5.7 0.8 + - - -
577A VAL* 3.6 23.8 - - + +
578A LEU 2.7 3.2 + - - -
579A ASP* 1.3 108.5 + - - +
581A ILE* 1.3 65.6 + - - +
582A LYS* 3.6 16.3 + - - +
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Residues in contact with ILE 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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522A THR* 3.1 10.2 - - - -
523A LEU* 3.0 41.9 + - + -
562A ILE* 3.7 34.5 - - + -
565A GLN* 3.6 10.5 - - + +
566A LEU* 3.7 32.8 - - + -
569A LEU* 4.1 11.0 - - + -
574A ILE* 4.2 13.5 - - + -
577A VAL* 2.9 20.2 - - + +
578A LEU* 2.8 13.2 + - - +
580A LYS* 1.3 77.3 - - - +
582A LYS* 1.3 64.0 + - - +
583A LEU* 5.1 2.2 - - + -
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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