Contacts of the helix formed by residues 471 - 475 (chain A) in PDB entry 4DKT
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 HIS 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ASP* 3.8 7.2 - - - -
403A GLY 2.8 28.2 + - - -
406A SER* 2.7 20.5 + - - -
408A GLY* 3.3 21.5 - - - +
409A ASN* 3.6 11.4 - - + -
464A SER* 4.2 1.8 - - - -
467A LEU* 3.2 7.8 - - - +
469A VAL* 3.4 25.3 - - + +
470A GLY* 1.3 82.2 - - - +
472A VAL* 1.3 64.0 + - - +
473A ASP* 3.2 17.3 - - - +
474A GLU* 2.6 35.5 + - - +
4B FIO 3.1 28.2 + - + +
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Residues in contact with VAL 472 (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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408A GLY 3.9 5.8 + - - +
409A ASN* 3.3 13.0 + - - +
411A GLU* 3.6 29.8 - - + -
429A LEU* 4.4 4.9 - - + +
430A PHE 3.8 3.8 - - - -
431A GLY* 3.4 34.8 - - - +
462A LEU* 4.2 17.0 - - + -
464A SER* 4.1 5.6 - - - -
471A HIS* 1.3 68.0 - - - +
473A ASP* 1.3 60.1 + - - +
474A GLU 3.0 6.1 + - - -
475A PHE* 3.2 14.4 + - + -
476A LEU* 3.0 42.8 + - + +
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Residues in contact with ASP 473 (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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349A GLN* 4.2 0.9 - - - +
408A GLY* 3.5 18.1 + - - +
411A GLU* 4.0 9.0 - - - +
471A HIS* 3.2 8.0 - - - +
472A VAL* 1.3 81.4 - - - +
474A GLU* 1.3 73.0 + - - +
475A PHE 3.4 0.4 - - - -
476A LEU* 3.4 20.0 + - - +
587A VAL* 4.0 0.9 - - - +
588A ASN* 3.7 22.8 - - - +
644A HIS* 2.7 42.4 + - + +
645A CYS* 4.2 0.5 - - - -
4B FIO 3.0 31.3 + - - -
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Residues in contact with GLU 474 (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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467A LEU* 3.4 27.6 - - + +
469A VAL* 3.3 23.3 + - - +
470A GLY* 2.9 12.7 + - - -
471A HIS* 2.6 38.3 + - + +
472A VAL 3.0 1.2 - - - -
473A ASP* 1.3 91.2 + - - +
475A PHE* 1.3 56.9 + - - +
571A PHE* 4.7 7.3 - - + -
579A ALA 4.9 3.3 - - - +
580A GLU* 5.7 2.4 - - - -
585A ASN* 2.6 32.8 + - - +
587A VAL* 3.1 6.8 - - - +
588A ASN* 4.3 6.1 - - - +
640A HIS 5.4 1.3 - - - +
4B FIO 4.2 9.4 - - + +
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Residues in contact with PHE 475 (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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462A LEU* 4.6 3.1 - - + -
463A TYR 3.9 14.4 - - - -
464A SER* 4.1 10.5 - - - -
466A TRP* 3.6 31.2 - + + -
467A LEU* 3.7 9.0 - - + -
472A VAL* 3.2 25.6 + - + -
474A GLU* 1.3 79.3 - - - +
476A LEU* 1.3 82.8 + - + +
491A LEU* 3.4 15.9 - - + +
492A ALA* 3.1 26.5 + - + -
546A ILE* 4.4 20.4 - - + -
549A ASN* 3.5 41.5 - - + -
571A PHE* 5.2 1.1 - - + -
587A VAL* 3.8 6.7 - - - -
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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