Contacts of the helix formed by residues 449 - 457 (chain A) in PDB entry 4L59
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A TYR* 5.0 2.3 + - - -
447A HIS 3.6 4.9 + - - -
448A PHE* 1.3 81.8 - - - +
450A TRP* 1.3 65.3 + - - +
451A ASP* 3.2 20.1 + - - +
452A LYS* 3.3 21.0 + - - +
453A TYR* 3.0 22.9 + - - +
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Residues in contact with TRP 450 (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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376A LYS* 3.8 21.8 - - + -
377A LEU 3.4 29.8 - - - -
378A GLU* 2.8 35.8 + - + -
390A VAL* 3.8 28.3 - - + -
426A VAL* 3.5 24.5 - - + -
427A GLY* 3.6 16.2 - - - +
436A LEU* 3.4 13.8 - - + +
448A PHE* 3.7 12.2 - + - -
449A SER* 1.3 71.4 + - - +
451A ASP* 1.3 62.0 + - - +
453A TYR* 3.7 24.1 - + - +
454A LEU* 2.8 49.8 + - + +
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Residues in contact with ASP 451 (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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449A SER* 3.2 9.7 + - - +
450A TRP* 1.3 78.7 + - - +
452A LYS* 1.3 67.4 + - - +
454A LEU* 3.5 8.7 + - - +
455A GLU* 3.2 21.3 + - - +
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Residues in contact with LYS 452 (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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442A TYR* 4.9 1.8 - - - +
449A SER* 3.3 19.8 + - - +
451A ASP* 1.3 78.6 - - - +
453A TYR* 1.3 58.2 + - - +
455A GLU* 3.2 7.8 + - - +
456A GLU* 2.8 46.2 + - - +
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Residues in contact with TYR 453 (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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376A LYS* 3.6 27.4 + - + -
390A VAL* 3.8 10.3 - - + -
406A ASP* 2.6 31.3 + - - +
407A ASN* 6.1 0.2 - - - -
439A PRO* 3.7 15.7 - - + +
442A TYR* 3.5 42.8 + + - +
448A PHE* 3.8 16.2 - + + -
449A SER 3.0 18.7 + - - +
450A TRP* 3.7 22.7 - + - +
452A LYS* 1.3 77.3 - - - +
454A LEU* 1.3 57.1 + - - +
456A GLU* 3.3 4.3 + - + +
457A THR* 2.9 50.7 + - + +
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Residues in contact with LEU 454 (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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376A LYS* 4.1 22.7 - - + -
426A VAL* 5.0 2.9 - - + -
450A TRP* 2.8 44.9 + - + +
451A ASP* 3.9 7.2 - - - +
453A TYR* 1.3 72.9 - - - +
455A GLU* 1.3 56.8 + - - +
457A THR* 3.7 3.1 - - - -
458A ASN* 3.0 5.4 + - - -
459A SER* 2.8 60.7 + - - +
460A LEU 3.7 14.4 - - - +
461A PRO* 3.8 25.8 - - + -
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Residues in contact with GLU 455 (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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451A ASP 3.2 12.6 + - - +
452A LYS* 3.2 10.5 + - - +
454A LEU* 1.3 71.6 - - - +
456A GLU* 1.3 63.6 + - + +
457A THR 3.1 1.3 - - - -
458A ASN* 2.9 21.8 + - - +
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Residues in contact with GLU 456 (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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442A TYR* 3.0 33.0 + - + -
452A LYS* 2.8 39.3 + - - +
453A TYR* 3.3 6.7 + - + +
455A GLU* 1.3 72.7 - - + +
457A THR* 1.3 62.6 + - + +
458A ASN 3.4 0.4 + - - -
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Residues in contact with THR 457 (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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376A LYS* 3.3 13.9 - - - +
453A TYR* 2.9 50.4 + - + +
454A LEU* 3.4 3.6 + - - -
456A GLU* 1.3 80.3 - - + +
458A ASN* 1.3 69.2 + - - +
459A SER* 2.8 31.9 + - - -
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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