Contacts of the strand formed by residues 448 - 453 (chain A) in PDB entry 4Z2A
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 ARG 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A PRO* 4.1 9.8 + - + +
447A GLN* 1.3 83.5 - - - +
449A LYS* 1.3 61.9 + - - +
477A GLU 4.0 1.8 + - - -
478A PRO* 3.1 32.1 + - - +
479A ASN* 3.9 8.7 - - - +
480A HIS* 2.9 38.9 + - - +
481A ILE* 3.8 13.5 - - + -
571A TYR* 3.3 6.6 - - - -
572A GLY 2.7 37.4 + - - +
573A THR* 4.3 1.1 - - - +
574A ALA* 3.5 28.0 - - - +
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Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN* 4.4 2.4 + - - +
448A ARG* 1.3 75.9 - - - +
450A CYS* 1.3 59.1 + - - +
451A ILE* 4.0 27.3 + - + +
479A ASN* 3.0 23.5 + - - +
569A VAL* 3.8 19.5 - - + -
570A LEU 3.3 3.4 - - - -
571A TYR* 3.5 39.0 + - + -
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Residues in contact with CYS 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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449A LYS* 1.3 73.0 - - - +
451A ILE* 1.3 59.9 + - - +
452A ILE* 3.9 16.9 + - - +
473A ALA* 3.5 11.4 - - - -
474A CYS* 2.1 57.2 - - + -
479A ASN* 3.7 13.0 - - - +
481A ILE* 4.0 11.4 - - + +
568A LEU 3.6 2.4 - - - +
569A VAL* 3.5 2.9 - - - -
570A LEU* 2.9 38.2 + - + +
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Residues in contact with ILE 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 LYS* 4.0 39.5 + - + +
450A CYS* 1.3 77.5 - - - +
452A ILE* 1.3 64.0 + - - +
453A ASP* 4.3 7.6 + - - +
474A CYS* 4.4 3.8 - - - -
479A ASN* 4.7 2.2 - - - +
567A THR* 3.6 23.8 - - + -
568A LEU 3.7 2.2 - - - -
569A VAL* 4.4 8.1 - - + +
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Residues in contact with ILE 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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450A CYS* 3.9 17.3 - - - +
451A ILE* 1.3 80.2 - - - +
453A ASP* 1.3 68.6 + - - +
454A ILE* 3.4 21.7 + - + +
469A LYS* 5.5 2.5 - - + -
471A VAL* 3.8 31.4 - - + -
473A ALA* 4.4 3.6 - - - +
474A CYS* 5.2 0.4 - - - +
567A THR* 3.4 3.2 - - - -
568A LEU* 2.8 50.7 + - + +
570A LEU* 3.8 31.0 - - + -
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Residues in contact with ASP 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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451A ILE* 4.2 6.9 + - - +
452A ILE* 1.3 76.1 - - - +
454A ILE* 1.3 63.1 + - - +
455A LEU 3.7 7.3 - - - +
469A LYS* 5.1 2.9 + - - +
565A LYS* 4.5 10.4 - - - -
566A PHE 4.1 3.6 - - - -
567A THR* 4.0 19.7 + - - +
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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