Contacts of the strand formed by residues 443 - 447 (chain A) in PDB entry 4OE4
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 THR 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A PHE* 3.7 2.8 - - - -
415A ILE* 4.0 14.9 - - + +
426A ILE* 4.2 5.4 - - + -
428A TYR 3.4 7.0 - - - +
430A GLY* 2.9 36.2 + - - +
440A VAL* 4.8 0.2 - - - +
441A GLY 2.9 12.8 + - - -
442A PRO* 1.3 71.1 - - - +
444A VAL* 1.3 67.7 + - - +
445A ILE* 3.8 26.9 - - + -
462A PRO 2.9 11.9 + - - +
463A ILE* 3.4 10.3 - - + +
464A LEU* 2.8 26.0 + - - +
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PHE* 4.0 18.6 - - + -
368A LEU* 4.6 5.8 - - + -
371A MET* 4.2 10.8 - - - -
372A PHE* 3.9 35.9 - - + -
375A LEU* 4.5 5.8 - - + -
426A ILE* 3.6 1.7 - - - -
427A LEU* 2.7 34.6 + - + -
428A TYR* 2.9 18.5 + - + +
443A THR* 1.3 76.5 - - - +
445A ILE* 1.3 59.5 + - - +
446A LYS 4.2 0.2 - - - -
464A LEU* 3.4 17.0 - - + +
466A VAL* 3.9 23.6 - - + -
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Residues in contact with ILE 445 (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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414A VAL* 4.6 5.2 - - + +
415A ILE* 5.0 3.8 - - - -
418A ALA* 3.8 23.8 - - + -
424A LEU* 4.0 22.0 - - + -
425A GLU 3.3 22.7 - - - +
426A ILE* 4.4 5.8 - - + -
443A THR* 3.8 19.1 - - + -
444A VAL* 1.3 76.7 - - - +
446A LYS* 1.3 57.6 - - - +
454A TYR* 4.0 15.7 - - + -
463A ILE* 3.9 20.9 - - + -
464A LEU 2.8 14.4 + - - +
465A THR* 3.1 10.3 - - + +
466A VAL* 2.7 34.6 + - - -
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Residues in contact with LYS 446 (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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423A GLU 3.5 1.0 - - - +
424A LEU* 3.3 6.2 - - - +
425A GLU* 2.7 49.5 + - + +
427A LEU* 3.5 31.3 - - + +
444A VAL 4.2 0.4 - - - -
445A ILE* 1.3 73.6 - - - +
447A ALA* 1.3 69.7 + - - +
448A LYS* 4.9 17.2 - - + +
466A VAL* 3.3 14.1 - - + +
468A GLU* 3.3 44.0 + - + +
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Residues in contact with ALA 447 (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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423A GLU 3.3 4.0 - - - -
424A LEU* 3.9 12.6 - - + -
445A ILE 3.8 1.2 + - - -
446A LYS* 1.3 80.2 - - - +
448A LYS* 1.3 61.3 + - - +
449A ARG 3.4 15.9 - - - +
452A HIS* 4.1 10.5 - - + -
455A MET* 4.3 6.1 - - + -
465A THR* 3.9 22.7 - - + -
466A VAL 2.8 14.2 + - - +
467A TYR* 3.4 19.7 - - + -
468A GLU 4.8 0.5 + - - -
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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