Contacts of the strand formed by residues 439 - 443 (chain A) in PDB entry 1B0K
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 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A PRO* 4.0 8.5 - - - -
351A ARG* 3.7 31.1 - - + +
430A ARG* 2.8 38.2 + - - +
433A ILE* 3.5 16.0 - - + +
437A GLU 3.9 5.0 - - - +
438A LYS* 1.3 76.5 - - - +
440A THR* 1.3 63.0 + - - +
441A ILE* 3.9 5.8 - - - +
456A ASN* 4.1 1.7 + - - -
458A GLU 3.5 3.8 + - - -
459A THR* 2.6 26.6 + - - -
460A HIS* 2.8 31.5 + - - +
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Residues in contact with THR 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 2.7 40.4 + - - +
349A ASP 3.6 13.8 + - - -
350A ILE* 3.4 21.1 - - + -
351A ARG* 3.0 28.9 + - - +
439A ASN* 1.3 78.5 + - - +
441A ILE* 1.4 65.3 + - - +
442A VAL* 4.4 3.8 - - + -
460A HIS* 3.4 8.3 - - - +
462A PHE* 3.6 27.7 - - + -
478A LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 441 (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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352A VAL* 3.4 20.9 - - + +
354A LEU* 4.3 7.2 - - + -
428A TRP* 4.3 11.7 - - + -
430A ARG* 3.4 33.4 - - - +
439A ASN* 3.9 5.8 + - - +
440A THR* 1.4 78.1 - - - +
442A VAL* 1.3 61.8 + - - +
443A THR* 4.3 11.4 - - + +
453A ASN* 3.8 30.3 - - + +
459A THR* 3.7 23.6 - - + -
460A HIS 3.0 6.1 + - - +
461A ALA* 3.4 16.3 - - + +
462A PHE* 3.3 19.4 + - - +
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Residues in contact with VAL 442 (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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322A ILE* 4.3 11.0 - - + -
350A ILE* 3.8 40.4 - - + +
352A VAL 3.2 5.9 + - - +
353A GLY* 3.4 8.2 - - - -
354A LEU* 3.1 22.9 + - - +
440A THR* 4.4 2.9 - - + -
441A ILE* 1.3 75.8 - - - +
443A THR* 1.3 60.1 + - - +
462A PHE* 3.5 11.2 - - + +
464A THR* 4.8 4.5 - - + -
469A VAL* 4.1 23.3 - - + +
472A LEU* 4.4 10.3 - - + -
473A ALA 5.5 0.9 - - - +
478A LEU* 4.2 18.8 - - + -
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Residues in contact with THR 443 (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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354A LEU* 3.5 28.0 - - + -
441A ILE* 4.3 17.0 - - + +
442A VAL* 1.3 78.4 - - - +
444A SER* 1.3 59.7 + - - +
445A TYR* 3.2 32.8 + - + +
447A ARG 5.1 0.7 + - - -
453A ASN* 5.1 3.8 - - - +
461A ALA* 5.3 3.7 - - + +
462A PHE 2.8 8.8 + - - +
463A VAL* 3.2 24.4 - - - +
464A THR* 2.8 28.1 + - - +
469A VAL* 3.7 5.4 - - - -
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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