Contacts of the strand formed by residues 442 - 448 (chain A) in PDB entry 3BJI
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 ASP 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A GLU 4.8 8.5 - - - +
392A ASN* 5.0 3.5 - - + +
434A CYS* 3.1 4.7 - - - -
435A LYS* 2.7 51.3 + - + +
437A ARG 5.5 0.7 + - - -
440A SER* 4.9 10.9 - - - +
441A TYR* 1.3 73.8 - - - +
443A LEU* 1.3 66.1 + - - +
444A LYS* 3.1 24.8 + - - +
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Residues in contact with LEU 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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390A ILE 5.6 0.4 + - - -
391A GLU* 5.2 1.1 - - - +
392A ASN* 3.6 46.2 - - + +
393A LEU* 3.7 30.5 - - + -
432A LEU* 4.6 9.6 - - + -
433A ILE 3.6 9.2 - - - +
434A CYS* 3.9 13.1 - - - -
441A TYR 3.8 3.4 + - - -
442A ASP* 1.3 70.8 - - - +
444A LYS* 1.3 71.7 + - - +
445A ASP 3.5 28.7 - - - +
446A PHE* 4.3 17.7 - - + +
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Residues in contact with LYS 444 (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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422A ARG* 4.8 19.3 - - - +
433A ILE* 2.8 12.5 + - + +
435A LYS* 3.4 34.9 - - + +
442A ASP* 3.1 20.9 + - - +
443A LEU* 1.3 79.3 - - - +
445A ASP* 1.3 64.7 - - + +
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Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER* 5.6 0.5 - - - -
431A LEU 3.9 0.2 - - - +
432A LEU 3.8 0.2 - - - -
433A ILE* 2.8 58.8 + - + +
443A LEU* 3.5 6.3 - - - +
444A LYS* 1.3 81.2 - - - +
446A PHE* 1.3 73.8 + - - +
447A VAL* 4.7 1.1 - - - -
480A GLN* 5.5 0.7 + - - -
482A TYR* 2.8 39.0 + - - -
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Residues in contact with PHE 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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393A LEU* 5.4 3.8 - - + -
400A TYR* 3.6 48.9 - + - -
429A LYS 5.3 0.2 - - - -
430A ALA* 3.6 20.9 - - + -
431A LEU 3.8 2.5 - - - -
432A LEU* 3.4 20.9 - - + -
443A LEU* 4.6 18.8 - - + -
445A ASP* 1.3 81.1 + - - +
447A VAL* 1.3 67.6 + - - +
448A ASN* 3.6 25.6 + - + -
482A TYR* 5.4 0.2 + - - -
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Residues in contact with VAL 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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430A ALA* 3.1 11.1 - - - +
431A LEU* 2.9 44.8 + - + +
433A ILE* 3.8 28.5 - - + -
445A ASP* 4.7 0.7 - - - +
446A PHE* 1.3 76.6 - - - +
448A ASN* 1.3 63.9 + - - +
449A LEU* 3.6 4.2 + - + -
452A PHE* 3.6 39.3 - - + -
473A LEU* 4.5 11.7 - - + -
482A TYR* 3.8 23.8 - - + +
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Residues in contact with ASN 448 (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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400A TYR* 5.8 1.0 - - - -
429A LYS 3.8 4.3 - - - +
446A PHE* 3.6 23.9 + - + -
447A VAL* 1.3 71.4 - - - +
449A LEU* 1.3 63.7 + - - +
450A HIS* 3.2 41.4 + - - +
451A SER* 3.5 11.7 + - - +
452A PHE* 3.0 28.2 - - + -
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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