Contacts of the strand formed by residues 453 - 458 (chain A) in PDB entry 2JED
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ILE* 5.9 0.8 - - - +
411A LEU 3.3 5.5 - - - +
412A LYS* 2.9 34.9 + - - +
413A LYS* 3.9 1.2 - - - -
449A GLN* 3.4 5.4 - - - +
450A THR* 2.8 45.6 + - - +
451A LYS 3.7 0.6 - - - -
452A GLU* 1.3 88.7 + - - +
454A LEU* 1.3 63.9 + - - +
455A PHE* 3.4 31.2 - - + -
675A LEU* 3.8 24.0 - - + +
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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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409A LYS 3.7 0.9 - - - +
410A ALA* 3.4 5.7 - - - -
411A LEU* 2.8 53.4 + - + +
413A LYS* 3.8 24.0 - - + -
416A VAL* 4.5 4.9 - - + -
425A THR* 3.7 25.4 - - + -
448A PHE 4.0 1.8 - - - -
449A GLN* 3.8 13.5 - - + -
453A ASN* 1.3 74.4 - - - +
455A PHE* 1.3 62.4 + - - +
456A PHE* 4.5 4.1 - - + -
691A PHE* 3.8 29.8 - - + -
694A PHE* 3.7 36.3 - - + -
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Residues in contact with PHE 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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377A ILE* 3.8 38.4 - - + -
382A LEU* 6.2 0.2 - - + -
408A ILE* 4.0 11.4 - - + -
409A LYS 3.4 1.1 - - - -
410A ALA* 3.8 13.2 - - + -
447A THR* 3.5 7.1 + - - -
448A PHE* 2.9 73.9 + + + +
449A GLN* 5.1 0.2 - - - -
450A THR* 4.1 12.8 - - - -
453A ASN* 3.4 32.1 - - + -
454A LEU* 1.3 76.6 - - - +
456A PHE* 1.3 63.9 + - - +
457A VAL 4.1 0.2 - - - -
675A LEU* 3.7 39.7 - - + -
694A PHE* 3.8 2.8 - - - -
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Residues in contact with PHE 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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407A ALA 3.6 0.3 - - - +
408A ILE* 3.3 5.6 - - - -
409A LYS* 2.9 76.8 + - + -
411A LEU* 4.1 12.6 - - + -
425A THR* 4.2 15.0 - - + -
428A GLU* 4.4 6.7 - - + -
429A LYS* 4.1 22.0 - - + -
432A LEU* 3.7 21.8 - - + -
444A MET* 4.8 3.1 - - + -
446A CYS 3.6 4.7 - - - +
447A THR* 3.8 12.6 - - - +
454A LEU* 4.5 4.3 - - + -
455A PHE* 1.3 75.7 - - - +
457A VAL* 1.3 62.6 + - - +
458A MET* 3.6 15.9 + - - +
694A PHE* 3.6 32.8 - + - -
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Residues in contact with VAL 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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380A PHE* 3.8 22.7 - - + -
406A PHE* 3.8 37.5 - - + -
407A ALA 3.8 1.8 - - - -
408A ILE* 3.8 22.9 - - + -
444A MET* 3.7 2.8 - - - +
445A PHE* 2.7 35.5 + - + +
446A CYS* 2.7 31.0 + - - +
448A PHE* 3.8 22.4 - - + -
456A PHE* 1.3 71.7 - - - +
458A MET* 1.3 59.5 + - - +
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Residues in contact with MET 458 (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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406A PHE* 3.4 11.1 - - - +
407A ALA* 2.7 46.1 + - + +
409A LYS 4.9 2.2 - - - +
432A LEU* 3.6 21.5 - - + -
442A THR* 3.6 31.2 - - + +
443A HIS 3.5 14.6 - - - +
444A MET* 3.7 23.6 - - - -
445A PHE* 3.7 5.4 - - - -
456A PHE* 3.8 18.8 - - + +
457A VAL* 1.3 75.0 - - - +
459A GLU* 1.3 67.4 + - - +
1701A LG8 3.7 31.6 - - + +
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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