Contacts of the strand formed by residues 526 - 530 (chain B) in PDB entry 4EHE
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 ALA 526 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B VAL* 4.0 19.7 - - + -
483B LYS 3.2 11.7 - - - +
484B MET* 4.0 9.2 - - + -
485B LEU* 4.2 1.1 - - - -
498B PHE* 3.5 3.2 - - - -
519B TYR* 3.3 10.7 - - - +
520B SER* 2.8 49.7 + - - +
524B GLN 4.2 0.7 - - - +
525B LEU* 1.3 77.2 - - - +
527B ILE* 1.3 69.6 + - - +
528B VAL* 5.0 1.1 - - + -
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Residues in contact with ILE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B ALA 3.6 1.2 - - - +
482B VAL* 3.4 2.1 - - - -
483B LYS* 2.8 36.5 + - + +
485B LEU* 4.1 4.3 - - + -
498B PHE* 3.3 34.5 - - + -
502B VAL* 5.0 2.5 - - + -
505B LEU* 3.8 17.9 - - + -
516B PHE* 4.2 11.2 - - + -
518B GLY 3.9 1.8 - - - -
519B TYR* 4.5 7.9 - - + -
526B ALA* 1.3 74.2 - - - +
528B VAL* 1.3 63.5 + - - +
529B THR* 4.1 6.5 - - + -
597B LEU* 3.5 24.5 - - + -
801B RI8 3.7 43.7 - - + +
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Residues in contact with VAL 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B ILE* 3.8 22.4 - - + -
457B ILE* 5.1 9.4 - - + -
476B TRP* 5.0 7.9 - - + -
480B VAL* 3.7 32.3 - - + -
481B ALA 3.2 9.4 - - - +
482B VAL* 4.3 17.3 - - + -
516B PHE* 3.8 2.3 - - - -
517B MET* 2.8 27.7 + - + -
518B GLY 2.8 24.4 + - - +
519B TYR* 4.4 5.6 - - - +
520B SER* 4.8 3.1 - - - +
526B ALA* 5.0 1.3 - - + -
527B ILE* 1.3 76.7 - - - +
529B THR* 1.3 67.7 + - - +
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Residues in contact with THR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B VAL* 3.4 7.8 - - - +
481B ALA* 2.7 54.1 + - - +
514B LEU* 3.7 16.1 - - + +
515B LEU 3.3 14.8 - - - +
516B PHE* 4.3 2.0 - - - -
517B MET* 4.0 7.6 - - - +
527B ILE* 4.1 3.4 - - + -
528B VAL* 1.3 80.1 - - - +
530B GLN* 1.3 61.5 + - - +
801B RI8 3.6 49.6 - - + -
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Residues in contact with GLN 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A VAL* 4.1 23.6 - - + +
479B ASP 4.5 1.3 - - - -
481B ALA* 3.8 0.2 - - - +
514B LEU* 3.8 15.1 - - + -
515B LEU* 2.9 47.6 + - + +
517B MET* 3.7 29.4 - - + +
529B THR* 1.3 83.5 + - - +
531B TRP* 1.3 63.4 + - - +
532B CYS* 4.5 4.4 - - - -
585B HIS* 4.7 7.7 + - - -
591B LYS* 3.4 35.0 - - - +
801B RI8 3.3 11.4 - - - -
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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