Contacts of the strand formed by residues 454 - 459 (chain B) in PDB entry 5BS8
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 GLU 454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LYS 4.1 8.5 - - - +
453B SER* 1.3 81.3 - - - +
455B LEU* 1.3 54.8 + - - +
456B TYR* 3.7 16.7 + - + -
475B PHE* 2.7 16.5 + - - +
476B GLN* 3.4 33.0 + - + +
477B ALA* 2.7 35.3 + - - +
524B TYR* 3.7 5.3 - - - -
526B LYS* 3.3 40.1 - - + +
528B VAL* 5.1 2.8 - - + +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B LEU* 3.9 27.6 - - + -
454B GLU* 1.3 72.1 - - - +
456B TYR* 1.3 62.0 + - - +
457B VAL* 3.5 21.1 + - + -
477B ALA* 3.8 16.4 - - + +
479B LEU* 4.0 17.3 - - + +
505B ILE* 5.6 1.1 - - + +
508B ALA* 4.4 11.2 - - + -
509B LEU* 3.7 28.9 - - + -
524B TYR* 3.6 29.1 - - + +
526B LYS 2.7 10.5 + - - +
527B ILE* 3.5 6.1 - - + +
528B VAL 2.8 27.9 + - - +
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLU* 3.7 23.8 + - + -
455B LEU* 1.3 72.8 - - - +
457B VAL* 1.3 63.2 + - - +
458B VAL* 3.4 10.4 + - + +
476B GLN* 3.9 27.9 + - + -
477B ALA 2.8 11.6 + - - -
478B ILE* 3.6 22.1 - - + -
479B LEU 3.0 24.6 + - - -
528B VAL* 3.4 40.7 - - + +
530B MET* 3.9 34.1 - - + -
564B ALA* 4.5 3.4 - - + -
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 4.1 23.8 - - + -
456B TYR* 1.3 70.3 - - - +
458B VAL* 1.3 59.7 + - - +
479B LEU* 3.5 11.2 - - + +
481B LEU* 3.1 40.6 - - + -
505B ILE* 5.1 9.2 - - + -
509B LEU* 5.9 0.2 - - + -
527B ILE* 4.2 11.9 - - + -
528B VAL 2.8 8.5 + - - +
529B LEU* 3.7 22.8 - - + +
530B MET 2.9 28.9 + - - +
544B LEU* 4.3 14.4 - - + +
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Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 3.5 21.1 - - + +
457B VAL* 1.3 74.6 - - - +
459B GLU* 1.3 63.5 + - - +
460B GLY 4.2 0.2 - - - +
463B ALA* 3.5 18.2 - - + +
464B GLY* 3.5 32.1 - - - +
467B ALA* 4.5 2.2 - - + -
478B ILE* 3.9 15.7 - - + -
479B LEU 3.1 10.0 + - - +
480B PRO* 3.5 2.9 - - + +
481B LEU* 2.7 35.8 + - - +
530B MET* 3.5 33.4 - - + +
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Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B VAL* 1.3 72.7 - - - +
460B GLY* 1.3 62.2 + - - +
463B ALA* 3.4 20.3 - - - +
481B LEU* 3.9 5.6 - - - +
530B MET 3.1 6.4 + - - +
531B ALA* 3.2 22.2 - - + +
532B ASP* 2.8 52.2 + - - +
534B ASP* 4.7 0.9 - - - +
536B ASP* 4.8 4.7 - - - +
537B GLY* 3.5 10.4 + - - -
540B ILE* 3.7 33.5 - - + +
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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