Contacts of the strand formed by residues 540 - 544 (chain B) in PDB entry 3K5N
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 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534B ILE* 5.0 0.4 - - - -
535B GLU* 4.8 6.7 - - - +
539B TYR* 1.3 79.8 - - - +
541B VAL* 1.3 64.2 + - - +
542B ILE* 4.1 0.7 - - + +
551B VAL* 3.4 7.8 - - - +
552B TRP* 2.9 61.0 + - + +
554B LYS* 2.6 24.4 + - - +
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Residues in contact with VAL 541 (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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406B ASP 5.1 0.9 - - - +
408B ARG* 4.6 6.5 - - - +
531B LYS* 4.0 42.2 + - + +
534B ILE* 3.8 28.7 - - + -
535B GLU* 4.8 7.6 + - + +
540B ASP* 1.3 74.7 + - - +
542B ILE* 1.3 60.9 + - - +
543B TYR 4.0 15.5 - - - +
544B GLY* 5.0 1.3 - - - +
549B THR* 4.7 14.1 - - - +
550B PHE 3.1 16.6 - - - +
551B VAL* 4.6 2.5 - - + -
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Residues in contact with ILE 542 (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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406B ASP 2.9 20.3 - - - +
407B SER* 3.3 2.6 - - - -
408B ARG* 2.7 57.3 + - + +
412B TYR* 2.7 32.5 - - + +
415B VAL* 3.9 21.5 - - + -
540B ASP* 5.2 0.6 - - + +
541B VAL* 1.3 73.6 - - - +
543B TYR* 1.3 55.9 + - - +
550B PHE* 2.9 11.4 + - + +
552B TRP* 3.8 32.3 - - + -
601B PHE* 4.8 0.4 - - + -
603B MET* 4.0 21.5 - - + -
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Residues in contact with TYR 543 (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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406B ASP 4.2 6.1 - - - -
407B SER* 4.2 20.6 - - - -
541B VAL* 3.6 6.5 - - - +
542B ILE* 1.3 82.5 - - - +
544B GLY* 1.3 63.7 + - - +
545B ASP* 3.1 36.8 + - + -
549B THR* 3.3 0.5 - - - -
550B PHE* 2.3 85.5 + + + +
603B MET* 3.7 23.3 - - + -
616B ARG 4.8 17.5 + - - -
617B TYR* 5.4 2.0 - + - -
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Residues in contact with GLY 544 (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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406B ASP 5.2 0.8 + - - -
527B MET* 5.3 3.8 - - - -
541B VAL* 5.0 2.6 - - - +
543B TYR* 1.3 89.4 - - - +
545B ASP* 1.3 65.3 + - - +
548B SER 2.9 11.9 - - - -
549B THR* 3.6 7.4 - - - -
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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