Contacts of the strand formed by residues 477 - 482 (chain B) in PDB entry 4WMJ
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 THR 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP 4.4 1.9 - - - +
61B LYS* 3.0 34.6 + - - +
62B ASN* 3.5 12.2 + - - -
407B CYS* 3.2 13.7 - - + +
409B PHE* 3.7 26.7 - - + -
436B THR* 3.3 31.1 + - + +
439B LEU* 3.8 18.4 - - + -
475B ARG 4.0 3.6 + - - +
476B PRO* 1.3 80.8 - - - +
478B ASN* 1.3 66.4 + - - +
479B SER* 4.7 0.9 + - - -
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Residues in contact with ASN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.1 14.1 - - + -
58B ASP 3.6 2.7 - - - -
59B TYR* 3.3 18.4 - - - +
62B ASN* 2.9 33.8 - - - +
323B LEU* 3.6 18.3 - - - +
326B LEU* 3.5 13.3 - - - +
339B HIS* 5.1 2.1 - - - -
407B CYS 3.0 7.0 + - - +
408B ASP* 2.9 28.0 - - + +
409B PHE* 2.9 27.9 + - - +
477B THR* 1.3 76.5 - - - +
479B SER* 1.3 63.1 + - - +
480B ILE* 4.1 2.0 - - + -
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 3.8 36.9 - - - +
56B LEU 3.5 1.6 - - - +
57B LEU* 3.6 1.4 - - - +
58B ASP* 2.7 44.2 + - - +
61B LYS* 4.3 2.0 + - - -
409B PHE* 3.4 3.6 - - - +
432B PHE* 4.1 13.7 + - - -
436B THR* 3.6 27.7 + - - +
477B THR* 4.7 0.9 + - - -
478B ASN* 1.3 71.2 - - - +
480B ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 480 (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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55B ILE* 4.7 5.4 - - + -
56B LEU 3.2 7.9 - - - +
57B LEU* 3.6 28.5 - - + -
323B LEU* 5.1 2.2 - - + -
408B ASP* 4.7 10.5 - - + -
409B PHE 2.9 9.7 + - - +
410B LEU* 3.2 22.7 - - + -
411B ALA 2.9 24.9 + - - +
432B PHE* 4.0 1.0 - - - -
478B ASN* 5.1 0.9 - - + -
479B SER* 1.3 73.6 - - - +
481B VAL* 1.3 69.3 + - - +
482B VAL* 4.8 1.3 - - + -
485B PHE* 6.2 0.2 - - + -
493B LEU* 4.0 25.8 - - + -
496B MET* 3.8 20.6 - - + -
497B TYR* 3.6 24.5 - - - +
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LEU* 3.8 29.2 - - + -
551A PHE* 3.6 26.2 - - + -
552A LEU* 3.6 30.3 - - + -
55B ILE* 3.6 4.2 - - - +
56B LEU* 2.9 39.0 + - + +
411B ALA 3.2 7.4 - - - +
413B ALA* 4.9 1.1 - - + -
432B PHE* 3.9 18.8 - - + -
480B ILE* 1.3 78.2 - - - +
482B VAL* 1.3 77.9 + - - +
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Residues in contact with VAL 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A PHE* 5.0 1.8 - - - -
54B GLU 4.1 5.8 - - - +
55B ILE* 4.2 24.9 - - + -
411B ALA 3.1 3.0 + - - +
412B PRO* 3.3 10.9 - - + +
413B ALA* 2.8 24.8 + - - +
480B ILE* 4.8 2.7 - - + -
481B VAL* 1.3 86.9 - - - +
483B LYS* 1.3 61.7 + - - +
484B LYS 3.5 29.8 - - - +
485B PHE* 3.7 23.3 - - + +
489B THR* 4.3 11.0 - - + -
493B LEU* 4.0 23.6 - - + -
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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