Contacts of the strand formed by residues 477 - 482 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP 4.4 1.6 - - - +
61A LYS* 3.0 34.7 + - - +
62A ASN* 3.4 13.0 + - - -
407A CYS* 3.2 12.6 - - + +
409A PHE* 3.7 15.0 - - + -
436A THR* 3.4 29.3 + - + +
439A LEU* 3.7 31.4 - - + -
475A ARG 3.9 4.2 + - - +
476A PRO* 1.3 81.0 - - - +
478A ASN* 1.3 65.9 + - - +
479A SER* 4.7 0.9 + - - -
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Residues in contact with ASN 478 (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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57A LEU* 4.3 10.3 - - + -
58A ASP 3.4 4.5 - - - +
59A TYR* 3.4 18.8 - - - +
62A ASN* 2.9 29.7 - - - +
323A LEU* 3.5 20.0 - - + +
326A LEU* 3.7 11.0 - - - +
339A HIS* 5.0 3.1 - - - -
407A CYS 2.9 6.0 + - - +
408A ASP* 2.8 26.8 - - + +
409A PHE* 2.8 32.3 + - - +
477A THR* 1.3 73.8 - - - +
479A SER* 1.4 59.7 + - - +
480A ILE* 5.2 1.8 - - + -
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Residues in contact with SER 479 (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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56A LEU 3.8 1.4 - - - +
57A LEU* 3.7 1.4 - - - +
58A ASP* 2.8 39.5 + - - +
61A LYS* 4.5 1.8 + - - -
409A PHE* 3.3 6.8 - - - +
432A PHE* 4.0 12.1 + - - -
436A THR* 3.6 24.6 + - - +
477A THR* 4.7 0.5 + - - -
478A ASN* 1.4 74.5 - - - +
480A ILE* 1.3 61.3 + - - +
548B LEU* 3.8 37.8 - - - +
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Residues in contact with ILE 480 (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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55A ILE* 4.6 6.5 - - + -
56A LEU 3.3 8.3 - - - +
57A LEU* 3.8 22.2 - - + -
323A LEU* 5.1 2.5 - - + -
408A ASP* 4.7 9.6 - - + -
409A PHE 2.8 12.5 + - - +
410A LEU* 3.1 25.1 - - + +
411A ALA 2.9 25.8 + - - +
432A PHE* 4.0 0.9 - - - -
478A ASN* 5.2 0.9 - - + -
479A SER* 1.3 79.0 - - - +
481A VAL* 1.3 69.1 + - - +
482A VAL* 4.4 1.1 + - + -
485A PHE* 6.4 0.2 - - + -
493A LEU* 4.0 26.0 - - + -
496A MET* 3.9 20.0 - - + -
497A TYR* 3.7 23.8 - - + +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.7 1.2 - - - +
56A LEU* 2.9 38.2 + - + +
411A ALA 3.3 8.5 - - - +
413A ALA* 4.5 1.1 - - + +
432A PHE* 3.8 19.3 - - + -
480A ILE* 1.3 77.7 - - - +
482A VAL* 1.3 77.6 + - - +
548B LEU* 3.8 29.4 - - + +
551B PHE* 3.7 25.4 - - + -
552B LEU* 3.6 32.1 - - + -
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Residues in contact with VAL 482 (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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54A GLU 4.1 7.2 - - - +
55A ILE* 4.3 17.3 - - + -
411A ALA 3.1 3.8 + - - +
412A PRO* 3.2 8.9 - - + +
413A ALA* 2.9 24.4 + - - +
480A ILE* 4.8 2.2 - - + -
481A VAL* 1.3 84.6 - - - +
483A LYS* 1.3 60.0 + - - +
484A LYS 3.5 30.5 - - - +
485A PHE* 3.8 21.1 - - + -
489A THR* 4.3 15.7 - - + -
493A LEU* 4.1 24.7 - - + -
551B PHE* 4.9 2.5 - - - -
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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