Contacts of the strand formed by residues 573 - 578 (chain A) in PDB entry 3BMW
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 TYR 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ASN 5.5 1.1 - - - -
317A PHE* 4.0 39.4 - + - +
319A ASN* 4.7 10.2 - - - +
320A ASP* 4.7 1.0 + - - -
501A ILE* 3.8 28.5 - - + -
502A GLY 3.5 21.6 + - - -
503A HIS* 3.6 20.8 - - - -
504A VAL* 3.5 48.2 + - + -
559A ASN* 3.6 0.3 - - - -
560A ILE* 2.8 41.4 + - + +
571A ASN* 4.1 1.5 + - - -
572A THR* 1.3 72.2 - - - +
574A ASN* 1.3 69.0 + - - +
576A ILE* 4.2 3.9 - - + +
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Residues in contact with ASN 574 (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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316A ASN 5.1 2.3 - - - +
317A PHE* 3.5 16.3 - - - -
559A ASN* 3.3 28.7 - - - +
572A THR* 2.9 29.4 + - - -
573A TYR* 1.3 80.9 - - - +
575A ASN* 1.3 84.9 + - - +
576A ILE 3.5 1.2 + - - -
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Residues in contact with ASN 575 (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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275A ASN 5.6 0.7 - - - +
316A ASN* 3.7 37.6 + - - +
317A PHE* 3.3 20.9 - - + -
507A THR 4.3 0.3 - - - +
557A LYS* 3.7 35.4 + - + +
558A TYR 3.4 3.1 + - - -
559A ASN* 3.2 11.4 + - - +
574A ASN* 1.3 88.5 - - - +
576A ILE* 1.3 65.1 + - - +
577A ASN* 3.4 4.7 + - - +
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Residues in contact with ILE 576 (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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317A PHE* 4.1 9.9 - - + -
504A VAL* 3.7 26.5 - - + -
506A PRO 4.6 4.3 - - - +
507A THR* 3.7 33.9 - - + +
509A THR* 4.1 22.7 - - + -
515A ILE* 4.7 7.6 - - + -
531A PHE* 5.2 1.8 - - + -
556A GLY 3.7 0.3 - - - +
557A LYS* 3.3 0.9 - - - -
558A TYR* 2.8 38.7 + - - +
560A ILE* 3.5 35.4 - - + -
573A TYR* 4.2 10.1 - - + +
575A ASN* 1.3 74.9 - - - +
577A ASN* 1.3 62.5 + - - +
578A ILE* 3.6 6.1 + - + +
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Residues in contact with ASN 577 (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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241A LYS* 4.4 13.1 - - - +
276A GLU* 4.5 16.6 + - - +
507A THR 2.8 16.5 + - - +
508A MET* 3.4 10.9 - - + +
509A THR* 2.9 30.5 + - - +
556A GLY* 3.7 12.3 - - - +
557A LYS* 3.8 23.9 - - + +
575A ASN 3.4 3.7 + - - +
576A ILE* 1.3 69.6 - - - +
578A ILE* 1.3 67.8 + - - +
579A LEU* 3.8 22.9 + - - +
608A ALA* 5.7 1.9 - - - +
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Residues in contact with ILE 578 (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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509A THR* 3.5 11.2 - - + -
510A LYS* 4.1 12.1 - - - -
511A ALA* 4.4 4.3 - - + +
531A PHE* 3.8 18.4 - - + -
550A VAL* 3.8 25.8 - - + -
551A PRO 5.0 1.3 - - - +
553A VAL* 3.4 36.8 - - + +
555A PRO* 3.3 10.5 - - + +
556A GLY* 2.8 44.0 + - - +
558A TYR* 3.6 15.5 - - + -
576A ILE* 4.3 5.4 - - + +
577A ASN* 1.3 76.6 + - - +
579A LEU* 1.3 71.9 + - - +
608A ALA* 4.9 1.6 - - - +
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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