Contacts of the strand formed by residues 574 - 581 (chain A) in PDB entry 2WMH
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 VAL 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A THR* 3.5 30.5 - - + -
543A LEU 3.3 4.5 - - - +
544A LYS* 4.0 28.3 - - + +
567A ASN 3.7 1.2 - - - +
568A TRP* 3.5 4.7 - - - -
569A ASP* 2.9 35.1 + - + +
572A THR* 3.1 30.0 - - - +
573A HIS* 1.3 76.6 - - - +
575A TYR* 1.3 61.6 + - - +
576A THR* 4.1 8.2 + - - +
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Residues in contact with TYR 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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541A LEU* 5.2 0.2 - - + -
542A THR* 3.4 2.3 - - - +
543A LEU* 2.7 61.7 + - + +
546A HIS* 5.0 1.1 - - + -
550A LYS* 6.2 0.2 - - + -
551A PRO* 4.1 30.3 - - + -
553A ILE* 3.3 22.8 - - + +
566A GLU* 2.7 48.1 + - + +
567A ASN 3.3 14.8 - - - -
568A TRP* 3.6 22.3 - + + -
574A VAL* 1.3 73.0 - - - +
576A THR* 1.3 61.2 + - - +
577A ILE* 3.6 30.5 - - + +
589A ILE* 4.3 15.3 - - + -
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Residues in contact with THR 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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540A THR* 3.7 26.5 - - + -
541A LEU 3.3 10.5 - - - +
542A THR* 3.8 17.8 + - - +
565A THR 3.9 0.3 - - - +
566A GLU* 3.3 4.3 - - - +
567A ASN* 2.8 54.5 + - + +
574A VAL* 4.1 5.9 - - - +
575A TYR* 1.3 78.7 + - - +
577A ILE* 1.3 63.8 + - - +
578A THR* 4.0 10.3 + - - +
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Residues in contact with ILE 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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539A THR 3.9 1.7 - - - +
540A THR* 3.7 1.2 - - - -
541A LEU* 2.8 57.4 + - + +
553A ILE* 3.5 31.0 - - + -
555A ILE* 3.9 13.0 - - + -
564A TYR* 3.6 23.3 - - + -
565A THR 3.4 10.5 - - - +
566A GLU* 4.3 0.9 - - + -
575A TYR* 3.6 22.3 - - + +
576A THR* 1.3 74.2 - - - +
578A THR* 1.3 63.3 + - - +
579A VAL* 3.8 9.9 + - + +
587A MET* 3.8 23.3 - - + -
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Residues in contact with THR 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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538A THR* 3.5 26.9 - - + -
539A THR 3.8 2.7 - - - -
540A THR* 4.1 10.4 - - - +
564A TYR* 3.1 5.7 - - - -
565A THR* 2.9 47.2 + - + +
576A THR* 4.0 14.1 - - - +
577A ILE* 1.3 72.2 - - - +
579A VAL* 1.3 59.6 + - - +
580A ASN* 4.0 10.3 + - - +
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Residues in contact with VAL 579 (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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489A LEU* 4.1 8.7 - - + -
538A THR* 3.2 2.6 - - - -
539A THR 2.8 45.0 + - - +
541A LEU* 5.9 0.7 - - + -
555A ILE* 5.0 0.7 - - + -
562A TYR* 4.6 2.5 - - + -
563A THR 3.5 9.9 - - - +
564A TYR* 4.2 4.0 - - + -
577A ILE* 3.8 19.1 - - + +
578A THR* 1.3 75.0 - - - +
580A ASN* 1.3 63.6 + - - +
581A HIS* 3.4 22.8 + - + +
585A VAL* 3.8 29.6 - - + -
587A MET* 3.7 29.6 - - + -
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Residues in contact with ASN 580 (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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536A PHE* 3.7 18.4 - - + -
537A ARG 3.5 4.9 - - - -
538A THR* 2.9 31.8 + - - +
562A TYR* 3.1 3.8 - - - -
563A THR* 2.8 58.7 + - - +
564A TYR* 4.3 3.1 + - - -
565A THR* 5.2 5.5 - - - +
578A THR* 4.2 11.3 - - - +
579A VAL* 1.3 72.2 - - - +
581A HIS* 1.3 62.2 + - - +
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Residues in contact with HIS 581 (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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474A THR* 4.6 0.8 - - - +
489A LEU* 3.9 18.4 - - + +
490A ASN 4.5 0.4 + - - -
491A ASN* 2.9 45.1 + - - +
536A PHE* 3.5 7.9 - - - +
537A ARG* 2.8 27.4 + - - +
539A THR* 2.8 37.4 + - - -
561A HIS 3.3 12.6 - - - +
562A TYR* 3.7 11.2 - - + -
579A VAL* 3.4 16.3 + - + +
580A ASN* 1.3 76.7 - - - +
582A ASN* 1.3 61.4 + - - +
583A GLY 2.9 27.7 + - - +
585A VAL* 3.8 15.5 - - + -
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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