Contacts of the strand formed by residues 537 - 544 (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 ARG 537 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A THR* 3.0 33.2 + - + +
472A PRO* 2.9 22.6 + - - +
473A HIS* 3.2 12.1 + - - +
491A ASN* 2.8 50.6 + - - +
493A ARG* 3.6 45.1 + - - +
535A ASP* 4.6 4.7 + - + +
536A PHE* 1.3 76.1 - - - +
538A THR* 1.3 63.7 + - - +
580A ASN* 4.3 0.9 - - - -
581A HIS* 2.8 35.5 + - - +
582A ASN* 4.1 13.9 + - - +
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Residues in contact with THR 538 (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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451A ASN* 4.8 3.1 + - - -
469A ASP* 3.9 6.6 - - - +
471A THR* 3.5 23.1 + - - +
537A ARG* 1.3 76.1 - - - +
539A THR* 1.3 63.3 + - - +
540A THR* 3.7 13.6 + - - +
578A THR* 3.5 31.4 - - + -
579A VAL 3.2 5.2 - - - +
580A ASN* 2.9 21.0 + - - +
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Residues in contact with THR 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 3.8 24.0 - - + -
469A ASP 3.4 12.5 + - - +
470A LEU* 4.4 11.5 - - + -
471A THR* 5.3 0.7 + - - -
474A THR* 3.7 15.1 + - + +
489A LEU* 4.1 20.9 - - + -
491A ASN* 4.6 0.7 + - - -
537A ARG 3.9 0.2 + - - -
538A THR* 1.3 74.4 + - - +
540A THR* 1.3 63.2 - - - +
541A LEU* 4.0 1.0 + - + +
577A ILE 3.9 1.6 - - - +
578A THR* 3.8 0.3 - - - -
579A VAL* 2.8 33.9 + - - +
581A HIS* 2.8 31.9 + - - -
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Residues in contact with THR 540 (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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467A SER 3.6 1.0 - - - +
468A LEU* 3.3 9.1 - - - +
469A ASP* 3.0 47.4 + - - +
538A THR* 3.7 15.6 - - - +
539A THR* 1.3 72.4 - - - +
541A LEU* 1.3 62.9 + - - +
542A THR* 4.2 7.3 + - - +
576A THR* 3.7 26.0 - - + -
577A ILE 3.7 2.0 - - - -
578A THR* 4.1 12.5 - - - +
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Residues in contact with LEU 541 (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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466A LEU* 3.3 29.6 - - + -
467A SER 3.2 16.8 - - - +
468A LEU* 3.4 17.5 - - + -
487A ILE* 4.1 24.7 - - + -
489A LEU* 5.7 3.4 - - + -
539A THR* 4.0 2.4 + - + +
540A THR* 1.3 73.3 - - - +
542A THR* 1.3 62.1 + - - +
543A LEU* 3.7 29.4 - - + -
575A TYR* 5.2 0.9 - - + -
576A THR* 3.3 3.7 - - - +
577A ILE* 2.8 61.7 + - + +
579A VAL* 5.9 0.7 - - + -
587A MET* 5.3 3.8 - - + -
589A ILE* 4.7 2.9 - - + -
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Residues in contact with THR 542 (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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465A SER 3.9 0.5 - - - +
466A LEU* 3.2 6.4 - - - +
467A SER* 2.8 49.5 + - - -
540A THR* 4.2 8.0 + - - +
541A LEU* 1.3 76.1 + - - +
543A LEU* 1.3 66.1 + - - +
544A LYS* 3.9 4.3 + - + +
574A VAL* 3.5 28.0 - - + -
575A TYR 3.4 2.2 - - - -
576A THR* 3.8 17.5 + - - +
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Residues in contact with LEU 543 (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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463A THR* 3.5 11.7 - - + +
465A SER 3.7 2.5 - - - -
466A LEU* 3.5 37.9 - - + -
485A LEU* 4.1 12.6 - - + -
487A ILE* 4.9 1.1 - - + -
541A LEU* 3.7 14.8 - - + -
542A THR* 1.3 72.0 - - - +
544A LYS* 1.3 62.2 + - - +
546A HIS* 3.4 30.8 - - + +
573A HIS 3.6 2.1 - - - +
574A VAL* 3.3 6.4 - - - -
575A TYR* 2.7 50.7 + - + +
589A ILE* 3.7 30.1 - - + -
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Residues in contact with LYS 544 (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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463A THR* 3.0 1.3 + - - -
464A LYS* 2.9 41.3 + - + +
465A SER* 2.9 32.5 + - - +
542A THR* 3.9 5.0 - - + +
543A LEU* 1.3 69.8 - - - +
545A GLY* 1.3 63.4 + - - +
572A THR 5.5 0.7 - - - +
574A VAL* 4.0 22.2 - - + +
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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