Contacts of the strand formed by residues 584 - 589 (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 MET 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PRO* 4.6 21.5 - - + -
488A LEU* 3.7 27.6 - - + -
489A LEU 3.3 5.8 - - - +
490A ASN* 3.5 14.3 - - - +
557A GLY* 3.2 6.8 - - - -
558A ASP* 2.9 57.5 + - - +
561A HIS 5.5 0.9 - - - +
562A TYR* 4.8 1.0 - - - +
583A GLY* 1.3 72.1 - - - -
585A VAL* 1.3 66.7 + - - +
586A GLU* 3.9 26.5 - - + +
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Residues in contact with VAL 585 (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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487A ILE 4.0 0.3 - - - +
488A LEU* 3.7 1.6 - - - -
489A LEU* 2.8 44.9 + - + +
555A ILE* 3.9 24.9 - - + -
556A SER 3.5 12.1 - - - +
557A GLY* 4.1 0.2 - - - -
561A HIS 5.2 0.2 - - - +
562A TYR* 3.5 34.1 - - + -
579A VAL* 3.8 22.7 - - + -
581A HIS* 3.8 11.4 - - + -
583A GLY 3.9 0.6 + - - -
584A MET* 1.3 78.8 - - - +
586A GLU* 1.3 64.9 + - - +
587A MET* 4.2 13.5 - - + -
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Residues in contact with GLU 586 (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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486A HIS* 3.6 25.5 + - + +
487A ILE 3.3 5.4 - - - +
488A LEU* 3.6 26.1 - - + +
554A ASN 4.0 0.2 - - - +
555A ILE* 3.3 3.3 - - - +
556A SER* 2.9 49.6 + - - +
557A GLY* 5.9 0.2 - - - -
584A MET* 3.9 28.2 - - + +
585A VAL* 1.3 73.2 - - - +
587A MET* 1.3 64.6 + - - +
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Residues in contact with MET 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU 3.8 0.2 - - - +
486A HIS* 3.2 11.0 + - - -
487A ILE* 2.8 49.6 + - + +
489A LEU* 4.0 19.7 - - + -
541A LEU* 5.3 2.5 - - + -
553A ILE* 4.5 4.0 - - + -
554A ASN 3.1 10.1 - - - +
555A ILE* 4.0 13.9 - - + -
577A ILE* 3.8 31.4 - - + -
579A VAL* 3.7 30.7 - - + -
585A VAL* 4.2 6.7 - - + -
586A GLU* 1.3 80.7 - - - +
588A SER* 1.3 61.7 + - - +
589A ILE* 4.3 24.0 - - + -
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Residues in contact with SER 588 (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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484A ASN* 4.2 17.5 + - - +
485A LEU 3.4 8.1 + - - -
486A HIS* 4.4 10.1 - - - -
552A GLN 4.7 0.9 - - - +
553A ILE* 3.6 5.0 - - - +
554A ASN* 2.9 41.3 + - - +
587A MET* 1.3 73.8 - - - +
589A ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 589 (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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462A ASN* 5.3 0.9 + - - -
483A ASN 4.7 1.5 - - - +
484A ASN* 3.3 15.2 - - - -
485A LEU* 2.9 42.6 + - + +
487A ILE* 4.0 22.7 - - + -
541A LEU* 4.7 2.2 - - + -
543A LEU* 3.7 24.7 - - + -
546A HIS* 3.5 37.4 + - + +
551A PRO* 3.8 21.8 - - + -
552A GLN 5.5 1.6 - - - -
553A ILE* 3.9 13.7 - - + +
575A TYR* 4.3 13.5 - - + -
587A MET* 4.3 21.8 - - + -
588A SER* 1.3 79.2 + - - +
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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