Contacts of the strand formed by residues 443 - 450 (chain A) in PDB entry 2WNT
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 GLU 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ARG* 3.2 33.7 + - + +
435A CYS 3.6 6.1 - - - +
436A VAL* 4.2 9.9 - - + +
441A ASN 5.8 0.2 - - - +
442A MET* 1.3 73.3 - - - +
444A TYR* 1.3 69.8 + - - +
491A LEU* 3.7 19.6 + - + +
493A ARG* 3.0 45.0 + - - +
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Residues in contact with TYR 444 (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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418A TYR* 4.0 11.0 - + - -
434A ARG* 3.6 9.9 - - - +
435A CYS* 2.8 36.2 + - - +
437A HIS* 3.7 24.9 - + + -
440A THR* 6.0 0.5 - - - -
442A MET* 3.2 42.8 - - + +
443A GLU* 1.3 76.8 - - - +
445A ALA* 1.3 61.7 + - - +
476A LYS* 4.6 14.6 - - + -
488A VAL* 3.7 21.5 - - + -
489A THR 3.6 19.5 - - - +
490A GLU* 4.6 6.3 - - + -
491A LEU* 4.0 8.0 - - - +
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Residues in contact with ALA 445 (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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424A ILE* 4.4 6.3 - - + -
432A CYS* 4.4 9.2 - - - -
433A LYS 3.6 7.0 - - - +
435A CYS* 4.5 1.6 - - - -
444A TYR* 1.3 76.5 - - - +
446A VAL* 1.3 60.5 + - - +
447A LYS 4.2 0.2 + - - -
487A LEU 3.5 0.9 - - - +
488A VAL* 3.3 2.6 - - - -
489A THR* 2.7 42.5 + - - +
490A GLU 3.8 19.1 - - - +
491A LEU* 3.8 19.9 - - + +
492A MET 5.1 0.9 - - - +
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Residues in contact with VAL 446 (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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420A VAL* 4.4 11.2 - - + -
431A GLU 3.7 1.4 - - - +
432A CYS* 3.4 4.9 - - - -
433A LYS* 2.8 60.1 + - + +
435A CYS* 4.1 24.7 - - + -
444A TYR 4.3 0.2 - - - -
445A ALA* 1.3 73.2 - - - +
447A LYS* 1.3 68.4 + - - +
448A VAL* 3.8 4.9 + - + -
486A TYR* 4.0 34.3 - - + -
487A LEU 3.2 10.1 - - - +
488A VAL* 4.5 8.1 - - + -
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Residues in contact with LYS 447 (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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430A SER* 3.4 35.2 - - - -
431A GLU 3.8 6.1 - - - +
432A CYS* 4.3 11.9 - - + +
445A ALA 4.2 0.4 - - - -
446A VAL* 1.3 71.5 - - - +
448A VAL* 1.3 60.5 + - - +
449A ILE* 3.7 17.7 + - + +
459A GLU* 3.3 21.7 + - - +
485A VAL 3.3 5.9 - - - +
486A TYR* 3.8 0.9 - - - -
487A LEU* 2.8 49.5 + - + +
489A THR* 5.9 2.5 - - + -
556A CYS 5.6 0.8 + - - -
557A ASP* 2.8 29.5 + - - +
559A GLY* 5.4 0.6 - - - -
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Residues in contact with VAL 448 (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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420A VAL* 6.5 0.2 - - + -
430A SER* 3.1 4.9 - - - -
431A GLU* 2.9 63.7 + - + +
433A LYS* 4.5 16.8 - - + -
446A VAL* 4.4 11.2 - - + +
447A LYS* 1.3 72.3 - - - +
449A ILE* 1.3 60.8 + - - +
450A ASP 4.1 0.7 + - - -
484A HIS* 3.9 32.5 - - + +
485A VAL 3.7 2.9 - - - -
486A TYR* 4.4 22.2 - - + -
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Residues in contact with ILE 449 (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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429A TYR* 3.2 20.9 - - + +
430A SER* 4.2 5.4 - - - -
447A LYS* 4.1 23.8 - - + +
448A VAL* 1.3 78.3 - - - +
450A ASP* 1.3 68.0 + - - +
451A LYS* 3.2 5.8 + - - +
455A ASP 5.9 1.3 - - - +
456A PRO* 3.9 35.9 - - + -
459A GLU* 4.1 9.9 - - - +
484A HIS* 3.3 7.8 - - - -
485A VAL* 3.0 35.9 + - + +
487A LEU* 3.7 31.4 - - + -
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Residues in contact with ASP 450 (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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429A TYR* 3.6 14.4 + - - +
448A VAL 4.1 1.4 + - - -
449A ILE* 1.3 76.7 - - - +
451A LYS* 1.3 67.4 + - - +
483A LYS 4.4 0.4 - - - -
484A HIS* 3.7 20.1 - - + +
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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