Contacts of the strand formed by residues 443 - 450 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B ARG* 3.2 34.5 + - + +
435B CYS 3.6 6.1 - - - +
436B VAL* 4.2 9.9 - - + +
441B ASN 5.8 0.4 - - - +
442B MET* 1.3 73.8 - - - +
444B TYR* 1.3 69.3 + - - +
491B LEU* 3.3 31.8 + - + +
493B ARG* 3.3 37.4 + - - +
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Residues in contact with TYR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B TYR* 4.3 8.5 - + - -
434B ARG* 3.6 9.5 - - - +
435B CYS* 2.8 42.6 + - - +
437B HIS* 3.7 21.1 - - + -
440B THR* 6.0 1.1 - - - -
442B MET* 3.3 41.5 - - + +
443B GLU* 1.3 77.8 - - - +
445B ALA* 1.3 61.3 + - - +
476B LYS* 3.5 39.0 + - + +
488B VAL* 4.0 13.7 - - + -
489B THR 3.4 17.5 - - - +
490B GLU* 4.3 4.5 - - - -
491B LEU* 3.7 9.3 - - - +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE* 4.2 8.7 - - + -
432B CYS* 4.4 9.4 - - - -
433B LYS 3.5 7.9 - - - +
435B CYS* 4.4 2.0 - - - -
444B TYR* 1.3 76.5 - - - +
446B VAL* 1.3 59.8 + - - +
473B ILE* 6.0 0.4 - - + -
487B LEU 3.5 1.2 - - - +
488B VAL* 3.5 2.1 - - - +
489B THR* 2.9 38.9 + - - +
490B GLU 3.9 16.6 - - - +
491B LEU* 4.0 17.2 - - + +
492B MET 5.1 1.1 - - - +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B VAL* 4.6 9.4 - - + -
431B GLU 3.7 0.3 - - - +
432B CYS* 3.4 4.9 - - - -
433B LYS* 2.8 59.9 + - + +
435B CYS* 4.1 25.7 - - + -
445B ALA* 1.3 74.5 - - - +
447B LYS* 1.3 63.1 + - - +
448B VAL* 3.6 15.3 + - + -
486B TYR* 4.0 28.7 - - + -
487B LEU 3.2 10.1 - - - +
488B VAL* 4.5 8.1 - - + -
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Residues in contact with LYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B SER* 3.7 24.0 - - - +
431B GLU 4.0 3.6 - - - +
432B CYS* 4.3 14.4 - - + +
445B ALA 4.2 0.4 - - - -
446B VAL* 1.3 71.1 - - - +
448B VAL* 1.3 60.4 + - - +
449B ILE* 3.6 19.7 + - + +
459B GLU* 2.7 32.5 + - - +
485B VAL 3.4 6.1 - - - +
486B TYR* 3.6 0.3 - - - -
487B LEU* 2.8 58.1 + - + +
489B THR* 6.0 2.0 - - + -
557B ASP* 2.8 24.2 + - - +
559B GLY* 4.4 3.2 - - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B VAL* 6.1 1.1 - - + -
430B SER* 3.2 4.7 - - - -
431B GLU* 2.9 57.8 + - + +
433B LYS* 4.3 17.7 - - + -
446B VAL* 4.1 14.4 - - + +
447B LYS* 1.3 71.8 - - - +
449B ILE* 1.3 62.1 + - - +
450B ASP 4.1 0.5 + - - -
484B HIS* 3.7 21.8 - - + -
485B VAL 3.7 2.5 - - - -
486B TYR* 3.7 35.2 - - + -
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B TYR* 3.8 12.3 - - + +
430B SER* 3.8 12.3 - - - -
447B LYS* 3.9 29.6 - - + +
448B VAL* 1.3 77.0 - - - +
450B ASP* 1.3 68.6 + - - +
451B LYS 3.2 2.6 + - - -
454B ARG* 4.4 13.5 - - + -
456B PRO* 3.9 31.6 - - + -
459B GLU* 3.9 4.7 - - - +
484B HIS* 3.4 5.9 - - - -
485B VAL* 2.8 54.0 + - + +
487B LEU* 3.9 19.7 - - + -
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Residues in contact with ASP 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B TYR* 3.3 17.6 + - - +
448B VAL 4.1 0.6 + - - -
449B ILE* 1.3 71.7 - - - +
451B LYS* 1.3 66.4 + - - +
452B SER* 3.1 9.6 - - - +
453B LYS* 3.0 23.2 + - + +
454B ARG* 3.1 10.6 + - - +
483B LYS 4.3 1.1 - - - +
484B HIS* 3.6 24.9 - - + +
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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