Contacts of the helix formed by residues 444 - 455 (chain B) in PDB entry 4WMJ
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 THR 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B LYS 5.7 2.7 - - - +
443B LYS* 1.3 76.1 - - - +
445B ASP* 1.3 66.7 + - - +
446B ALA* 3.3 10.0 + - - +
447B GLU* 3.0 35.9 + - - +
448B ALA* 2.9 22.3 + - - +
470B VAL* 4.2 6.1 - - - -
471B PHE 5.0 0.7 - - - +
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Residues in contact with ASP 445 (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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444B THR* 1.3 72.2 - - - +
446B ALA* 1.3 57.8 + - - +
449B LYS* 2.9 31.9 + - - +
466B LEU* 3.7 21.8 - - + +
467B PRO* 5.3 3.5 - - - +
470B VAL* 3.8 31.0 - - - +
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Residues in contact with ALA 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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444B THR* 3.1 8.7 + - - +
445B ASP* 1.3 74.4 - - - +
447B GLU* 1.3 62.4 + - + +
449B LYS* 3.4 5.7 + - - +
450B ALA* 2.9 32.6 + - - +
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Residues in contact with GLU 447 (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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441B LYS* 3.9 28.0 + - - +
442B GLY 4.2 3.5 - - - +
443B LYS* 3.4 24.4 + - + +
444B THR* 3.0 39.8 + - - +
446B ALA* 1.3 81.4 - - + +
448B ALA* 1.3 62.9 + - - +
450B ALA* 3.3 6.3 + - - +
451B GLU* 3.2 26.8 + - - +
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Residues in contact with ALA 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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443B LYS* 3.8 21.8 - - + +
444B THR 2.9 16.7 + - - +
445B ASP 4.5 0.2 - - - -
447B GLU* 1.3 76.0 - - - +
449B LYS* 1.3 62.5 + - - +
451B GLU* 3.3 8.3 + - - +
452B LEU* 3.1 26.3 + - - +
466B LEU* 3.7 18.8 - - + -
469B LYS* 4.0 24.9 - - + +
470B VAL* 4.5 2.2 - - + -
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Residues in contact with LYS 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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445B ASP 2.9 19.3 + - - +
446B ALA* 3.8 5.6 - - - +
448B ALA* 1.3 75.3 - - - +
450B ALA* 1.3 58.8 + - - +
452B LEU* 3.1 6.6 + - - +
453B GLU* 2.9 57.2 + - + +
462B ILE* 4.5 20.6 - - + -
466B LEU* 3.7 23.1 - - + +
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Residues in contact with ALA 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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446B ALA 2.9 18.8 + - - +
447B GLU* 3.7 6.5 - - - +
449B LYS* 1.3 76.6 - - - +
451B GLU* 1.3 63.3 + - + +
453B GLU* 3.4 17.0 + - - +
454B LYS* 3.2 37.2 + - - +
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Residues in contact with GLU 451 (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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519A GLU* 3.8 9.9 - - - +
523A GLN* 4.0 11.1 + - - +
443B LYS* 2.9 41.8 + - - +
447B GLU* 3.2 16.8 + - - +
448B ALA* 3.6 6.7 - - - +
449B LYS 3.2 0.4 - - - -
450B ALA* 1.3 75.3 - - + +
452B LEU* 1.3 61.3 + - + +
454B LYS* 2.9 28.2 + - + +
455B SER* 3.2 11.4 + - - -
469B LYS* 5.6 2.4 - - - +
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Residues in contact with LEU 452 (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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448B ALA 3.1 15.7 + - - +
449B LYS 3.6 6.1 - - - +
451B GLU* 1.3 79.6 - - + +
453B GLU* 1.3 59.4 + - - +
455B SER* 2.9 32.0 + - - +
457B MET* 3.5 37.8 + - + +
462B ILE* 3.8 27.4 - - + +
465B ILE* 4.0 23.1 - - + -
466B LEU* 4.0 23.8 - - + -
469B LYS* 4.1 26.9 - - + +
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Residues in contact with GLU 453 (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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449B LYS* 2.9 41.6 + - + +
450B ALA* 3.5 20.9 - - - +
452B LEU* 1.3 76.3 - - - +
454B LYS* 1.3 59.3 + - + +
455B SER 3.0 10.9 - - - +
457B MET 4.9 0.7 + - - +
462B ILE* 4.0 17.3 - - + -
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Residues in contact with LYS 454 (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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450B ALA* 3.2 24.4 + - - +
451B GLU* 2.9 13.4 + - - +
453B GLU* 1.3 76.9 - - + +
455B SER* 1.3 59.4 + - - +
456B GLY 4.1 0.2 + - - -
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Residues in contact with SER 455 (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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451B GLU 3.2 9.0 + - - -
452B LEU* 2.9 24.6 + - - +
453B GLU 3.0 10.9 - - - +
454B LYS* 1.3 76.9 - - - +
456B GLY* 1.3 54.7 + - - +
457B MET* 2.5 37.9 + - - +
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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