Contacts of the helix formed by residues 439 - 453 (chain B) in PDB entry 2BEX
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 SER 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B ASP* 2.5 41.7 + - - -
437B TYR* 4.3 10.7 - - - -
438B TRP* 1.3 76.7 - - - +
440B GLU* 1.3 64.8 + - - +
441B GLU* 3.5 3.3 + - - -
442B MET* 3.1 13.5 + - - +
443B GLU* 3.2 22.3 + - - +
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Residues in contact with GLU 440 (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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439B SER* 1.3 74.9 - - - +
441B GLU* 1.3 60.7 + - - +
443B GLU* 3.5 6.7 + - - +
444B ASP* 2.7 40.4 + - - +
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Residues in contact with GLU 441 (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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411B ASP* 3.1 21.5 - - + +
439B SER* 3.2 1.7 + - - +
440B GLU* 1.3 80.1 - - - +
442B MET* 1.3 59.8 + - - +
444B ASP* 4.0 4.4 - - - +
445B ARG* 3.0 27.9 + - - +
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Residues in contact with MET 442 (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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409B LEU 4.3 2.7 - - - +
410B GLY* 3.8 5.2 - - - -
411B ASP* 3.3 50.0 + - - +
414B ILE* 3.1 35.7 - - + -
436B ILE* 4.3 9.2 - - + -
437B TYR* 3.0 29.4 - - - +
438B TRP* 3.8 21.3 - - + -
439B SER* 3.1 17.2 + - - +
440B GLU 3.4 0.2 - - - -
441B GLU* 1.3 79.9 - - - +
443B GLU* 1.3 57.7 + - - +
445B ARG* 3.6 4.8 - - - +
446B LEU* 3.1 34.3 + - - +
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Residues in contact with GLU 443 (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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438B TRP* 3.9 17.6 - - + -
439B SER 3.2 14.1 + - - +
440B GLU* 4.0 7.2 - - - +
442B MET* 1.3 77.3 - - - +
444B ASP* 1.3 65.2 + - - +
446B LEU* 3.4 1.6 + - - +
447B GLN* 2.8 37.3 + - + +
0D MET* 4.8 7.6 - - + +
1D LYS* 3.8 12.6 + - - +
7D TRP* 3.3 41.3 + - + -
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Residues in contact with ASP 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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440B GLU* 2.7 29.0 + - - +
441B GLU* 4.0 4.2 - - - +
443B GLU* 1.3 80.0 - - - +
445B ARG* 1.3 63.7 + - - +
447B GLN* 3.7 5.8 - - - +
448B ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 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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414B ILE* 5.8 2.5 - - + -
415B LEU* 5.6 10.8 - - + -
418B VAL* 5.0 12.5 - - + +
441B GLU 3.0 20.2 + - - +
442B MET* 3.6 7.2 - - - +
444B ASP* 1.3 78.8 - - - +
446B LEU* 1.3 60.2 + - + +
448B ALA* 3.5 5.9 + - - +
449B LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 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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414B ILE* 3.9 19.3 - - + -
418B VAL* 3.5 29.2 - - + -
431B LEU* 5.2 6.5 - - + -
433B LEU* 4.0 6.5 - - + -
438B TRP* 3.2 37.2 - - + -
442B MET 3.1 15.4 + - - +
445B ARG* 1.3 74.5 - - + +
447B GLN* 1.3 60.8 + - - +
449B LEU* 3.3 18.7 + - + +
450B GLU* 3.0 27.9 + - - +
458B VAL* 3.9 22.0 - - + +
0D MET* 3.6 18.6 - - + +
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Residues in contact with GLN 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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443B GLU* 2.8 25.6 + - + +
444B ASP* 3.3 7.2 + - - +
446B LEU* 1.3 76.5 - - - +
448B ALA* 1.3 61.3 + - - +
450B GLU* 3.4 6.9 + - - +
451B LYS* 3.4 18.5 + - - +
0D MET* 4.2 13.4 - - - -
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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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444B ASP 3.0 17.3 + - - +
445B ARG* 3.7 5.6 - - - +
447B GLN* 1.3 76.0 - - - +
449B LEU* 1.3 65.9 + - - +
451B LYS* 2.9 9.2 + - - +
452B ASP* 2.9 24.9 + - - +
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Residues in contact with LEU 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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418B VAL* 3.9 14.4 - - + -
421B VAL* 3.5 25.6 - - + -
422B ARG* 4.0 27.6 - - + -
431B LEU* 6.0 0.4 - - + -
445B ARG 3.1 14.3 + - - +
446B LEU* 3.5 31.2 - - + +
448B ALA* 1.3 75.9 - - - +
450B GLU* 1.3 54.8 + - - +
452B ASP* 4.5 6.5 - - + -
453B LYS* 2.8 50.6 + - + +
456B LEU* 3.8 15.0 - - + -
458B VAL* 4.7 3.6 - - + -
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Residues in contact with GLU 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 LEU 3.0 15.9 + - - +
447B GLN* 3.5 8.1 - - - +
448B ALA 3.1 0.2 - - - -
449B LEU* 1.3 78.8 - - - +
451B LYS* 1.3 59.6 + - - +
453B LYS 3.6 17.6 - - - +
454B PRO* 3.7 8.8 - - + +
456B LEU* 4.0 12.8 - - - +
457B ARG* 4.0 4.3 - - - +
458B VAL* 3.2 31.2 + - + +
0D MET* 3.3 36.0 + - - +
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Residues in contact with LYS 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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447B GLN 3.4 9.0 + - - +
448B ALA* 2.9 11.3 + - - +
450B GLU* 1.3 78.4 - - - +
452B ASP* 1.3 63.9 + - - +
453B LYS 3.5 0.2 + - - -
454B PRO* 3.7 15.0 - - - +
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Residues in contact with ASP 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 2.9 15.1 + - - +
449B LEU* 3.9 8.5 - - + +
451B LYS* 1.3 78.9 - - - +
453B LYS* 1.3 57.8 + - + +
454B PRO* 3.6 5.9 - - - +
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Residues in contact with LYS 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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421B VAL* 2.9 31.1 + - - +
422B ARG* 4.1 6.6 + - - +
423B GLN 3.0 22.4 + - - -
424B PRO* 4.4 5.9 + - - +
426B CYS* 3.0 19.8 + - - -
427B LEU* 5.5 0.4 - - - +
428B LEU 4.6 6.1 - - - +
449B LEU* 2.8 27.1 + - + +
450B GLU 3.6 5.5 - - - +
452B ASP* 1.3 77.4 - - - +
454B PRO* 1.3 65.3 - - - +
455B SER* 3.1 21.9 + - - +
456B LEU* 3.0 48.1 + - + +
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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