Contacts of the helix formed by residues 437 - 448 (chain B) in PDB entry 2O8C
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 HIS 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366B TYR* 4.1 24.9 - + - -
367B HIS* 3.6 40.1 + - + +
373B LEU* 6.0 0.2 - - + -
410B MET* 3.9 20.3 - - + -
413B TRP* 3.5 27.6 - + + -
414B TRP* 3.8 20.3 + + + -
436B TYR* 1.3 77.3 - - + +
438B MET* 1.3 70.3 + - + +
440B ALA 3.0 11.4 + - - -
441B LEU* 3.3 10.0 + - - +
456B TRP* 4.0 24.4 - + + +
457B ALA* 2.8 29.4 + - - +
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Residues in contact with MET 438 (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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367B HIS* 3.7 19.1 + - + -
373B LEU* 5.0 13.0 - - + -
413B TRP* 4.3 4.9 - - + -
414B TRP* 5.1 3.8 - - - -
417B LYS* 3.5 39.5 - - + +
421B PHE* 3.7 38.4 - - + +
436B TYR 3.9 4.7 - - - +
437B HIS* 1.3 82.4 - - + +
439B ASP* 1.3 75.6 + - - +
441B LEU* 3.3 22.2 + - + +
442B ILE* 3.5 14.0 + - + +
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Residues in contact with ASP 439 (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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413B TRP* 4.0 2.9 - - - -
417B LYS* 2.9 28.1 + - - -
424B VAL* 3.9 14.9 - - + +
425B ILE* 2.7 37.3 + - - +
435B LEU* 3.7 22.6 - - + +
436B TYR 2.9 15.4 + - - +
438B MET* 1.3 81.8 - - - +
440B ALA* 1.3 59.6 + - - +
442B ILE* 3.2 16.9 + - - +
443B GLY 2.9 22.7 + - - -
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.3 23.1 - - - +
436B TYR 3.7 2.0 + - - -
437B HIS 3.0 12.2 + - - +
439B ASP* 1.3 76.0 - - - +
441B LEU* 1.3 59.4 + - - +
443B GLY* 3.6 0.7 - - - +
444B VAL* 3.0 34.8 + - - +
451B PHE* 4.0 4.7 - - + -
457B ALA* 3.5 26.0 - - + +
458B HIS 3.8 1.1 - - - +
459B SER* 3.6 15.9 - - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 3.4 33.4 - - + +
367B HIS* 3.4 25.8 - - + +
368B GLU* 4.0 11.9 - - - +
437B HIS 3.6 9.6 - - - +
438B MET* 3.3 12.3 - - + +
439B ASP 3.2 0.2 - - - -
440B ALA* 1.3 79.8 - - - +
442B ILE* 1.3 58.1 + - + +
444B VAL* 4.1 1.4 - - - +
445B SER* 3.0 30.5 + - - -
451B PHE* 3.7 15.9 - - + -
457B ALA* 4.4 0.9 - - + -
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Residues in contact with ILE 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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424B VAL* 3.9 19.3 - - + -
438B MET* 3.5 15.0 + - + +
439B ASP* 3.2 14.8 + - - +
441B LEU* 1.3 77.5 - - + +
443B GLY* 1.3 57.1 + - - +
445B SER* 4.6 3.6 - - - -
446B GLU* 2.8 36.7 + - + +
473B LEU* 3.8 21.8 - - + -
478B TYR* 3.6 48.9 - - + +
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Residues in contact with GLY 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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435B LEU* 3.7 24.0 - - - +
439B ASP 2.9 10.7 + - - -
440B ALA* 3.3 5.1 + - - -
442B ILE* 1.3 77.4 - - - +
444B VAL* 1.3 57.6 + - - +
447B LEU* 3.3 25.0 + - - +
449B LEU* 3.3 28.4 + - - +
459B SER* 4.8 0.4 - - - -
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Residues in contact with VAL 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 ALA 3.0 16.3 + - - +
441B LEU 4.2 0.9 - - - +
443B GLY* 1.3 77.5 - - - +
445B SER* 1.3 65.5 + - - +
448B GLY* 3.4 17.8 + - - -
449B LEU 3.2 27.8 - - - +
450B VAL* 5.1 0.7 - - - -
451B PHE* 3.6 51.6 - - + +
459B SER* 4.1 6.7 - - - +
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Residues in contact with SER 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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441B LEU 3.0 19.4 + - - -
442B ILE* 4.1 3.4 - - - -
444B VAL* 1.3 79.3 - - - +
446B GLU* 1.3 69.1 + - - +
448B GLY 4.9 0.4 - - - -
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Residues in contact with GLU 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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2A ALA* 4.9 4.0 - - - -
3A VAL* 4.7 1.6 - - - +
83A MET* 5.9 0.3 - - - +
442B ILE* 2.8 23.4 + - + +
445B SER* 1.3 86.4 + - - +
447B LEU* 1.3 61.9 + - - +
448B GLY 3.7 0.7 - - - -
472B SER* 4.4 1.6 + - - -
473B LEU* 4.3 11.0 - - + -
476B LYS* 3.1 55.0 + - + +
478B TYR* 2.8 39.8 + - + +
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Residues in contact with LEU 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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3A VAL* 3.7 26.0 - - + +
83A MET* 3.6 17.4 - - - +
435B LEU* 4.6 4.7 - - + -
443B GLY* 3.3 25.7 + - - +
446B GLU* 1.3 85.4 - - + +
448B GLY* 1.3 62.1 + - - +
449B LEU* 3.5 9.6 + - + -
461B PHE* 4.7 1.6 - - + -
469B TYR* 3.6 55.6 - - + +
472B SER* 3.8 9.6 - - - +
473B LEU* 3.7 41.1 - - + -
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Residues in contact with GLY 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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83A MET* 3.8 22.7 - - - +
444B VAL 3.4 15.8 + - - -
445B SER 4.9 0.2 - - - -
446B GLU 3.7 1.2 - - - -
447B LEU* 1.3 79.4 - - - +
449B LEU* 1.3 65.2 + - - +
450B VAL* 3.9 4.9 + - - +
24F G 4.6 1.7 + - - -
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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