Contacts of the helix formed by residues 447 - 455 (chain A) in PDB entry 3U78
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 LEU 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LEU* 3.5 46.7 - - + +
444A LYS* 2.9 19.1 + - + +
446A GLU* 1.3 87.9 - - + +
448A VAL* 1.3 66.4 + - - +
449A SER* 3.0 5.7 + - - -
450A GLU* 3.3 19.4 - - + +
451A HIS* 3.2 31.8 - - + +
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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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442A TRP 3.7 15.7 - - - +
443A MET* 3.5 34.3 - - + +
444A LYS 2.8 13.5 + - - +
445A LYS* 3.5 19.7 - - - +
446A GLU 3.4 1.0 - - - -
447A LEU* 1.3 76.7 - - - +
449A SER* 1.3 66.6 + - - +
450A GLU 3.2 0.2 - - - -
451A HIS 3.9 0.4 - - - -
452A ALA* 3.1 35.6 + - + +
455A ILE* 5.4 0.7 - - + -
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Residues in contact with SER 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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445A LYS 4.7 1.7 + - - -
446A GLU 4.9 6.4 + - - -
447A LEU 3.0 2.9 + - - -
448A VAL* 1.3 82.7 - - - +
450A GLU* 1.3 64.1 + - - +
451A HIS 3.6 0.2 - - - -
452A ALA* 4.5 7.7 + - - +
453A PHE* 5.3 3.1 + - - -
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Residues in contact with GLU 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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386A LYS* 5.8 1.7 + - - -
400A GLU* 5.2 0.2 - - - +
447A LEU* 3.3 20.8 - - - +
449A SER* 1.3 82.8 + - - +
451A HIS* 1.3 82.3 + - + +
452A ALA 3.6 0.4 - - - -
453A PHE* 3.2 27.4 - - + -
454A GLU* 5.1 0.7 - - - +
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Residues in contact with HIS 451 (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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386A LYS* 6.0 6.1 - - + -
400A GLU* 3.0 38.9 + - - +
404A TRP* 5.4 1.1 + - + -
442A TRP* 3.3 57.0 - + + +
443A MET* 6.2 0.2 - - - -
447A LEU* 3.2 35.5 + - + +
448A VAL* 3.3 2.3 + - + +
450A GLU* 1.3 98.1 + - + +
452A ALA* 1.3 66.6 + - - +
453A PHE* 3.1 3.6 - - - -
454A GLU* 3.0 23.0 + - - +
455A ILE* 3.6 10.3 + - + +
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Residues in contact with ALA 452 (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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448A VAL* 3.1 24.3 + - + +
449A SER* 4.5 7.4 - - - +
450A GLU 3.6 0.4 - - - -
451A HIS* 1.3 77.9 - - - +
453A PHE* 1.3 61.5 + - - +
454A GLU 3.2 0.2 - - - -
455A ILE* 3.2 34.4 + - + +
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Residues in contact with PHE 453 (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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261A PHE* 3.4 19.6 - + - -
397A PRO 5.7 1.1 - - - -
398A PHE* 4.7 14.6 - + - -
449A SER 5.3 2.8 + - - -
450A GLU* 3.2 31.2 - - + -
451A HIS 3.1 1.4 + - - -
452A ALA* 1.3 80.6 - - - +
454A GLU* 1.3 86.4 + - + +
455A ILE 3.6 2.6 + - - +
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Residues in contact with GLU 454 (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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261A PHE* 3.4 13.0 - - - -
382A TYR* 4.3 4.7 + - - -
397A PRO 3.3 16.2 - - - +
398A PHE* 3.1 40.2 - - - +
399A PHE 4.5 0.2 + - - -
400A GLU* 3.6 48.9 + - + +
401A ALA* 3.5 12.6 + - - +
404A TRP* 4.5 2.5 - - - +
450A GLU 5.1 0.4 - - - +
451A HIS* 3.0 10.4 + - - +
453A PHE* 1.3 100.2 - - + +
455A ILE* 1.3 59.8 + - - +
456A PRO* 3.1 15.4 - - - +
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Residues in contact with ILE 455 (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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261A PHE* 4.3 1.4 - - - -
404A TRP* 3.9 20.0 - - + +
443A MET* 3.5 33.2 - - + -
448A VAL* 5.4 0.4 - - + -
451A HIS* 4.0 9.2 - - + +
452A ALA* 3.2 29.1 + - + +
453A PHE 4.4 3.1 - - - +
454A GLU* 1.3 74.8 - - - +
456A PRO* 1.3 78.6 - - + +
457A ASP* 4.5 1.2 - - - +
459A VAL* 4.2 5.4 - - + +
461A PRO* 3.5 33.4 - - + -
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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