Contacts of the helix formed by residues 439 - 445 (chain I) in PDB entry 5FUR
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 439 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437I HIS* 2.5 22.7 + - + +
438I PRO* 1.3 78.3 - - + +
440I THR* 1.3 67.4 + - + +
442I SER* 2.8 15.2 + - - -
443I TRP* 2.8 24.9 + - + +
965I TRP* 3.3 44.4 - + + +
968I ARG* 3.2 57.9 + - + +
969I CYS* 3.1 20.4 - - - -
972I VAL* 3.9 15.3 - - + -
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Residues in contact with THR 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I HIS 5.3 0.9 - - - +
433I PHE* 3.2 48.5 - - + +
434I SER* 4.8 1.3 - - - -
435I ILE* 3.6 7.6 - - - +
436I LYS* 3.0 26.3 + - + +
437I HIS 2.9 17.4 + - - +
439I HIS* 1.3 95.7 - - + +
441I LEU* 1.3 58.5 + - - +
443I TRP* 3.9 9.5 + - - +
444I GLU* 3.5 23.6 + - - +
969I CYS* 4.9 0.2 - - - -
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Residues in contact with LEU 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I TYR* 3.1 27.4 - - - +
183I GLN* 4.4 15.3 - - + +
196I TYR* 6.1 4.0 - - + -
364I TRP* 3.5 48.0 - - + +
367I GLU* 4.9 2.7 - - + -
435I ILE* 3.3 26.2 - - + -
436I LYS 5.2 4.5 - - - +
437I HIS 5.0 0.2 - - - -
438I PRO 3.4 21.7 + - - +
439I HIS 3.2 0.4 - - - -
440I THR* 1.3 73.6 + - - +
442I SER* 1.3 65.7 + - - +
443I TRP 2.9 3.1 + - - -
444I GLU* 2.9 27.6 + - - +
445I TYR* 5.1 4.4 - - - -
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Residues in contact with SER 442 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I TYR* 4.5 8.9 + - - -
315I GLU 5.0 0.3 + - - -
316I VAL* 3.6 15.0 - - - +
438I PRO 3.2 3.5 + - - -
439I HIS 2.8 2.5 + - - -
441I LEU* 1.3 79.6 - - - +
443I TRP* 1.3 61.0 + - - +
444I GLU 3.4 0.9 + - - -
445I TYR* 3.6 23.2 + - - -
965I TRP* 3.0 51.5 + - - +
966I ARG* 3.6 20.5 + - - +
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Residues in contact with TRP 443 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433I PHE* 5.2 7.9 - + + -
439I HIS* 2.8 24.0 + - - +
440I THR* 3.9 5.4 + - - +
441I LEU 2.9 0.6 + - - -
442I SER* 1.3 74.8 - - - +
444I GLU* 1.3 57.6 + - - +
445I TYR 3.1 5.4 - - - -
446I TYR* 3.3 36.3 + + + +
449I PHE* 3.6 7.9 - - + -
924I HIS* 3.7 14.6 - + - -
928I ASN* 4.7 11.9 - - - -
965I TRP 2.6 18.8 + - - -
966I ARG* 2.8 64.7 - - + +
969I CYS* 2.6 55.2 - - + +
970I GLY* 3.5 9.2 - - - -
973I ASP* 5.3 6.7 - - - -
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Residues in contact with GLU 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367I GLU* 4.5 19.5 - - + +
371I LYS* 5.0 3.8 - - - +
417I ILE 4.2 6.1 - - - +
435I ILE* 3.1 40.1 - - - +
440I THR 3.5 18.0 - - - +
441I LEU* 2.9 19.1 + - - +
443I TRP* 1.3 78.6 - - - +
445I TYR* 1.3 66.9 + - - -
446I TYR 3.4 2.9 - - - -
449I PHE* 3.2 56.4 - - + +
450I GLN 4.6 0.2 + - - -
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Residues in contact with TYR 445 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I TYR* 6.1 4.9 - + - -
315I GLU 5.6 5.2 - - - -
316I VAL* 6.3 5.4 - - + -
352I GLN* 4.6 10.7 + - - -
370I LEU* 3.9 24.5 - - + +
371I LYS* 3.6 46.4 - - + +
441I LEU 5.2 4.7 - - - -
442I SER* 3.6 19.8 + - - +
443I TRP 3.1 3.0 - - - -
444I GLU* 1.3 84.8 - - - +
446I TYR* 1.3 64.3 + - - +
447I SER* 3.9 1.2 + - - -
449I PHE* 4.8 0.2 - - - -
450I GLN* 4.9 10.4 - - - +
966I ARG* 5.0 10.8 + - - +
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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