Contacts of the helix formed by residues 3838 - 3850 (chain F) in PDB entry 6X34
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 ASP3838 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3836F VAL* 3.5 6.8 + - + +
3837F LEU* 1.3 77.3 - - - +
3839F LEU* 1.3 61.4 - - - +
3840F ASN* 3.3 21.1 - - - +
3841F ALA* 4.3 11.5 - - + +
3842F PHE* 3.3 22.7 + - - +
3869F VAL* 5.1 9.4 + - - +
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Residues in contact with LEU3839 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838F ASP* 1.3 71.8 - - - +
3840F ASN* 1.3 66.0 + - - +
3842F PHE* 3.5 8.0 + - - +
3843F GLU* 3.4 20.6 + - - +
3927F ASP* 4.7 27.6 - - + +
3928F PHE* 6.0 0.9 - - - -
3931F TYR* 5.4 16.7 - - + -
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Residues in contact with ASN3840 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838F ASP* 3.3 19.1 - - - +
3839F LEU* 1.3 76.5 - - - +
3841F ALA* 1.3 78.6 + - - +
3843F GLU* 3.5 13.6 + - - +
3844F ARG* 3.7 21.5 + - - +
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Residues in contact with ALA3841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838F ASP* 3.9 12.5 + - + +
3839F LEU 3.4 0.4 - - - -
3840F ASN* 1.3 85.9 + - - +
3842F PHE* 1.3 64.2 + - - +
3844F ARG* 3.4 20.0 + - - +
3845F GLN* 3.5 12.1 + - - +
3868F LYS* 4.8 25.2 - - + +
3869F VAL* 5.7 5.7 - - + +
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Residues in contact with PHE3842 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838F ASP 3.3 18.2 + - - +
3839F LEU* 3.8 8.7 - - - +
3840F ASN 3.3 0.6 - - - -
3841F ALA* 1.3 80.2 - - - +
3843F GLU* 1.3 63.9 + - - +
3845F GLN* 3.4 14.7 + - + +
3846F ASN* 3.3 42.2 + - - -
3869F VAL* 4.0 24.4 - - + +
3928F PHE* 4.7 14.8 - + - -
3931F TYR* 5.1 13.7 - + - -
3932F TYR* 3.7 20.0 - + - -
3941F GLN* 4.4 1.3 - - + -
3942F GLY* 3.8 26.9 - - - -
3945F ASN* 3.2 30.1 - - + -
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Residues in contact with GLU3843 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2349F GLU* 5.5 10.9 - - + +
3839F LEU 3.4 10.6 + - - +
3840F ASN* 3.8 9.6 - - - +
3841F ALA 3.3 0.4 - - - -
3842F PHE* 1.3 83.5 - - - +
3844F ARG* 1.3 61.6 + - + +
3846F ASN* 3.7 4.5 + - - +
3847F LYS* 3.2 24.1 + - - +
3931F TYR* 5.1 12.8 - - + +
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Residues in contact with ARG3844 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2288F ALA 4.8 3.0 + - - -
2289F LEU* 3.0 41.4 + - + +
2290F ALA* 5.2 4.0 - - - +
2291F LEU 4.5 12.5 + - - -
2347F VAL* 5.3 1.6 - - - +
2349F GLU* 3.6 53.3 + - + +
2350F ASN* 4.6 7.1 - - - +
2353F VAL* 4.6 14.8 - - - +
3840F ASN* 3.7 18.3 + - - +
3841F ALA* 3.4 11.4 + - - +
3842F PHE 3.3 0.6 - - - -
3843F GLU* 1.3 75.1 - - - +
3845F GLN* 1.3 63.6 + - - +
3847F LYS* 3.9 6.2 - - - +
3848F ALA* 3.3 24.3 + - - +
3868F LYS* 6.2 0.9 - - - +
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Residues in contact with GLN3845 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3841F ALA 3.5 9.1 + - - +
3842F PHE* 3.4 14.5 + - + +
3843F GLU 3.2 0.8 - - - -
3844F ARG* 1.3 77.6 - - - +
3846F ASN* 1.3 69.3 + - - +
3848F ALA* 3.5 2.8 + - - +
3849F GLU* 3.1 24.5 + - - +
3868F LYS* 5.8 8.7 - - + +
3869F VAL* 4.7 16.6 - - + -
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Residues in contact with ASN3846 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3842F PHE* 3.3 43.7 + - - -
3843F GLU* 3.7 5.7 + - - +
3845F GLN* 1.3 78.8 - - - +
3847F LYS* 1.3 63.4 + - - +
3849F GLU* 3.6 6.4 + - - +
3850F GLY* 3.3 18.5 + - - -
3932F TYR* 4.8 3.8 + - - -
3941F GLN* 3.9 25.1 - - - +
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Residues in contact with LYS3847 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2289F LEU* 6.1 2.2 - - + -
2349F GLU* 5.1 12.1 - - - +
3843F GLU 3.2 18.9 + - - +
3844F ARG* 4.1 7.0 - - - +
3845F GLN 3.2 0.2 - - - -
3846F ASN* 1.3 79.9 - - - +
3848F ALA* 1.3 60.7 + - - +
3850F GLY* 3.6 8.7 + - - -
3851F LEU* 4.4 10.0 + - - +
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Residues in contact with ALA3848 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2285F ASN* 5.6 6.7 - - - +
2286F GLU* 5.5 8.7 - - - +
2289F LEU* 4.4 18.1 - - + +
3844F ARG 3.3 16.6 + - - +
3845F GLN* 4.1 3.8 - - - +
3847F LYS* 1.3 78.6 - - - +
3849F GLU* 1.3 61.6 + - - +
3850F GLY 3.4 0.7 + - - -
3851F LEU* 3.6 18.4 + - - +
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Residues in contact with GLU3849 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3845F GLN 3.1 18.0 + - - +
3846F ASN* 3.6 7.6 + - - +
3847F LYS 3.4 0.2 - - - -
3848F ALA* 1.3 75.3 - - - +
3850F GLY* 1.3 62.7 + - - +
3851F LEU 3.2 9.6 + - - +
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Residues in contact with GLY3850 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3846F ASN 3.3 14.6 + - - -
3847F LYS 3.6 4.6 + - - -
3848F ALA 3.2 1.6 - - - -
3849F GLU* 1.3 77.0 - - - +
3851F LEU* 1.3 64.4 + - - +
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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