Contacts of the helix formed by residues 3838 - 3850 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3836D VAL* 3.5 7.3 + - + +
3837D LEU* 1.3 76.8 - - - +
3839D LEU* 1.3 62.9 + - - +
3840D ASN* 3.3 20.9 - - - +
3841D ALA* 4.3 11.1 - - + +
3842D PHE* 3.3 22.0 + - - +
3869D VAL* 5.1 10.0 + - - +
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Residues in contact with LEU3839 (chain D).
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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3838D ASP* 1.3 71.6 - - - +
3840D ASN* 1.3 65.0 + - - +
3842D PHE* 3.5 7.5 + - - +
3843D GLU* 3.4 20.8 + - - +
3927D ASP* 4.7 28.1 - - + +
3928D PHE* 6.0 1.1 - - - -
3931D TYR* 5.4 16.4 - - + -
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Residues in contact with ASN3840 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838D ASP* 3.3 19.7 - - - +
3839D LEU* 1.3 75.1 - - - +
3841D ALA* 1.3 78.6 + - - +
3843D GLU* 3.5 12.6 + - - +
3844D ARG* 3.7 21.6 + - - +
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Residues in contact with ALA3841 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838D ASP* 3.9 12.5 + - + +
3840D ASN* 1.3 85.7 + - - +
3842D PHE* 1.3 64.3 + - - +
3844D ARG* 3.4 20.7 + - - +
3845D GLN* 3.5 11.6 + - - +
3868D LYS* 4.8 24.5 - - + +
3869D VAL* 5.7 5.6 - - - +
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Residues in contact with PHE3842 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3838D ASP 3.3 18.6 + - - +
3839D LEU* 3.8 8.7 - - - +
3840D ASN 3.3 0.6 - - - -
3841D ALA* 1.3 79.7 - - - +
3843D GLU* 1.3 63.9 + - - +
3845D GLN* 3.3 14.4 + - + +
3846D ASN* 3.3 41.5 + - - -
3869D VAL* 4.0 23.9 - - + +
3928D PHE* 4.7 14.6 - + - -
3931D TYR* 5.1 13.7 - + - -
3932D TYR* 3.7 19.5 - + - -
3939D GLU* 5.9 0.2 - - + -
3941D GLN* 4.4 2.0 - - + -
3942D GLY* 3.8 27.4 - - - -
3945D ASN* 3.2 29.4 - - + -
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Residues in contact with GLU3843 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2349D GLU* 5.5 10.4 - - + +
3839D LEU 3.4 11.0 + - - +
3840D ASN* 3.8 10.1 - - - +
3841D ALA 3.3 0.6 - - - -
3842D PHE* 1.3 83.6 - - - +
3844D ARG* 1.3 60.8 + - + +
3846D ASN* 3.7 4.3 + - - +
3847D LYS* 3.2 24.4 + - - +
3931D TYR* 5.1 13.0 - - + +
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Residues in contact with ARG3844 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2288D ALA 4.8 2.4 + - - -
2289D LEU* 3.0 41.6 + - + +
2290D ALA* 5.2 3.4 - - - +
2291D LEU 4.5 13.0 + - - -
2347D VAL* 5.3 1.6 - - - +
2349D GLU* 3.6 52.7 + - + +
2350D ASN* 4.6 6.9 - - - +
2353D VAL* 4.6 14.8 - - - +
3840D ASN* 3.7 18.2 + - - +
3841D ALA* 3.4 12.5 + - - +
3842D PHE 3.3 0.4 - - - -
3843D GLU* 1.3 75.7 - - + +
3845D GLN* 1.3 64.5 + - - +
3847D LYS* 3.9 6.6 - - - +
3848D ALA* 3.3 24.4 + - - +
3868D LYS* 6.2 1.1 - - - +
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Residues in contact with GLN3845 (chain D).
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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3841D ALA 3.5 8.6 + - - +
3842D PHE* 3.3 13.8 + - + +
3843D GLU 3.2 0.8 - - - -
3844D ARG* 1.3 76.8 - - - +
3846D ASN* 1.3 70.8 + - - +
3848D ALA* 4.0 2.8 - - - +
3849D GLU* 3.1 24.4 + - - +
3868D LYS* 5.8 8.7 - - + +
3869D VAL* 4.7 16.8 - - + -
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Residues in contact with ASN3846 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3842D PHE* 3.3 44.5 + - - -
3843D GLU* 3.7 5.5 + - - +
3845D GLN* 1.3 78.2 - - - +
3847D LYS* 1.3 64.0 + - - +
3849D GLU* 4.0 6.8 - - - +
3850D GLY* 3.3 18.5 + - - -
3932D TYR* 4.8 3.8 + - - -
3941D GLN* 3.9 26.0 - - - +
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Residues in contact with LYS3847 (chain D).
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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2289D LEU* 6.1 2.7 - - + -
2349D GLU* 5.1 12.3 - - - +
3843D GLU 3.2 19.1 + - - +
3844D ARG* 4.1 7.0 - - - +
3845D GLN 3.2 0.2 - - - -
3846D ASN* 1.3 78.9 - - - +
3848D ALA* 1.3 61.2 + - - +
3850D GLY* 3.6 10.0 + - - -
3851D LEU* 4.4 9.7 + - - +
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Residues in contact with ALA3848 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2285D ASN* 5.6 6.7 - - - +
2286D GLU* 5.5 8.7 - - + +
2289D LEU* 4.4 17.7 - - + +
3844D ARG 3.3 17.2 + - - +
3845D GLN* 4.1 3.1 - - - +
3847D LYS* 1.3 78.8 - - - +
3849D GLU* 1.3 63.4 + - - +
3850D GLY 3.4 0.7 + - - -
3851D LEU* 3.6 18.6 + - - +
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Residues in contact with GLU3849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3845D GLN 3.1 17.5 + - - +
3846D ASN* 4.1 7.0 - - - +
3847D LYS 3.4 0.4 - - - -
3848D ALA* 1.3 74.5 - - - +
3850D GLY* 1.3 62.0 + - - +
3851D LEU 3.2 9.5 + - - +
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Residues in contact with GLY3850 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3846D ASN 3.3 14.1 + - - -
3847D LYS 3.6 5.2 + - - -
3848D ALA 3.2 1.8 - - - -
3849D GLU* 1.3 77.5 - - - +
3851D 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