Contacts of the helix formed by residues 839 - 843 (chain D) in PDB entry 4AY6
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 GLN 839 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465D ILE* 5.9 2.1 - - - +
836D ASN* 5.3 0.2 - - - +
837D PHE 3.9 0.6 + - - -
838D ASN* 1.3 82.9 - - - +
840D LEU* 1.3 65.4 + - - +
841D TYR* 3.2 38.7 + - + -
842D LYS* 3.4 12.5 + - + +
843D ILE* 4.8 1.9 + - - +
868D PHE* 3.7 42.8 - - + +
914D THR* 5.8 0.2 - - - +
1200D 12V 3.2 28.6 + - - +
1394H TYR* 3.6 38.4 - - - +
1395H DNP 4.0 5.3 + - - -
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Residues in contact with LEU 840 (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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465D ILE 4.4 4.3 - - - +
467D CYS* 3.3 27.5 - - - -
838D ASN 4.5 6.5 - - - +
839D GLN* 1.3 67.4 - - - +
841D TYR* 1.3 66.3 + - - +
842D LYS 2.9 4.8 + - - -
843D ILE* 3.0 33.5 + - + +
865D LEU* 4.8 6.5 - - + -
866D LEU 3.4 29.8 - - - +
867D ARG* 4.8 0.7 - - - -
868D PHE* 3.0 17.2 + - + +
869D PRO* 3.5 25.4 - - + +
872D GLY* 3.8 23.8 - - - -
873D GLU 4.4 1.1 - - - +
876D ILE* 5.0 6.1 - - + -
892D PHE* 4.7 13.0 - - + -
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Residues in contact with TYR 841 (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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461D HIS* 5.2 5.6 - - - +
464D GLN* 2.9 51.6 + - + +
465D ILE* 3.7 27.1 + - + +
498D HIS* 5.0 7.3 + + - -
499D HIS* 6.4 0.9 - + - -
501D MET* 5.8 2.5 - - - -
502D LEU* 3.9 34.0 - - + +
839D GLN* 3.2 48.7 + - + -
840D LEU* 1.3 76.9 - - - +
842D LYS* 1.3 79.7 - - + +
843D ILE 3.3 0.3 + - - -
916D LEU* 4.4 2.9 - - - +
917D CYS* 5.2 2.7 - - - -
1200D 12V 3.7 28.1 + - + +
1395H DNP 5.2 2.6 + - - -
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Residues in contact with LYS 842 (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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502D LEU* 5.1 0.2 - - - -
838D ASN* 2.9 37.3 + - + +
839D GLN 3.8 10.3 - - - +
840D LEU 2.9 1.2 + - - -
841D TYR* 1.3 109.7 - - + +
843D ILE* 1.3 57.7 + - - +
844D ASP 3.9 0.2 + - - -
847D THR* 4.7 1.0 + - - -
914D THR* 3.7 24.0 - - + +
916D LEU* 3.7 27.4 - - - +
917D CYS* 3.4 25.8 - - + +
918D ASN 3.2 15.4 + - - -
1200D 12V 2.5 47.0 + - - +
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Residues in contact with ILE 843 (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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464D GLN* 3.5 17.7 + - - -
467D CYS* 4.4 1.6 - - - -
469D TRP* 3.2 33.9 + - + -
836D ASN* 5.0 4.5 - - - +
838D ASN 5.9 0.4 - - - +
839D GLN 5.2 1.3 - - - +
840D LEU* 3.0 40.3 + - + +
841D TYR 3.6 1.1 - - - +
842D LYS* 1.3 79.2 - - + +
844D ASP* 1.3 70.0 + - - +
847D THR* 4.2 10.3 - - + -
848D LEU* 4.2 9.2 - - + +
851D TRP* 3.8 23.1 - - + -
865D LEU* 4.7 10.5 - - + -
876D ILE* 4.7 11.0 - - + -
914D THR* 3.6 20.9 - - + -
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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