Contacts of the helix formed by residues 799 - 804 (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 ALA 799 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784D GLN 5.7 0.2 - - - -
785D ILE* 3.8 44.2 - - + -
796D ASN* 3.1 12.7 + - + +
798D LEU* 1.3 81.4 - - + +
800D THR* 1.3 53.0 + - - +
801D THR* 3.2 4.5 - - - -
802D GLN* 2.8 37.8 + - - +
803D ILE* 3.1 13.8 + - + +
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Residues in contact with THR 800 (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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795D SER* 5.5 0.2 - - - -
796D ASN 4.2 10.5 - - - +
797D GLY* 4.4 2.7 - - - -
798D LEU 3.6 2.5 - - - -
799D ALA* 1.3 75.5 + - - +
801D THR* 1.3 60.8 + - - +
803D ILE* 3.0 13.2 + - + -
804D ASN* 2.7 34.1 + - - +
807D ALA* 5.8 2.7 - - - -
808D ALA* 3.6 21.0 - - - +
818D ILE* 4.2 20.6 - - + -
897D PRO* 5.5 0.7 - - - +
899D GLU* 3.9 12.7 + - - +
900D GLU* 4.9 7.4 + - - +
903D ARG* 3.9 22.5 + - - +
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Residues in contact with THR 801 (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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798D LEU 5.6 0.5 + - - -
799D ALA* 3.2 1.6 + - - -
800D THR* 1.3 77.1 + - - +
802D GLN* 1.3 69.6 + - - +
805D ASN* 3.5 27.6 + - - +
808D ALA* 3.6 22.9 - - + -
809D THR* 6.3 1.1 - - + -
897D PRO* 3.7 24.7 - - + -
1390H VAL* 5.1 8.5 - - + -
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Residues in contact with GLN 802 (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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785D ILE* 3.6 32.4 - - + +
798D LEU 5.2 1.4 + - - -
799D ALA* 2.8 21.2 + - + +
801D THR* 1.3 85.2 - - - +
803D ILE* 1.3 68.0 - - + +
804D ASN* 3.4 0.7 + - - -
805D ASN* 5.1 1.6 + - - -
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Residues in contact with ILE 803 (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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573A PRO* 4.5 16.5 - - + +
785D ILE* 3.5 33.7 - - + +
786D GLN* 3.5 20.0 - - - +
795D SER* 3.7 32.1 - - - +
796D ASN 4.2 2.5 - - - +
799D ALA* 3.4 23.3 - - + +
800D THR* 3.0 9.6 + - + +
802D GLN* 1.3 80.1 - - - +
804D ASN* 1.3 62.5 + - + +
816D THR* 5.1 7.9 - - + -
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Residues in contact with ASN 804 (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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800D THR* 2.7 17.4 + - - +
803D ILE* 1.3 79.3 - - + +
805D ASN* 1.3 68.4 + - - +
806D LYS* 3.0 19.1 + - - +
807D ALA* 3.0 31.5 + - + +
808D ALA 3.3 8.1 + - - -
812D GLU* 3.1 19.9 + - - +
813D VAL 5.2 0.6 + - - -
815D ARG* 3.2 27.5 - - - +
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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