Contacts of the helix formed by residues 800 - 804 (chain A) in PDB entry 2Y48
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 GLY 800 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A SER* 3.4 7.6 + - - -
624A THR* 5.0 1.1 - - - -
799A ALA* 1.3 75.1 - - - +
801A GLU* 1.3 57.1 + - - -
802A HIS* 3.1 10.1 - - - -
803A THR* 2.4 38.0 + - - -
804A ILE 3.7 2.4 + - - -
817A SER* 2.7 22.0 + - - -
900A FAD 3.3 14.6 - - - -
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Residues in contact with GLU 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 2.9 30.3 + - - -
627A LEU 5.4 0.2 + - - -
656A PHE* 4.1 4.7 - - - -
761A TYR* 4.2 0.4 - - - -
762A SER* 2.3 48.7 + - - -
800A GLY* 1.3 69.4 - - - +
802A HIS* 1.3 64.0 + - - +
803A THR 3.1 4.3 + - - -
804A ILE* 3.7 10.8 + - - +
808A PRO* 3.6 19.6 - - - +
809A ALA* 3.0 29.6 + - - +
810A THR 3.8 5.4 - - - +
813A GLY 4.9 0.2 - - - -
814A ALA* 4.0 11.6 - - + +
900A FAD 3.1 34.8 + - - +
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Residues in contact with HIS 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 5.3 1.0 + - - -
623A CYS* 5.6 0.6 + - - -
624A THR 4.8 0.7 - - - -
625A LEU 3.1 29.3 + - - -
626A PRO* 4.6 1.0 - - + +
627A LEU* 3.8 34.6 + - + -
630A LEU* 3.6 12.8 - - + +
654A MET* 3.7 10.7 - - + +
762A SER* 4.2 4.5 - - - +
773A TYR* 3.4 18.3 - - - -
776A MET* 3.6 42.4 - - + +
798A PHE* 5.6 3.8 - - - -
799A ALA 3.6 21.5 + - - -
800A GLY* 3.9 7.0 - - - -
801A GLU* 1.3 91.0 + - - +
803A THR* 1.3 63.9 + - + +
804A ILE 3.7 0.2 - - - -
900A FAD 5.2 1.5 + - - -
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Residues in contact with THR 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A TYR 3.2 19.1 - - - +
774A ASP* 5.0 2.1 - - - +
776A MET* 3.8 25.8 - - + +
777A ALA* 3.5 10.7 - - - +
798A PHE* 4.2 4.9 - - + +
799A ALA* 3.9 17.5 - - - +
800A GLY 2.4 37.1 + - - +
802A HIS* 1.3 89.1 - - - +
804A ILE* 1.3 58.9 + - - +
805A ARG 3.6 3.0 + - - -
817A SER* 3.4 3.3 - - - -
820A ARG* 3.3 28.9 + - - -
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Residues in contact with ILE 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A TYR* 4.4 3.1 - - - -
800A GLY 4.3 4.3 - - - +
801A GLU* 3.7 10.7 + - - +
802A HIS 3.7 0.2 - - - -
803A THR* 1.3 77.8 + - - +
805A ARG* 1.3 53.9 + - - +
806A ASN* 4.4 2.7 - - + +
807A TYR* 2.8 63.7 + - + +
808A PRO* 3.1 11.0 - - - +
813A GLY 3.2 27.1 - - - +
816A LEU* 3.5 33.0 - - + -
817A SER* 3.9 15.0 - - - +
820A ARG* 4.3 7.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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