Contacts of the helix formed by residues 801 - 808 (chain A) in PDB entry 3BA6
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 801 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.6 21.2 - - - +
101A ASN* 4.7 2.7 - - - -
796A ASN 4.2 1.6 + - - -
797A LEU 4.6 5.7 + - - -
799A THR 3.4 4.2 - - - +
800A ASP* 1.3 79.0 - - - +
802A LEU* 1.3 58.1 + - - -
803A PRO* 3.2 4.4 - - - +
804A ALA* 2.8 26.9 + - - +
805A THR* 2.9 20.1 + - - -
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Residues in contact with LEU 802 (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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100A ALA* 3.9 35.9 - - + +
101A ASN* 4.2 13.0 - - - +
104A VAL* 4.6 15.0 - - + -
801A GLY* 1.3 67.5 - - - -
803A PRO* 1.3 72.7 - - + +
805A THR* 4.0 7.9 - - + +
806A ALA* 3.1 16.1 + - - +
936A SER* 3.0 26.9 + - - +
939A LEU* 3.8 27.6 - - + -
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Residues in contact with PRO 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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763A TYR* 4.3 9.0 - - + +
797A LEU 5.8 0.4 - - - +
798A VAL 3.9 11.4 - - - +
799A THR* 4.5 1.6 - - - +
801A GLY* 3.3 11.7 - - - +
802A LEU* 1.3 93.9 - - + +
804A ALA* 1.3 56.9 + - - +
806A ALA* 3.4 2.8 - - - +
807A LEU* 3.0 19.8 - - - +
909A MET* 3.9 25.8 - - + -
912A ALA* 5.2 2.0 - - + -
933A LEU* 3.1 19.8 - - + +
936A SER* 3.7 18.8 - - - +
937A ILE* 5.0 3.8 - - + -
940A SER* 3.7 23.3 - - - +
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Residues in contact with ALA 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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760A PHE* 3.5 28.5 - - + -
763A TYR* 3.9 8.9 - - + -
764A LEU* 3.8 24.2 - - + -
800A ASP 4.5 7.6 - - - +
801A GLY 2.8 10.7 + - - +
803A PRO* 1.3 76.7 - - - +
805A THR* 1.3 63.3 + - - +
806A ALA 2.8 6.3 + - - -
807A LEU* 2.8 30.5 + - - +
808A GLY 4.0 0.2 + - - -
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Residues in contact with THR 805 (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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101A ASN* 2.6 34.8 + - - +
104A VAL* 4.3 27.6 - - + -
310A GLY* 5.0 2.8 + - - -
313A ALA* 5.9 2.5 - - + -
314A VAL* 4.2 19.1 - - + +
317A THR* 5.3 4.8 - - + +
760A PHE* 4.0 9.5 - - - -
801A GLY 2.9 13.1 + - - -
802A LEU* 4.3 9.2 - - - -
804A ALA* 1.3 75.9 - - - +
806A ALA* 1.3 60.0 + - - +
808A GLY* 3.2 14.7 + - - -
809A PHE* 3.9 10.7 - - + -
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Residues in contact with ALA 806 (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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802A LEU 3.1 21.3 + - - +
803A PRO 3.4 7.9 - - - +
804A ALA 2.8 0.8 + - - -
805A THR* 1.3 75.2 - - - +
807A LEU* 1.3 56.1 + - - +
808A GLY 2.9 2.2 - - - -
809A PHE* 2.6 35.2 + - - +
930A ASN* 3.2 14.0 + - - -
932A TRP* 3.9 11.4 - - + +
933A LEU* 3.8 27.8 - - + +
936A SER* 3.9 1.3 - - - +
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Residues in contact with LEU 807 (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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756A ASN* 3.7 7.4 - - - +
759A GLN 4.8 0.2 - - - +
760A PHE* 4.5 22.9 - - + +
763A TYR* 4.7 13.0 - - + -
803A PRO 3.0 28.7 - - - +
804A ALA* 2.8 20.9 + - + +
806A ALA* 1.3 77.6 - - - +
808A GLY* 1.3 55.6 + - - +
810A ASN* 2.7 51.8 + - - +
912A ALA* 4.2 10.1 - - + +
915A SER* 2.8 45.8 - - - +
933A LEU* 4.2 13.9 - - + -
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Residues in contact with GLY 808 (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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314A VAL* 4.3 9.4 - - - +
317A THR* 6.1 0.2 - - - -
318A CYS* 3.7 27.6 - - - -
321A LEU* 4.2 11.1 - - - +
325A ARG* 5.4 0.3 + - - -
756A ASN* 3.2 21.7 + - - -
760A PHE* 5.6 0.4 - - - +
804A ALA 4.0 0.6 + - - -
805A THR 3.2 14.3 + - - -
806A ALA 2.9 1.6 - - - -
807A LEU* 1.3 77.4 - - - +
809A PHE* 1.3 64.4 + - - +
810A ASN 3.3 0.4 - - - +
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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