Contacts of the helix formed by residues 778 - 793 (chain A) in PDB entry 3OSE
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 THR 778 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A ASP* 4.4 17.1 + - + +
752A LEU 4.7 0.6 + - - -
774A ARG* 3.8 0.4 - - - +
777A GLY* 1.3 76.0 - - - -
779A SER* 1.3 64.7 + - - +
780A ILE* 3.6 12.8 - - - +
781A ALA* 3.1 29.3 + - - +
782A PHE* 3.0 23.2 + - - +
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Residues in contact with SER 779 (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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774A ARG* 3.4 31.5 + - - +
778A THR* 1.3 72.5 - - - +
780A ILE* 1.3 57.5 + - - +
782A PHE* 3.8 4.4 - - - +
783A LYS* 2.9 31.2 + - - +
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Residues in contact with ILE 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A THR* 3.6 13.0 - - - +
779A SER* 1.3 76.7 - - - +
781A ALA* 1.3 64.6 + - + +
783A LYS* 3.3 16.8 + - + +
784A ASN* 2.9 53.2 + - - +
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Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ASP 4.7 8.3 - - - +
751A SER* 4.5 8.7 - - - +
752A LEU 5.4 0.2 - - - +
753A VAL* 3.3 23.5 - - + +
778A THR* 3.1 25.3 + - - +
780A ILE* 1.3 79.5 - - + +
782A PHE* 1.3 62.1 + - - +
784A ASN* 3.8 6.1 - - - +
785A ILE* 3.1 26.9 + - - +
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Residues in contact with PHE 782 (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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753A VAL* 3.8 25.9 - - + +
755A TRP* 3.6 29.2 - + + -
772A PHE* 4.7 11.4 - - + -
773A LYS* 4.4 2.5 - - - -
774A ARG* 3.7 49.1 - - + -
778A THR 3.0 17.2 + - - +
779A SER* 3.8 4.0 - - - +
781A ALA* 1.3 74.5 - - - +
783A LYS* 1.3 71.2 + - + +
785A ILE* 4.3 0.2 - - - -
786A ALA* 2.9 53.5 + - + +
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Residues in contact with LYS 783 (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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779A SER 2.9 18.6 + - - +
780A ILE* 3.3 19.9 + - + +
782A PHE* 1.3 82.6 - - + +
784A ASN* 1.3 69.0 + - - +
786A ALA* 5.1 0.7 - - - -
787A SER* 2.7 41.2 + - - +
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Residues in contact with ASN 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A ILE* 2.9 45.3 + - - +
781A ALA* 3.8 5.9 - - - +
783A LYS* 1.3 88.5 - - - +
785A ILE* 1.3 61.3 + - - +
787A SER* 4.0 2.7 - - - -
788A LYS* 3.2 23.2 + - - +
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Residues in contact with ILE 785 (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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728A ASN* 4.5 14.4 - - + +
730A CYS* 4.0 8.7 - - - -
744A HIS* 3.8 45.1 - - + +
753A VAL* 4.1 16.2 - - + -
755A TRP* 3.9 33.0 - - + -
781A ALA 3.1 20.0 + - - +
782A PHE 3.9 3.6 - - - +
784A ASN* 1.3 77.1 - - - +
786A ALA* 1.3 69.9 + - + +
788A LYS* 3.2 12.5 + - + +
789A ILE* 3.0 27.9 + - + +
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Residues in contact with ALA 786 (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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755A TRP* 4.9 4.5 - - - +
772A PHE* 3.8 22.2 - - + -
782A PHE* 2.9 48.1 + - + +
783A LYS* 4.5 1.1 - - - +
785A ILE* 1.3 80.2 - - + +
787A SER* 1.3 58.3 + - - +
789A ILE* 3.4 5.7 + - - +
790A ALA* 2.9 30.4 + - - +
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Residues in contact with SER 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LYS* 2.7 37.4 + - - +
784A ASN* 4.0 3.1 - - - -
786A ALA* 1.3 78.2 - - - +
788A LYS* 1.3 55.9 + - - +
790A ALA* 3.4 5.2 + - - +
791A ASN* 2.9 45.3 + - - +
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Residues in contact with LYS 788 (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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728A ASN* 2.8 28.0 + - - +
784A ASN 3.2 18.2 + - - +
785A ILE* 3.2 15.7 + - + +
787A SER* 1.3 77.0 - - - +
789A ILE* 1.3 62.9 + - - +
791A ASN* 3.4 7.0 + - - +
792A GLU* 2.6 59.6 + - - +
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Residues in contact with ILE 789 (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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724A VAL* 3.9 16.5 - - + +
725A LEU* 3.9 26.2 - - + -
728A ASN* 3.6 39.0 - - + +
730A CYS* 4.1 3.6 - - - -
755A TRP* 4.3 10.3 - - + -
757A MET* 4.0 31.4 - - + -
772A PHE* 4.3 4.9 - - + -
785A ILE* 3.0 23.9 + - + +
786A ALA 3.7 6.3 - - - +
788A LYS* 1.3 75.1 - - - +
790A ALA* 1.3 65.5 + - - +
792A GLU* 3.1 12.3 + - - +
793A LEU* 3.2 22.9 + - + +
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Residues in contact with ALA 790 (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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707A LYS* 4.7 8.7 - - + -
708A THR* 4.3 12.8 + - - +
772A PHE* 3.9 23.1 - - + -
786A ALA 2.9 18.0 + - - +
787A SER* 3.8 7.0 - - - +
789A ILE* 1.3 76.3 - - - +
791A ASN* 1.3 66.2 + - - +
792A GLU 3.3 0.7 + - - -
793A LEU* 3.5 20.1 + - - +
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Residues in contact with ASN 791 (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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787A SER* 2.9 29.9 + - - +
788A LYS* 3.7 7.2 - - - +
789A ILE 3.2 0.2 - - - -
790A ALA* 1.3 79.8 - - - +
792A GLU* 1.3 62.5 + - + +
793A LEU 3.8 3.5 + - - +
794A LYS* 5.5 2.1 - - - +
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Residues in contact with GLU 792 (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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724A VAL* 3.8 23.4 - - + +
727A ALA* 5.3 3.3 - - - +
728A ASN* 2.9 23.8 + - - -
788A LYS* 2.6 50.1 + - - +
789A ILE 3.1 2.4 + - - -
791A ASN* 1.3 81.3 - - + +
793A LEU* 1.3 63.0 + - - +
794A LYS* 3.3 17.7 + - - +
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Residues in contact with LEU 793 (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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708A THR* 4.1 23.1 - - + -
720A GLU* 4.0 6.5 - - + +
721A ILE* 3.8 35.7 - - + +
724A VAL* 3.9 20.0 - - + -
757A MET* 4.4 9.2 - - + -
770A VAL* 4.7 2.2 - - + -
772A PHE* 4.3 13.9 - - + -
789A ILE* 3.2 18.3 + - + +
790A ALA* 3.9 16.7 - - - +
791A ASN 3.5 4.7 - - - +
792A GLU* 1.3 76.4 - - - +
794A LYS* 1.3 65.3 + - - +
795A LEU* 3.7 20.6 + - + +
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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
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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