Contacts of the helix formed by residues 767 - 777 (chain A) in PDB entry 2N8Z
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 767 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766A LEU* 1.3 79.5 - - - +
768A PRO* 1.3 74.9 - - - +
769A GLU 3.3 2.7 - - - -
770A GLU* 3.8 15.8 - - - +
771A PHE* 3.1 23.2 + - - +
805A GLY 4.1 6.5 - - - -
806A VAL* 4.9 2.2 - - - -
807A VAL* 4.7 1.6 - - - -
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Residues in contact with PRO 768 (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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767A GLY* 1.3 82.4 - - - +
769A GLU* 1.3 61.4 + - + +
771A PHE* 4.6 1.3 - - + +
772A LYS* 3.2 23.7 + - - +
792A PHE* 3.4 31.7 - - + -
796A MET* 5.2 8.1 - - + -
805A GLY* 3.4 23.6 - - - +
807A VAL* 4.5 14.3 - - + -
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Residues in contact with GLU 769 (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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767A GLY 3.3 0.2 - - - -
768A PRO* 1.3 81.9 - - + +
770A GLU* 1.3 78.4 + - + +
772A LYS* 3.2 24.1 + - - +
773A ALA* 3.0 25.2 + - + +
784A ASN* 5.0 8.6 + - - +
792A PHE* 5.6 0.2 - - - -
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Residues in contact with GLU 770 (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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758A PHE* 3.7 16.8 - - + -
766A LEU* 3.9 22.0 - - + -
767A GLY* 3.3 25.1 + - - +
769A GLU* 1.3 88.3 - - - +
771A PHE* 1.3 59.0 + - - +
773A ALA* 3.2 5.8 + - - -
774A CYS* 2.9 27.0 + - - +
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Residues in contact with PHE 771 (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 PHE* 4.0 25.1 - + + -
764A GLY 5.4 0.2 - - - -
766A LEU* 3.4 40.2 - - + -
767A GLY 3.1 12.6 + - - +
768A PRO 4.6 1.8 - - - +
770A GLU* 1.3 79.4 - - - +
772A LYS* 1.3 61.6 + - - +
774A CYS* 3.3 22.2 + - + +
775A LEU* 3.3 17.2 + - + +
807A VAL* 3.3 34.5 - - + -
808A THR 3.2 23.6 - - - -
809A PHE* 3.7 23.1 - - - -
812A PHE* 3.4 27.8 - + + -
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Residues in contact with LYS 772 (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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768A PRO 3.2 14.2 + - - +
769A GLU* 3.2 32.1 + - - +
770A GLU 3.2 1.0 - - - -
771A PHE* 1.3 76.6 - - - +
773A ALA* 1.3 63.4 + - + +
775A LEU* 3.2 28.3 + - + +
776A ILE 3.7 1.4 + - - -
782A ILE* 3.2 40.1 - - + +
783A GLY* 4.7 7.6 - - - -
784A ASN* 5.3 4.7 - - - +
788A GLY 5.4 0.7 - - - +
789A GLU* 2.8 31.0 + - + +
792A PHE* 3.6 40.5 - - + -
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Residues in contact with ALA 773 (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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758A PHE* 3.7 20.3 - - + -
769A GLU* 3.0 16.6 + - + +
770A GLU* 3.7 4.9 - - - +
772A LYS* 1.3 75.7 - - + +
774A CYS* 1.3 65.1 + - - +
776A ILE* 3.1 35.9 + - + +
777A SER 3.6 3.5 + - - -
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Residues in contact with CYS 774 (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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754A SER* 3.6 42.7 - - - -
755A PHE* 3.7 10.1 - - - -
758A PHE* 3.7 19.5 - - + -
770A GLU 2.9 14.4 + - - +
771A PHE* 3.3 25.1 - - + +
772A LYS 3.2 0.2 - - - -
773A ALA* 1.3 78.8 - - - +
775A LEU* 1.3 61.3 + - - +
777A SER* 3.4 15.9 + - - -
778A LEU* 4.0 8.4 - - - +
812A PHE* 6.1 4.0 - - - -
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Residues in contact with LEU 775 (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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771A PHE* 3.4 13.7 - - + +
772A LYS* 3.4 21.1 - - - +
773A ALA 3.2 0.4 - - - -
774A CYS* 1.3 75.3 - - - +
776A ILE* 1.3 60.5 + - + +
778A LEU* 2.8 31.1 + - + +
779A GLY 3.3 0.5 + - - -
780A TYR* 3.1 44.5 - - + -
782A ILE* 4.0 31.2 - - + -
792A PHE* 6.4 0.7 - - + -
795A ILE* 4.5 13.0 - - + -
812A PHE* 5.0 11.7 - - + -
815A PHE* 4.1 23.8 - - + -
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Residues in contact with ILE 776 (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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772A LYS 3.8 2.2 - - - +
773A ALA* 3.1 27.3 + - + +
775A LEU* 1.3 76.6 - - + +
777A SER* 1.3 57.3 + - - +
779A GLY* 3.0 19.4 + - - -
780A TYR 3.5 22.4 - - - +
782A ILE 3.5 27.1 - - - +
783A GLY* 3.7 17.0 - - - +
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Residues in contact with SER 777 (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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750A GLU* 5.7 0.2 - - - +
754A SER* 4.6 11.8 - - - -
757A HIS* 6.0 0.5 - - - -
758A PHE* 4.3 19.3 - - - -
773A ALA 3.6 2.2 + - - -
774A CYS 3.4 15.2 + - - -
775A LEU 3.1 0.4 - - - -
776A ILE* 1.3 78.6 - - - +
778A LEU* 1.3 60.0 + - - +
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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