Contacts of the helix formed by residues 770 - 783 (chain A) 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 ASN 770 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A PRO* 5.6 4.4 - - - +
740A ASP* 4.1 17.1 + - - +
767A ILE* 6.1 0.2 - - + -
768A PRO* 2.7 37.2 + - - +
769A MET* 1.3 77.5 - - - +
771A THR* 1.3 59.0 + - - +
772A ILE* 3.2 10.8 - - + +
773A ALA* 3.0 5.1 + - - +
774A GLU* 2.7 41.5 + - - +
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Residues in contact with THR 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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770A ASN* 1.3 74.0 + - - +
772A ILE* 1.3 57.8 - - - +
774A GLU* 3.0 17.5 + - + +
775A ALA* 2.6 38.1 + - + +
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Residues in contact with ILE 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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711A ILE* 6.4 0.2 - - + -
734A PHE* 5.0 5.2 - - + -
738A LEU* 3.9 34.5 - - + -
739A PRO* 5.6 7.6 - - + -
767A ILE* 4.4 17.7 - - + -
770A ASN* 4.8 6.7 - - + -
771A THR* 1.3 83.0 - - - +
773A ALA* 1.3 69.7 + - - +
775A ALA* 2.8 20.9 + - - +
776A VAL* 3.0 16.3 + - + +
789A ILE* 4.0 28.2 - - + +
790A ASN* 5.8 4.3 - - - +
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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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711A ILE* 3.9 32.2 - - + +
767A ILE* 4.3 4.9 - - + -
768A PRO 3.6 10.1 + - - +
769A MET* 3.8 12.6 - - - -
770A ASN* 3.0 26.2 + - - +
772A ILE* 1.3 80.7 - - - +
774A GLU* 1.3 58.2 + - - +
776A VAL* 3.4 4.0 + - - +
777A ILE* 3.0 31.4 + - - +
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Residues in contact with GLU 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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769A MET* 3.9 34.3 - - + +
770A ASN 2.7 19.9 + - - +
771A THR* 3.4 22.8 + - + +
773A ALA* 1.3 70.3 - - - +
775A ALA* 1.3 59.9 + - - +
777A ILE* 3.2 9.4 - - + +
778A GLU* 2.9 31.6 + - - +
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Residues in contact with ALA 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 THR* 2.6 16.7 + - + +
772A ILE* 2.8 14.9 + - - +
774A GLU* 1.3 69.4 - - - +
776A VAL* 1.3 63.5 + - - +
778A GLU* 3.1 12.3 + - - +
779A MET* 3.0 21.0 + - - +
787A ILE* 4.2 15.6 - - + +
789A ILE* 4.6 7.6 - - + -
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Residues in contact with VAL 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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711A ILE* 4.0 22.0 - - + -
724A ILE* 5.4 1.1 - - + -
726A LEU* 4.8 5.4 - - + -
734A PHE* 5.7 3.6 - - + -
772A ILE* 3.0 12.2 + - + +
773A ALA* 3.6 7.4 - - - +
775A ALA* 1.3 76.8 - - - +
777A ILE* 1.3 65.2 + - + +
779A MET* 3.1 15.6 + - + +
780A ILE* 3.2 12.8 + - - +
787A ILE* 4.1 9.9 - - + -
789A ILE* 3.7 25.6 - - + -
794A ILE* 4.4 9.0 - - + -
819A VAL* 3.9 37.5 - - + -
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Residues in contact with ILE 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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711A ILE* 6.1 2.5 - - + -
713A PHE* 4.9 14.4 - - + -
724A ILE* 4.3 26.0 - - + -
769A MET* 4.5 15.9 - - + -
773A ALA 3.0 20.6 + - - +
774A GLU* 3.2 21.8 - - + +
776A VAL* 1.3 78.0 - - + +
778A GLU* 1.3 56.7 + - - +
780A ILE* 3.2 11.1 + - + +
781A ASN* 2.9 49.6 + - - +
823A SER* 6.0 2.0 - - - +
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Residues in contact with GLU 778 (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 GLU 2.9 18.6 + - - +
775A ALA* 3.6 8.1 - - - +
777A ILE* 1.3 73.1 - - - +
779A MET* 1.3 60.2 + - - +
781A ASN* 4.0 10.3 - - + +
782A ARG* 2.8 58.9 + - + +
784A GLN* 4.8 4.0 + - - +
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Residues in contact with MET 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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775A ALA 3.0 11.3 + - - +
776A VAL 3.3 11.2 - - - +
778A GLU* 1.3 74.3 - - - +
780A ILE* 1.3 82.6 + - + +
782A ARG* 3.4 0.3 + - - -
783A GLY 2.9 18.7 + - - -
784A GLN* 3.0 44.7 + - + +
786A GLN* 3.9 7.0 - - - -
787A ILE* 3.8 33.7 - - + -
794A ILE* 3.7 22.4 - - + +
795A SER 3.8 4.5 - - - -
796A ASN* 3.5 30.3 - - - +
819A VAL* 3.9 15.9 - - + -
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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
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776A VAL* 3.2 14.5 + - + +
777A ILE* 3.2 13.7 + - + +
779A MET* 1.3 100.0 - - + +
781A ASN* 1.3 65.5 + - - +
783A GLY* 3.2 12.8 + - - -
796A ASN* 4.0 9.6 + - - +
819A VAL* 4.0 20.0 - - + -
821A THR* 4.0 15.0 - - + -
823A SER* 4.0 17.5 - - - +
824A GLN* 3.6 44.7 - - + +
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Residues in contact with ASN 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A ILE* 2.9 42.1 + - - +
778A GLU* 3.6 11.3 - - + +
779A MET 3.2 0.2 - - - -
780A ILE* 1.3 80.3 - - - +
782A ARG* 1.3 65.6 + - + +
783A GLY* 3.1 5.0 + - - -
823A SER* 4.9 7.4 + - - -
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Residues in contact with ARG 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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778A GLU* 2.8 45.0 + - + +
781A ASN* 1.3 78.3 - - + +
783A GLY* 1.3 63.1 + - - +
784A GLN* 3.1 35.3 + - + +
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Residues in contact with GLY 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 MET 2.9 6.2 + - - -
780A ILE 3.2 8.9 + - - -
781A ASN 3.1 4.8 - - - -
782A ARG* 1.3 79.9 - - - +
784A GLN* 1.3 62.3 + - - +
785A ILE* 4.1 5.4 + - - +
796A ASN* 4.1 9.4 - - - -
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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