Contacts of the helix formed by residues 770 - 783 (chain A) in PDB entry 3V53
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 ARG 770 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734A LYS* 3.7 13.7 - - - +
766A LEU* 3.2 7.5 + - - +
769A ARG* 1.3 83.1 - - + +
771A ILE* 1.3 64.5 + - + +
773A PRO* 3.7 4.3 - - - +
774A TRP* 3.0 68.6 + - - +
829A LEU* 3.5 23.2 - - + +
833A GLU* 3.6 40.3 + - + +
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Residues in contact with ILE 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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762A VAL* 4.3 14.6 - - + -
766A LEU* 3.1 34.5 + - + +
767A MET* 3.9 23.8 - - + +
770A ARG* 1.3 80.5 - - + +
772A ARG* 1.3 60.7 + - - +
774A TRP* 3.1 6.7 + - - +
775A ILE* 2.9 51.8 + - + +
798A VAL* 5.2 3.8 - - + -
826A MET* 5.5 5.2 - - + -
829A LEU* 4.6 14.1 - - + -
830A LEU* 3.8 31.0 - - + -
833A GLU* 5.4 8.7 - - + -
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Residues in contact with ARG 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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767A MET* 2.5 38.5 + - + +
768A GLU* 4.4 10.2 - - - +
771A ILE* 1.3 73.1 - - - +
773A PRO* 1.4 63.6 - - + +
775A ILE* 3.3 12.1 + - - +
776A ASN* 3.1 24.3 + - + +
791A VAL* 4.6 8.9 - - + +
792A ASP* 2.9 30.3 + - - -
795A CYS* 3.7 24.2 - - - +
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Residues in contact with PRO 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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767A MET 3.4 2.2 - - - +
768A GLU 3.2 27.8 - - - +
769A ARG 3.9 9.0 - - - +
770A ARG 3.7 7.9 - - - +
771A ILE 3.5 2.9 - - - -
772A ARG* 1.4 92.6 - - + +
774A TRP* 1.3 52.1 + - - +
776A ASN* 3.2 6.5 + - + +
777A LYS* 2.8 37.6 + - - +
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Residues in contact with TRP 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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770A ARG* 3.0 54.8 + - - +
771A ILE 3.1 4.4 + - - +
773A PRO* 1.3 78.8 - - - +
775A ILE* 1.3 72.2 + - + +
777A LYS* 3.6 5.2 + - - +
778A LYS* 3.1 27.9 + - + +
822A PHE* 3.6 34.3 - + - -
825A LYS* 4.1 21.5 - - + -
826A MET* 3.7 39.7 - - + -
829A LEU* 3.7 21.8 - - + +
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Residues in contact with ILE 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 ILE* 2.9 38.5 + - + +
772A ARG 3.6 5.6 - - - +
774A TRP* 1.3 86.0 - - + +
776A ASN* 1.3 58.3 + - - +
778A LYS* 3.3 2.8 + - - +
779A ILE* 3.0 32.7 + - + +
791A VAL* 4.1 24.5 - - + +
794A VAL* 4.5 10.8 - - + -
795A CYS* 3.8 31.2 - - - +
798A VAL* 5.2 1.3 - - + -
822A PHE* 4.0 17.8 - - + -
826A MET* 3.6 26.5 - - + -
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Residues in contact with ASN 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 ARG* 3.1 20.1 + - + +
773A PRO* 3.7 6.7 - - + +
775A ILE* 1.3 77.1 - - - +
777A LYS* 1.3 57.8 + - - +
779A ILE* 3.0 22.7 - - - +
780A ILE* 3.1 19.4 - - - +
788A ALA* 5.8 0.5 - - - -
791A VAL* 3.7 28.6 - - + +
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Residues in contact with LYS 777 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A PRO 2.8 21.3 + - - +
774A TRP* 4.0 5.6 - - - +
776A ASN* 1.3 74.3 - - - +
778A LYS* 1.3 59.9 + - - +
779A ILE 3.4 0.5 + - - -
780A ILE* 3.4 11.7 + - - +
781A GLU* 3.0 23.0 - - - +
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Residues in contact with LYS 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 TRP* 3.1 30.1 + - + +
775A ILE 3.3 0.4 + - - +
777A LYS* 1.3 75.4 - - - +
779A ILE* 1.3 61.1 + - - +
780A ILE 3.3 0.6 + - - -
781A GLU* 3.6 21.7 + - - +
782A TYR* 3.3 23.7 - - + -
822A PHE* 3.9 24.9 - - + -
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Residues in contact with ILE 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 ILE* 3.0 17.6 + - + +
776A ASN* 3.0 36.8 - - - +
778A LYS* 1.3 75.1 - - - +
780A ILE* 1.3 68.5 + - + +
781A GLU 3.3 0.2 - - - -
782A TYR* 3.4 8.2 + - + +
783A ILE* 3.2 26.6 + - + +
784A GLY 4.2 0.5 + - - +
788A ALA 5.1 6.5 - - - +
790A LEU* 4.7 12.3 - - + -
791A VAL* 3.8 31.4 - - + +
794A VAL* 5.7 4.5 - - + -
815A LEU* 5.0 18.2 - - + -
822A PHE* 5.1 7.8 - - + -
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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 ASN* 3.1 32.8 - - - +
777A LYS* 3.4 10.5 + - - +
778A LYS 3.3 0.6 - - - -
779A ILE* 1.3 89.8 - - + +
781A GLU* 1.3 72.4 + - + +
783A ILE 3.8 0.2 - - - -
784A GLY* 2.9 44.2 + - - +
765D ILE* 5.8 4.6 - - + +
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Residues in contact with GLU 781 (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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777A LYS 3.0 23.1 - - - +
778A LYS* 3.8 16.6 - - - +
779A ILE 3.3 0.8 - - - -
780A ILE* 1.3 88.6 - - - +
782A TYR* 1.3 68.7 + - + +
765D ILE* 4.7 33.6 - - + +
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Residues in contact with TYR 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 LYS* 3.3 28.3 - - + -
779A ILE* 3.4 7.5 + - - +
780A ILE 3.2 0.4 - - - -
781A GLU* 1.3 86.2 - - + +
783A ILE* 1.4 58.2 + - - +
815A LEU* 3.8 36.1 - - + +
818A GLU* 3.7 44.0 + - + -
821A VAL* 4.5 9.2 - - + +
822A PHE* 4.0 35.8 + + + -
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Residues in contact with ILE 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 ILE* 3.2 15.5 + - + +
780A ILE 3.4 0.6 + - - -
782A TYR* 1.4 80.4 - - - +
784A GLY* 1.3 64.9 + - - +
815A LEU* 4.8 12.1 - - + -
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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