Contacts of the helix formed by residues 770 - 783 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734B LYS* 5.6 8.5 - - - +
766B LEU* 3.3 11.1 + - + +
769B ARG* 1.3 80.1 - - + +
771B ILE* 1.3 68.9 + - + +
772B ARG 3.7 0.4 - - - -
773B PRO* 3.7 3.3 - - - +
774B TRP* 3.4 21.8 + - - +
829B LEU* 4.9 8.3 - - + +
833B GLU* 5.6 8.7 - - + -
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Residues in contact with ILE 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B VAL* 4.1 15.0 - - + -
766B LEU* 3.2 28.5 + - + +
767B MET* 3.8 28.9 - - + -
770B ARG* 1.3 79.0 - - + +
772B ARG* 1.3 62.3 + - - +
774B TRP* 3.2 6.4 + - - +
775B ILE* 3.0 50.7 + - + +
826B MET* 4.1 14.4 - - + -
829B LEU* 4.4 19.7 - - + -
830B LEU* 4.1 17.5 - - + -
833B GLU* 5.4 10.3 - - + -
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Residues in contact with ARG 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A GLU* 5.0 5.4 + - - -
767B MET* 2.9 26.8 + - + +
768B GLU* 4.8 7.0 - - - +
771B ILE* 1.3 77.1 - - - +
773B PRO* 1.4 60.9 - - + +
775B ILE* 3.3 9.3 + - - +
776B ASN* 2.9 43.3 + - - +
788B ALA* 4.1 10.7 + - - +
791B VAL* 3.7 24.1 - - + +
792B ASP* 2.6 36.0 + - - -
795B CYS* 3.5 23.1 - - - +
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Residues in contact with PRO 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767B MET 4.0 0.2 - - - +
768B GLU 3.8 15.5 - - - +
769B ARG 3.1 24.2 - - - +
770B ARG* 3.7 7.0 - - - +
771B ILE 3.8 0.4 - - - -
772B ARG* 1.4 94.7 - - + +
774B TRP* 1.3 56.8 + - - +
776B ASN* 3.3 9.5 + - + +
777B LYS* 2.9 45.9 + - - +
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Residues in contact with TRP 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770B ARG 3.4 17.7 - - - +
771B ILE 3.2 3.8 + - - +
772B ARG 3.2 0.4 - - - -
773B PRO* 1.3 80.4 - - - +
775B ILE* 1.3 72.2 + - + +
777B LYS* 3.3 9.0 + - - +
778B LYS* 3.0 63.5 + - + +
822B PHE* 3.7 23.6 - + - -
825B LYS* 3.9 20.2 - - + -
826B MET* 3.7 40.8 - - + -
829B LEU* 3.7 33.5 - - + +
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Residues in contact with ILE 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B ILE* 3.0 26.7 + - + +
772B ARG 3.6 4.0 - - - +
774B TRP* 1.3 86.3 - - + +
776B ASN* 1.3 64.6 + - - +
778B LYS* 3.0 7.0 + - - +
779B ILE* 2.9 34.8 + - + +
791B VAL* 3.9 15.5 - - + -
794B VAL* 4.0 17.7 - - + -
795B CYS* 3.8 27.1 - - - +
822B PHE* 3.8 20.2 - - + -
826B MET* 3.5 33.2 - - + -
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Residues in contact with ASN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772B ARG* 2.9 28.5 + - - +
773B PRO* 3.3 10.8 + - + +
775B ILE* 1.3 76.1 - - - +
777B LYS* 1.3 66.6 + - - +
779B ILE* 3.4 3.3 + - - +
780B ILE* 3.1 37.9 + - - +
786B GLU* 3.5 37.6 + - - +
787B GLU 5.3 0.2 + - - -
788B ALA* 5.7 0.3 - - - -
791B VAL* 4.0 24.1 - - + +
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Residues in contact with LYS 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B PRO* 2.9 29.8 + - - +
774B TRP* 3.6 7.4 - - - +
776B ASN* 1.3 79.6 - - - +
778B LYS* 1.3 65.8 + - + +
780B ILE* 3.3 13.7 + - + +
781B GLU* 2.9 27.5 + - - +
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Residues in contact with LYS 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B TRP* 3.0 61.1 + - + +
775B ILE 3.0 8.2 + - - +
777B LYS* 1.3 79.2 - - - +
779B ILE* 1.3 60.3 + - - +
781B GLU* 3.2 38.3 + - - +
782B TYR* 2.9 50.7 + - + +
822B PHE* 3.7 16.8 - - + -
825B LYS* 5.7 2.9 - - + -
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Residues in contact with ILE 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775B ILE* 2.9 23.6 + - + +
776B ASN 3.7 7.4 - - - +
778B LYS* 1.3 75.8 - - - +
780B ILE* 1.3 58.9 + - - +
781B GLU 3.1 0.2 - - - -
782B TYR* 4.4 4.3 - - + +
783B ILE* 2.9 37.5 + - + +
785B GLU 4.0 2.9 - - - +
787B GLU* 4.3 26.0 - - + +
790B LEU* 3.9 43.7 - - + +
791B VAL* 4.1 17.0 - - + -
794B VAL* 5.4 0.4 - - + -
815B LEU* 4.1 16.8 - - + -
822B PHE* 4.3 16.8 - - + -
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Residues in contact with ILE 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B ASN* 3.1 34.2 + - - +
777B LYS* 3.3 14.5 + - + +
779B ILE* 1.3 76.1 - - - +
781B GLU* 1.3 56.1 + - - +
783B ILE 2.5 18.3 - - - +
784B GLY 3.5 16.1 - - - +
785B GLU* 3.8 8.7 - - - -
786B GLU* 3.8 33.2 - - + +
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Residues in contact with GLU 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777B LYS 2.9 13.6 + - - +
778B LYS* 3.4 43.9 + - - +
779B ILE 3.1 0.2 - - - -
780B ILE* 1.3 80.8 - - - +
782B TYR* 1.3 76.6 + - + +
783B ILE 4.2 0.5 - - - +
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Residues in contact with TYR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778B LYS* 2.9 33.5 + - + +
779B ILE* 3.3 5.4 + - + +
781B GLU* 1.3 100.3 + - + +
783B ILE* 1.3 64.7 + - - +
815B LEU* 4.1 29.6 - - + -
818B GLU* 4.1 40.9 + - + +
821B VAL* 4.2 8.7 + - + +
822B PHE* 3.4 55.1 + + + -
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Residues in contact with ILE 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE* 2.9 22.6 + - + +
780B ILE 2.5 31.4 - - - +
781B GLU 3.8 1.0 - - - +
782B TYR* 1.3 79.5 + - + +
784B GLY* 1.3 68.8 + - - +
785B GLU* 3.6 21.3 - - - +
787B GLU* 5.1 9.9 - - + +
790B LEU* 4.6 21.3 - - + -
814B VAL* 5.1 4.3 - - + +
815B LEU* 3.7 29.4 - - + -
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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