Contacts of the helix formed by residues 770 - 784 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734D LYS* 3.9 15.6 - - - +
766D LEU* 2.9 22.0 + - + +
768D GLU 3.6 0.2 - - - -
769D ARG* 1.3 87.0 - - + +
771D ILE* 1.3 60.3 + - + +
772D ARG 3.8 0.7 - - - -
773D PRO* 3.8 5.4 - - - +
774D TRP* 3.4 40.8 + - - +
829D LEU* 3.6 25.1 - - + +
833D GLU* 2.8 45.5 + - + +
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Residues in contact with ILE 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762D VAL* 4.5 2.2 - - + -
766D LEU* 3.1 42.8 + - + +
767D MET* 3.6 33.0 - - + -
770D ARG* 1.3 82.2 - - + +
772D ARG* 1.3 62.0 + - - +
773D PRO 3.4 0.2 - - - -
774D TRP* 3.3 3.8 + - - +
775D ILE* 2.9 46.7 + - + +
798D VAL* 5.0 3.8 - - + -
826D MET* 5.1 5.2 - - + -
829D LEU* 4.4 18.8 - - + -
830D LEU* 3.6 27.4 - - + -
833D GLU* 5.7 2.0 - - + -
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Residues in contact with ARG 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767D MET* 3.0 23.1 + - + +
768D GLU* 5.2 2.5 - - - +
771D ILE* 1.3 74.6 - - - +
773D PRO* 1.4 65.9 - - + +
775D ILE* 3.7 1.4 - - - +
776D ASN* 2.8 50.4 + - - +
786D GLU* 5.5 3.6 + - - -
788D ALA* 4.6 13.3 - - - +
791D VAL* 3.5 20.2 - - + +
792D ASP* 2.4 40.2 + - - +
795D CYS* 3.7 27.6 - - - -
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Residues in contact with PRO 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767D MET 3.6 8.1 - - - +
768D GLU 3.7 12.1 - - - +
769D ARG 3.4 20.9 - - - +
770D ARG* 3.8 3.4 - - - +
771D ILE 3.6 8.3 - - - +
772D ARG* 1.4 97.4 - - + +
774D TRP* 1.3 55.3 + - - +
776D ASN* 3.7 8.8 + - + +
777D LYS* 3.0 29.6 + - - +
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Residues in contact with TRP 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D ARG* 3.4 39.8 + - - +
771D ILE 3.3 4.6 + - - +
772D ARG 3.2 0.6 - - - -
773D PRO* 1.3 77.3 - - - +
775D ILE* 1.3 77.6 + - + +
777D LYS* 3.3 5.9 + - + +
778D LYS* 3.0 60.9 + - + +
822D PHE* 3.6 28.0 - + - -
825D LYS* 3.7 22.9 - - + -
826D MET* 3.4 42.4 - - + -
829D LEU* 3.7 26.7 - - + +
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Residues in contact with ILE 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767D MET* 4.8 0.9 - - + -
771D ILE* 2.9 39.6 + - + +
772D ARG* 3.9 3.4 - - - +
774D TRP* 1.3 90.0 - - + +
776D ASN* 1.3 58.4 + - - +
778D LYS* 3.4 2.3 + - - +
779D ILE* 2.9 49.9 + - + +
791D VAL* 4.1 21.5 - - + +
794D VAL* 4.2 14.6 - - + -
795D CYS* 3.9 24.2 - - - +
798D VAL* 4.9 2.2 - - + -
822D PHE* 4.3 11.4 - - + -
826D MET* 4.2 20.0 - - - -
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Residues in contact with ASN 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772D ARG* 2.8 37.2 + - - +
773D PRO* 3.7 7.7 + - + +
775D ILE* 1.3 74.3 - - - +
777D LYS* 1.3 64.6 + - - +
779D ILE* 3.4 2.4 + - - +
780D ILE* 3.2 40.2 + - - +
786D GLU* 3.6 30.7 + - - +
791D VAL* 3.8 24.8 - - + +
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Residues in contact with LYS 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773D PRO 3.0 17.4 + - - +
774D TRP* 3.3 6.7 + - + +
776D ASN* 1.3 77.4 - - - +
778D LYS* 1.3 69.8 + - + +
780D ILE* 3.2 14.6 + - - +
781D GLU* 3.2 21.4 + - - +
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Residues in contact with LYS 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D TRP* 3.0 64.5 + - + +
775D ILE 3.8 3.4 - - - +
777D LYS* 1.3 81.7 - - - +
779D ILE* 1.3 62.0 + - - +
781D GLU* 3.2 41.0 + - - +
782D TYR* 3.0 34.2 + - + +
822D PHE* 4.1 17.9 - - + -
825D LYS* 4.4 18.4 - - + +
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Residues in contact with ILE 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775D ILE* 2.9 34.9 + - + +
776D ASN 3.9 3.6 - - - +
777D LYS 3.4 0.2 - - - -
778D LYS* 1.3 75.9 - - - +
780D ILE* 1.3 61.5 + - - +
782D TYR* 3.2 5.1 + - + +
783D ILE* 3.0 29.8 + - + +
785D GLU 3.9 2.5 - - - +
786D GLU* 5.6 0.2 - - - -
787D GLU* 4.5 18.6 - - + +
790D LEU* 3.9 38.4 - - + -
791D VAL* 4.1 17.9 - - + +
794D VAL* 5.1 2.9 - - + -
811D VAL* 5.9 1.6 - - + -
815D LEU* 4.6 17.9 - - + -
822D PHE* 4.6 18.6 - - + -
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Residues in contact with ILE 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776D ASN* 3.2 37.4 + - - +
777D LYS* 3.5 11.0 - - - +
778D LYS 3.2 0.2 - - - -
779D ILE* 1.3 76.2 - - + +
781D GLU* 1.3 56.6 + - - +
784D GLY* 2.7 37.9 + - - -
785D GLU* 3.3 27.4 - - - +
786D GLU* 3.8 23.8 - - + +
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Residues in contact with GLU 781 (chain D).
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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777D LYS 3.2 10.8 + - - +
778D LYS* 3.2 49.0 + - - +
780D ILE* 1.3 77.1 - - - +
782D TYR* 1.3 78.0 + - + +
784D GLY* 4.5 2.0 + - - -
825D LYS* 5.7 2.8 + - - -
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Residues in contact with TYR 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778D LYS* 3.0 33.4 + - + +
779D ILE* 3.2 9.1 + - + +
780D ILE 3.0 0.8 - - - -
781D GLU* 1.3 104.0 + - - +
783D ILE* 1.3 61.9 + - + +
784D GLY 3.6 0.7 - - - -
815D LEU* 3.5 35.6 - - + +
818D GLU* 3.7 38.0 + - + -
821D VAL* 4.1 11.7 - - + +
822D PHE* 3.7 41.3 + + + +
825D LYS* 4.8 3.6 + - - +
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Residues in contact with ILE 783 (chain D).
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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738C ILE* 4.2 18.4 - - + -
779D ILE* 3.0 20.4 + - + +
782D TYR* 1.3 84.5 - - + +
784D GLY* 1.3 64.1 + - - +
785D GLU* 3.0 20.3 + - + +
787D GLU* 5.1 7.2 - - + -
790D LEU* 3.8 29.2 - - + -
814D VAL* 4.4 9.0 - - + +
815D LEU* 4.5 7.2 - - + -
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Residues in contact with GLY 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780D ILE* 2.7 24.0 + - - -
781D GLU 4.5 1.4 - - - -
782D TYR 3.6 1.8 - - - -
783D ILE* 1.3 70.7 - - - +
785D GLU* 1.3 58.7 + - - +
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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