Contacts of the helix formed by residues 771 - 785 (chain C) in PDB entry 6DBT
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 SER 771 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769C THR 4.5 0.9 - - - -
770C ARG* 1.3 72.7 - - - +
772C HIS* 1.3 66.7 + - - +
773C ASP* 3.0 10.6 + - - +
774C GLU* 2.2 46.3 + - - -
775C ASN* 2.9 20.1 + - - +
811C PRO* 5.7 6.5 - - - -
971C ARG* 5.6 6.3 - - - +
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Residues in contact with HIS 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702C LYS* 5.9 5.0 + - - -
738C GLU* 4.3 8.0 + - - +
771C SER* 1.3 74.0 - - - +
773C ASP* 1.3 73.2 + - + +
775C ASN* 3.2 14.4 + - - +
776C LEU* 3.0 31.8 + - + +
805C PRO* 4.4 28.7 - - + +
806C PHE 4.8 1.8 - - - -
807C MET 4.0 9.0 + - - -
808C GLU* 3.4 54.5 + - + +
809C THR 4.9 4.7 + - - +
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Residues in contact with ASP 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771C SER* 3.0 7.9 + - - +
772C HIS* 1.3 89.4 - - + +
774C GLU* 1.3 66.4 + - - +
776C LEU* 3.1 10.6 + - - +
777C GLU* 2.9 26.6 + - - +
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Residues in contact with GLU 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769C THR 2.5 20.8 - - - +
770C ARG* 2.8 1.2 - - - -
771C SER* 2.2 59.1 + - - +
773C ASP* 1.3 86.4 + - - +
775C ASN* 1.3 62.6 + - - +
777C GLU* 3.3 11.6 + - + +
778C ARG* 2.9 55.9 + - - +
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Residues in contact with ASN 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738C GLU* 2.2 42.7 + - + +
740C LEU* 5.9 2.7 - - + -
770C ARG* 3.4 29.7 + - - +
771C SER* 2.9 29.9 + - - +
772C HIS* 3.3 6.4 - - - +
773C ASP 3.2 0.2 - - - -
774C GLU* 1.3 78.6 - - - +
776C LEU* 1.3 65.9 + - - +
778C ARG* 3.3 8.1 + - - +
779C TYR* 2.9 20.4 + - - +
801C VAL* 3.5 19.5 - - + +
805C PRO* 4.6 7.9 - - + -
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Residues in contact with LEU 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772C HIS* 3.0 24.5 + - - +
773C ASP* 3.2 14.8 - - - +
775C ASN* 1.3 74.9 - - - +
777C GLU* 1.3 62.9 + - - +
779C TYR* 3.3 6.0 + - + +
780C GLU* 3.0 49.3 + - + +
804C LYS* 4.0 37.2 - - + -
805C PRO* 4.5 14.1 - - + +
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Residues in contact with GLU 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C ASP* 2.9 16.0 + - - +
774C GLU* 3.3 16.6 - - + +
775C ASN 3.2 0.2 - - - -
776C LEU* 1.3 78.9 - - - +
778C ARG* 1.3 66.3 + - + +
780C GLU* 3.1 13.8 + - - +
781C ILE* 3.0 40.2 + - + +
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Residues in contact with ARG 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753C ASP* 3.9 22.6 + - - -
769C THR* 5.4 7.7 + - - -
770C ARG* 5.1 3.4 - - - +
774C GLU* 2.9 56.7 + - - +
775C ASN* 3.8 7.2 + - - +
777C GLU* 1.3 78.9 - - + +
779C TYR* 1.3 59.1 + - - +
781C ILE* 3.2 8.1 + - + -
782C TRP* 2.9 23.4 + - - +
797C ARG 5.8 0.2 + - - -
798C VAL* 3.1 45.0 + - + +
799C LYS* 4.3 10.1 - - - +
801C VAL* 3.6 22.2 - - + -
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Residues in contact with TYR 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775C ASN 2.9 14.0 + - - +
776C LEU* 3.6 11.7 - - + +
778C ARG* 1.3 77.0 - - - +
780C GLU* 1.3 69.7 + - - +
782C TRP* 3.1 16.4 + + - +
783C ARG* 2.9 53.3 + - + +
801C VAL* 3.7 12.9 - - + +
802C SER* 3.9 9.6 - - - -
803C ALA* 3.4 21.5 - - - +
804C LYS* 3.2 54.8 - - + +
805C PRO* 4.7 0.7 - - + -
36D TRP* 4.0 17.8 - + - -
70D PRO* 4.3 11.3 - - - +
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Residues in contact with GLU 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776C LEU* 3.0 40.6 + - + +
777C GLU* 3.1 15.2 + - - +
779C TYR* 1.3 86.1 - - + +
781C ILE* 1.3 62.6 + - - +
783C ARG* 3.2 25.5 + - - +
784C LYS* 3.0 40.3 + - + +
804C LYS* 5.6 4.3 - - - -
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Residues in contact with ILE 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C GLU* 3.0 38.6 + - + +
778C ARG* 3.2 14.1 + - + +
780C GLU* 1.3 75.2 - - - +
782C TRP* 1.3 58.4 + - - +
784C LYS* 5.2 2.2 - - - +
785C ASN* 2.8 29.1 + - - -
786C PRO* 3.4 18.6 - - + +
787C PHE* 5.9 0.4 - - + -
794C LEU* 4.7 9.6 - - + +
797C ARG* 5.5 17.3 - - + +
798C VAL* 4.1 14.6 - - + -
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Residues in contact with TRP 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778C ARG 2.9 14.1 + - - +
779C TYR* 3.1 22.6 + + - +
781C ILE* 1.3 77.4 - - - +
783C ARG* 1.3 73.8 + - + +
785C ASN* 3.2 17.7 + - - +
791C ALA* 5.1 3.1 - - - -
794C LEU* 3.8 35.1 - - + +
795C ARG* 4.3 22.9 - - + -
798C VAL* 4.1 7.8 - - + +
800C GLY* 6.0 1.1 - - - -
801C VAL 3.3 26.7 - - - +
802C SER* 4.5 25.0 + - - -
37D PRO* 6.4 1.8 - - + -
42D PRO* 4.6 17.3 - - + -
68D TYR* 3.4 52.1 + + + +
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Residues in contact with ARG 783 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779C TYR* 2.9 47.5 + - + +
780C GLU* 3.2 18.4 + - - +
782C TRP* 1.3 82.9 - - + +
784C LYS* 1.3 80.0 + - - +
67D SER* 2.9 24.5 + - - -
68D TYR 3.9 15.7 + - - +
70D PRO* 4.6 9.2 - - + -
105D SER* 5.3 4.1 + - - -
107D TYR* 2.6 34.3 + - - +
126D GLU* 3.4 23.7 + - - +
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Residues in contact with LYS 784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780C GLU* 3.0 25.9 + - + +
781C ILE* 5.2 1.6 - - - +
783C ARG* 1.3 101.1 - - - +
785C ASN* 1.3 70.5 + - - +
786C PRO* 3.5 17.5 - - + +
67D SER* 3.9 10.1 - - - -
126D GLU* 4.9 8.3 - - - +
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Residues in contact with ASN 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C ILE 2.8 15.7 + - - -
782C TRP 3.2 11.1 + - - +
784C LYS* 1.3 79.2 - - - +
786C PRO* 1.3 62.9 - - - +
787C PHE 2.9 7.2 + - - -
788C SER* 3.2 20.8 + - - -
789C GLU* 3.5 19.8 + - - +
790C SER 5.4 0.2 + - - -
794C LEU* 3.7 19.0 - - - +
66D SER 3.1 23.9 + - - -
67D SER* 4.2 11.8 - - - -
68D TYR* 3.6 21.4 - - - -
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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