Contacts of the helix formed by residues 788 - 798 (chain C) in PDB entry 4OQB
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 ASP 788 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C LYS* 4.3 12.1 - - + +
663C SER* 3.5 40.8 - - - +
787C LYS* 1.3 74.4 - - - +
789C PRO* 1.3 77.4 - - + +
790C ILE 3.3 0.2 - - - -
791C ASP* 3.1 12.5 + - - +
792C VAL* 3.0 25.3 + - - +
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Residues in contact with PRO 789 (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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662C LYS* 5.8 4.0 - - + -
663C SER* 5.7 0.2 - - - -
787C LYS 4.7 0.9 - - - +
788C ASP* 1.3 89.8 - - + +
790C ILE* 1.3 65.6 + - + +
792C VAL* 3.4 10.1 + - + +
793C ASN* 3.4 27.2 + - - +
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Residues in contact with ILE 790 (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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663C SER* 4.2 15.9 - - - +
665C LEU* 4.5 6.7 - - + -
670C GLN* 4.0 48.2 - - + +
673C ILE* 3.4 31.4 - - + +
674C LYS* 4.4 18.4 - - + +
788C ASP* 3.3 1.0 - - - +
789C PRO* 1.3 79.9 - - + +
791C ASP* 1.3 58.8 + - - +
793C ASN* 3.4 7.9 + - - +
794C TYR 3.0 22.0 + - - -
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Residues in contact with ASP 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C SER* 3.3 30.8 - - - -
664C LYS* 3.5 7.6 + - - +
665C LEU* 3.2 31.1 - - - +
787C LYS* 4.6 7.6 - - + -
788C ASP* 3.1 19.1 + - - +
790C ILE* 1.3 75.7 - - - +
792C VAL* 1.3 64.6 + - - +
794C TYR* 3.6 7.2 - - - +
795C GLU* 3.1 36.3 + - + +
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Residues in contact with VAL 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C GLY 5.2 2.0 - - - +
781C GLY* 5.9 1.8 - - - -
782C SER 5.8 6.1 - - - +
787C LYS* 4.4 16.6 - - + +
788C ASP 3.0 21.6 + - - +
789C PRO* 3.6 10.8 - - + +
790C ILE 3.3 0.2 - - - -
791C ASP* 1.3 76.8 - - - +
793C ASN* 1.3 62.8 + - - +
795C GLU* 3.6 10.4 + - - +
796C LYS* 3.3 49.4 + - - +
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Residues in contact with ASN 793 (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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673C ILE* 4.0 24.7 - - + +
677C PHE* 3.9 20.6 - - + +
778C LEU* 3.5 31.9 - - - +
789C PRO* 3.4 13.8 + - - +
790C ILE* 3.4 8.4 + - - +
791C ASP 3.3 0.2 - - - -
792C VAL* 1.3 76.7 - - - +
794C TYR* 1.3 64.4 + - - +
795C GLU 3.4 0.2 - - - -
796C LYS* 3.5 22.6 + - - +
797C LEU* 3.4 24.3 + - - +
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Residues in contact with TYR 794 (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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665C LEU* 4.1 21.3 - - + -
669C VAL* 3.9 25.4 - - + -
673C ILE* 3.5 27.3 - - + +
790C ILE 3.0 11.6 + - - +
791C ASP* 3.6 10.8 - - - +
792C VAL 3.3 0.4 - - - -
793C ASN* 1.3 76.4 - - - +
795C GLU* 1.3 69.9 + - + +
797C LEU* 3.2 23.3 + - + +
798C LYS 3.8 2.6 + - - -
799C THR* 3.6 19.4 + - - +
800C ASP* 3.7 6.5 + - - -
801C ILE* 2.8 55.1 + - + -
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Residues in contact with GLU 795 (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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787C LYS* 5.4 9.1 - - - +
791C ASP* 3.1 26.8 + - + +
792C VAL* 4.0 8.6 - - - +
794C TYR* 1.3 84.1 - - + +
796C LYS* 1.3 61.1 + - + +
798C LYS* 3.4 21.1 + - - +
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Residues in contact with LYS 796 (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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677C PHE* 5.2 2.7 - - + -
777C LEU* 3.2 53.6 + - + +
778C LEU* 2.8 28.9 + - - -
780C GLY 3.2 27.9 + - - -
781C GLY* 4.3 7.2 - - - +
792C VAL* 3.3 35.2 + - - +
793C ASN* 3.6 24.1 + - - +
794C TYR 3.2 0.4 - - - -
795C GLU* 1.3 77.0 - - + +
797C LEU* 1.3 64.2 + - - +
798C LYS* 3.2 12.5 + - - +
874C SER* 4.5 1.2 - - - -
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Residues in contact with LEU 797 (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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673C ILE* 4.2 17.9 - - + -
676C ILE* 4.0 24.2 - - + -
677C PHE* 3.6 21.5 - - + -
777C LEU* 5.3 1.1 - - + -
793C ASN 3.4 14.1 + - - +
794C TYR* 3.2 15.2 + - + +
796C LYS* 1.3 76.0 - - - +
798C LYS* 1.3 71.3 + - - +
799C THR* 3.5 12.1 - - - +
801C ILE* 4.6 18.4 - - + -
870C ALA* 3.9 16.2 - - - +
873C LEU* 3.5 26.7 - - + +
874C SER* 3.4 22.2 - - - -
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Residues in contact with LYS 798 (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 LEU* 5.8 0.7 - - + -
794C TYR 3.8 2.0 + - - -
795C GLU* 3.4 17.4 + - - +
796C LYS* 3.2 17.0 - - - +
797C LEU* 1.3 78.6 - - - +
799C THR* 1.3 64.2 + - - +
841C ARG* 4.9 1.5 + - - +
842C GLU* 3.2 49.2 + - + +
873C LEU 4.6 0.9 - - - +
874C SER* 4.8 15.1 + - - +
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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