Contacts of the helix formed by residues 787 - 801 (chain C) 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 GLU 787 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776C ASN* 4.7 2.2 + - - -
779C ILE* 4.4 18.0 - - + +
783C ILE* 5.8 3.1 - - + -
785C GLU* 3.8 12.0 + - + +
786C GLU* 1.3 79.8 - - - +
788C ALA* 1.3 65.1 + - - +
789C THR* 2.8 27.5 + - - +
790C LEU* 3.3 19.2 + - + +
791C VAL* 3.4 15.4 + - - +
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Residues in contact with ALA 788 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C ASN* 5.6 1.1 - - - -
786C GLU* 4.2 8.1 - - + +
787C GLU* 1.3 72.4 - - - +
789C THR* 1.3 60.2 + - + +
790C LEU 3.3 0.2 - - - -
791C VAL* 3.6 9.6 - - + -
792C ASP* 2.9 43.6 + - - +
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Residues in contact with THR 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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787C GLU* 2.8 25.4 + - - +
788C ALA* 1.3 76.2 - - + +
790C LEU* 1.3 62.0 + - - +
792C ASP* 4.0 3.7 - - - +
793C PHE* 3.1 24.3 + - - +
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Residues in contact with LEU 790 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779C ILE* 4.6 20.0 - - + -
787C GLU* 3.3 20.8 + - + +
788C ALA 3.3 0.2 - - - -
789C THR* 1.3 80.0 + - - +
791C VAL* 1.3 62.8 + - - +
793C PHE* 3.5 6.6 + - - +
794C VAL* 3.2 29.8 + - + +
814C VAL* 5.8 11.4 - - + -
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Residues in contact with VAL 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772C ARG* 4.0 30.3 - - + +
775C ILE* 4.0 19.4 - - + +
776C ASN* 3.6 34.8 - - + +
779C ILE* 4.1 12.1 - - + -
787C GLU 3.4 15.5 - - - +
788C ALA* 3.2 12.9 + - + +
790C LEU* 1.3 76.3 - - - +
792C ASP* 1.3 66.0 + - - +
793C PHE 3.3 0.3 + - - -
794C VAL* 3.3 5.0 + - - +
795C CYS* 3.0 31.7 + - - -
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Residues in contact with ASP 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772C ARG* 3.0 26.2 + - - +
788C ALA* 2.9 26.9 + - - +
789C THR* 4.3 3.8 - - - +
791C VAL* 1.3 75.5 - - - +
793C PHE* 1.3 60.6 + - - +
795C CYS* 3.7 9.3 - - - +
796C SER* 3.0 27.4 + - - -
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Residues in contact with PHE 793 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C THR 3.1 19.5 + - - +
790C LEU* 3.5 7.4 - - - +
791C VAL 3.2 0.2 - - - -
792C ASP* 1.3 74.1 - - - +
794C VAL* 1.3 76.8 - - + +
796C SER* 2.6 26.5 + - - -
797C LYS* 3.0 40.4 + - + +
807C ILE* 5.3 1.6 - - + -
810C ASP* 3.8 34.5 - - + -
811C VAL* 4.4 13.0 - - + -
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Residues in contact with VAL 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C ILE* 3.7 26.7 - - + -
779C ILE* 5.2 2.9 - - + -
790C LEU* 3.2 16.2 + - + +
791C VAL 3.8 6.3 - - - +
793C PHE* 1.3 80.9 - - + +
795C CYS* 1.3 58.3 + - - +
797C LYS* 3.4 5.7 + - - +
798C VAL* 3.0 33.8 + - - +
807C ILE* 4.5 5.8 - - + +
811C VAL* 3.8 27.4 - - + -
822C PHE* 4.1 17.5 - - + -
826C MET* 3.8 26.7 - - + -
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Residues in contact with CYS 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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767C MET* 4.0 20.8 - - + +
772C ARG* 3.9 44.2 - - - +
775C ILE* 3.7 20.2 - - - -
791C VAL* 3.0 24.9 + - - +
792C ASP* 3.7 9.0 - - - +
794C VAL* 1.3 75.3 - - - +
796C SER* 1.3 58.6 + - - +
798C VAL* 3.4 3.6 + - - +
799C MET* 3.0 35.0 + - + +
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Residues in contact with SER 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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792C ASP 3.0 14.6 + - - -
793C PHE* 2.6 24.2 + - - -
795C CYS* 1.3 76.0 - - - +
797C LYS* 1.3 62.9 + - - +
799C MET* 3.4 6.2 + - - +
800C ALA* 2.7 36.5 + - - +
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Residues in contact with LYS 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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793C PHE* 3.0 45.0 + - + +
794C VAL* 3.8 4.9 - - - +
795C CYS 3.3 0.2 - - - -
796C SER* 1.3 87.9 + - - +
798C VAL* 1.3 62.2 + - - +
800C ALA* 4.0 4.8 - - + +
801C HIS 3.2 2.4 + - - -
802C SER* 2.9 51.5 + - - +
806C SER* 6.0 0.9 - - - -
807C ILE* 3.7 27.4 - - + +
810C ASP* 4.4 16.5 + - - +
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Residues in contact with VAL 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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759C TRP* 3.2 24.2 - - + -
762C VAL* 4.3 4.6 - - + +
767C MET* 3.6 21.1 - - + -
771C ILE* 5.0 1.1 - - + -
775C ILE* 5.0 3.8 - - + -
794C VAL* 3.0 23.6 + - + +
795C CYS* 3.8 5.4 - - - +
797C LYS* 1.3 75.4 - - - +
799C MET* 1.3 59.9 + - - +
801C HIS* 2.9 17.0 + - - -
807C ILE* 4.2 8.5 - - + -
826C MET* 4.0 31.6 - - + -
827C TRP* 5.2 0.4 - - + -
830C LEU* 4.0 32.5 - - + -
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Residues in contact with MET 799 (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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762C VAL* 4.2 17.9 - - - +
763C ASP* 3.6 30.1 - - - +
764C SER* 3.8 14.1 - - - +
767C MET* 3.3 36.8 - - + -
795C CYS 3.0 21.0 + - - +
796C SER* 3.7 6.1 - - - +
798C VAL* 1.3 75.4 - - - +
800C ALA* 1.3 56.6 + - - +
801C HIS* 2.9 22.9 + - - -
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Residues in contact with ALA 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796C SER 2.7 22.6 + - - +
797C LYS* 3.6 12.6 - - + +
799C MET* 1.3 72.6 - - - +
801C HIS* 1.3 69.0 + - - +
802C SER* 3.8 11.7 - - - +
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Residues in contact with HIS 801 (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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759C TRP* 3.4 75.9 + + + +
760C SER* 5.7 0.9 - - - -
762C VAL* 4.8 8.4 + - + -
798C VAL 2.9 16.3 + - - -
799C MET* 2.9 28.4 + - - -
800C ALA* 1.3 80.2 + - - +
802C SER* 1.3 66.9 + - - +
803C SER 3.8 0.2 + - - -
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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