Contacts of the strand formed by residues 792 - 798 (chain C) in PDB entry 6VVT
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 ILE 792 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764C ILE* 5.4 3.8 - - + -
767C VAL* 5.7 3.8 - - + -
771C VAL* 3.6 42.1 + - + +
772C LEU* 4.8 6.5 - - + -
775C LEU* 3.3 36.8 - - + +
781C VAL* 4.2 5.2 - - - +
787C VAL* 5.1 1.0 - - - +
790C GLY 4.6 2.7 - - - +
791C ASP* 1.3 82.9 - - + +
793C LEU* 1.3 64.9 + - - +
794C VAL 3.8 24.9 - - - +
795C GLY* 4.2 0.7 - - - +
827C SER* 3.8 20.0 - - - +
828C LEU 3.8 3.1 - - - +
829C LYS* 4.3 14.1 - - + +
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Residues in contact with LEU 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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746C HIS* 4.0 37.9 - - + +
775C LEU* 4.9 0.2 - - - -
779C GLY 3.8 1.3 - - - +
780C ILE* 3.3 1.9 - - - -
781C VAL* 2.6 48.8 + - + +
787C VAL* 3.7 33.0 - - + -
792C ILE* 1.3 74.8 - - - +
794C VAL* 1.3 67.3 + - + +
828C LEU* 2.7 25.5 + - + +
830C VAL* 3.8 26.7 - - + -
838C VAL* 4.6 4.0 - - + -
862C VAL* 4.6 12.3 - - + -
864C VAL* 4.7 6.3 - - + -
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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
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748C ILE* 3.6 28.9 - - + -
760C ILE* 4.6 10.8 - - + -
779C GLY 3.4 3.4 - - - -
780C ILE* 4.1 15.9 - - + -
792C ILE* 3.8 4.0 - - - +
793C LEU* 1.3 86.5 - - + +
795C GLY* 1.3 68.3 + - - +
796C LYS* 3.5 2.3 + - + +
827C SER* 3.4 4.2 - - - -
828C LEU* 2.8 37.5 + - + +
860C VAL* 3.9 25.1 - - + +
862C VAL* 3.9 20.9 - - + -
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Residues in contact with GLY 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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760C ILE* 3.2 5.6 - - - +
761C THR 2.5 47.5 + - - +
764C ILE* 3.8 17.3 - - - -
775C LEU* 4.8 2.0 - - - -
778C ARG 4.9 0.7 - - - +
779C GLY* 2.9 16.2 + - - -
792C ILE* 4.2 3.5 - - - +
794C VAL* 1.3 73.8 - - - +
796C LYS* 1.3 53.0 + - - -
827C SER* 3.9 3.8 - - - -
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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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748C ILE* 3.9 24.5 - - + +
749C ASP* 2.2 43.5 + - - +
750C ALA* 4.1 1.7 - - + +
751C ARG* 4.7 2.0 - - - +
758C GLU* 3.2 28.6 - - - +
759C GLU 4.3 4.0 - - - +
760C ILE* 3.7 15.7 - - + +
794C VAL* 3.5 4.6 + - + +
795C GLY* 1.3 73.2 - - - +
797C VAL* 1.3 74.4 + - - +
798C THR* 3.4 12.0 - - - +
825C ASP* 4.3 0.3 - - - +
826C THR* 2.6 53.9 + - - +
827C SER* 3.8 3.0 + - - +
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Residues in contact with VAL 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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757C ALA 4.7 0.3 - - - +
758C GLU* 3.6 0.5 - - - -
759C GLU* 2.7 49.4 + - + +
761C THR* 3.4 29.8 - - + +
763C ASP 3.7 15.7 - - - +
764C ILE* 4.7 4.7 - - + -
765C PRO* 5.1 9.0 - - + -
796C LYS* 1.3 81.5 - - - +
798C THR* 1.3 60.1 + - - +
821C ARG* 5.4 6.3 - - - +
823C VAL* 3.1 33.4 - - + +
824C ARG 3.1 13.7 - - - +
825C ASP* 5.2 0.2 - - - -
826C THR* 3.9 2.5 - - - -
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Residues in contact with THR 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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753C THR* 5.2 7.9 - - + -
758C GLU* 3.3 30.5 - - + +
796C LYS* 3.4 18.2 - - - +
797C VAL* 1.3 74.6 - - - +
799C PRO* 1.3 75.5 + - - +
823C VAL* 3.0 19.2 - - - +
824C ARG* 3.2 13.5 + - - +
826C THR* 3.0 22.6 - - + +
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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