Contacts of the helix formed by residues 806 - 817 (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 THR 806 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804C GLU 5.3 1.1 - - - +
805C LEU* 1.3 82.5 - - + +
807C PRO* 1.3 74.2 - - + +
808C GLU* 3.9 9.2 - - - -
809C GLU* 2.9 30.3 + - - +
810C ARG* 3.0 11.7 + - - +
391F PHE* 3.7 23.2 - - + -
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Residues in contact with PRO 807 (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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805C LEU 3.8 4.9 - - - +
806C THR* 1.3 84.2 - - - +
808C GLU* 1.3 84.1 + - - +
810C ARG* 3.0 8.3 + - + +
811C LEU* 3.0 22.3 + - - +
417F PHE* 3.2 28.2 - - + +
418F GLY 3.8 15.0 - - - +
419F LEU* 3.3 20.1 - - + +
422F GLY* 4.9 11.4 - - - +
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Residues in contact with GLU 808 (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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806C THR* 3.9 1.0 - - - -
807C PRO* 1.3 95.1 - - - +
809C GLU* 1.3 57.5 + - - +
811C LEU 4.1 0.4 + - - -
812C LEU* 3.2 28.8 + - - +
391F PHE* 3.5 25.3 - - + -
394F LEU* 4.0 11.6 - - + +
395F GLN* 3.1 46.1 + - + -
398F LEU* 3.7 15.5 - - + +
419F LEU* 3.7 25.9 - - + +
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Residues in contact with GLU 809 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805C LEU* 4.1 17.9 - - + -
806C THR* 2.9 24.3 + - - +
808C GLU* 1.3 79.3 - - - +
810C ARG* 1.3 62.5 + - - +
811C LEU 3.2 0.6 + - - -
812C LEU* 3.4 7.1 + - - +
813C ARG* 2.9 34.6 + - - +
391F PHE* 5.3 1.3 - - + -
394F LEU* 5.2 4.9 - - + -
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Residues in contact with ARG 810 (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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805C LEU* 5.5 7.5 - - + +
806C THR 3.0 11.1 + - - +
807C PRO* 3.0 12.0 + - + +
809C GLU* 1.3 76.9 - - - +
811C LEU* 1.3 62.5 + - - +
813C ARG* 2.9 28.2 + - + +
814C ALA 3.1 6.1 + - - -
417F PHE* 3.8 25.0 - - + +
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Residues in contact with LEU 811 (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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807C PRO 3.0 14.3 + - - +
808C GLU 4.2 5.6 - - - +
809C GLU 3.2 0.2 - - - -
810C ARG* 1.3 76.3 - - - +
812C LEU* 1.3 62.7 + - + +
813C ARG 3.2 0.2 + - - -
814C ALA* 3.2 3.6 + - - +
815C ILE* 3.0 46.1 + - + +
398F LEU* 4.0 23.6 - - + -
402F LEU* 4.5 11.2 - - + -
413F VAL* 3.5 29.6 - - + -
417F PHE* 3.6 22.8 - - + -
419F LEU* 3.6 28.5 - - + -
449F MET* 5.0 1.6 - - + -
452F LEU* 4.2 6.1 - - + -
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Residues in contact with LEU 812 (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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808C GLU 3.2 17.5 - - - +
809C GLU* 3.4 8.8 + - - +
810C ARG 3.4 0.2 - - - -
811C LEU* 1.3 76.4 - - - +
813C ARG* 1.3 63.2 + - - +
815C ILE* 4.0 6.7 - - + -
816C PHE* 3.1 34.6 + - + +
818C GLU* 5.7 0.3 - - - +
394F LEU* 3.6 26.5 - - + -
398F LEU* 3.5 34.5 - - + -
461F LEU* 4.1 22.7 - - + +
464F TYR* 3.8 25.1 - - + +
465F LEU 5.3 6.3 - - - +
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Residues in contact with ARG 813 (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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766C ASN* 3.7 32.2 + - - +
805C LEU* 5.2 12.4 - - + +
809C GLU* 2.9 32.6 + - - +
810C ARG* 2.9 21.8 + - + +
812C LEU* 1.3 76.1 - - - +
814C ALA* 1.3 54.5 + - - +
817C GLY* 2.8 24.3 + - - -
818C GLU* 3.1 49.5 + - - +
819C LYS* 4.5 2.8 + - - -
820C ALA* 3.9 34.1 - - + +
821C ARG 5.2 1.6 - - - +
465F LEU 4.3 9.0 + - - -
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Residues in contact with ALA 814 (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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810C ARG 3.1 3.6 + - - +
811C LEU 3.9 0.7 - - - +
813C ARG* 1.3 77.9 - - - +
815C ILE* 1.3 67.6 + - - +
817C GLY* 3.3 7.5 + - - +
417F PHE* 3.6 27.8 - - + -
445F GLU* 5.8 0.7 - - - +
449F MET* 3.3 19.7 - - + -
453F ARG* 3.0 25.3 + - - +
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Residues in contact with ILE 815 (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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811C LEU* 3.0 41.0 + - + +
812C LEU* 3.8 10.1 - - + +
813C ARG 3.3 0.2 - - - -
814C ALA* 1.3 79.4 - - - +
816C PHE* 1.3 78.7 + - + +
398F LEU* 4.8 0.9 - - + -
401F VAL* 5.6 2.7 - - + -
449F MET* 3.4 8.7 - - + -
452F LEU* 3.6 57.0 - - + +
453F ARG* 3.1 31.4 + - - +
458F SER* 4.6 5.2 - - - -
461F LEU* 4.5 18.6 - - + -
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Residues in contact with PHE 816 (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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812C LEU* 3.1 26.3 + - + +
815C ILE* 1.3 90.5 - - + +
817C GLY* 1.3 64.0 + - - +
818C GLU* 3.2 19.7 + - + +
453F ARG* 5.2 1.6 - - - -
458F SER* 3.0 39.7 - - - -
459F GLN* 5.5 0.2 - - - -
461F LEU* 3.6 24.5 - - + -
462F ARG* 3.2 48.7 - - + -
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Residues in contact with GLY 817 (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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813C ARG 2.8 10.1 + - - -
814C ALA* 3.3 11.9 + - - -
815C ILE 3.3 0.6 + - - -
816C PHE* 1.3 77.7 - - - +
818C GLU* 1.3 60.4 + - - +
819C LYS 3.8 2.3 + - - -
453F ARG* 5.0 6.7 - - - -
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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