Contacts of the helix formed by residues 807 - 819 (chain C) in PDB entry 6V3O
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 ARG 807 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712C GLU* 4.9 15.0 + - - +
805C ASP* 2.8 34.5 + - - +
806C VAL* 1.3 83.6 - - + +
808C ASN* 1.3 67.1 + - - +
809C PHE 3.3 1.7 + - - -
810C GLN* 3.3 14.0 + - - +
811C VAL* 3.3 19.3 + - + +
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Residues in contact with ASN 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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712C GLU* 4.7 4.9 - - - +
716C LEU* 3.8 31.2 - - + +
719C GLU* 5.3 0.4 + - - -
801C ALA* 2.9 35.0 + - + +
802C ILE* 4.3 0.2 - - - -
804C LYS* 4.2 10.3 - - - +
805C ASP* 2.9 33.1 + - - +
806C VAL 3.2 0.2 - - - -
807C ARG* 1.3 80.6 + - - +
809C PHE* 1.3 65.9 + - - +
811C VAL* 3.2 9.9 + - - +
812C LEU* 2.9 28.4 + - - +
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Residues in contact with PHE 809 (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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802C ILE* 3.9 44.7 + - + +
805C ASP 4.6 0.2 + - - -
806C VAL 4.4 6.1 + - - +
807C ARG 3.3 0.8 + - - -
808C ASN* 1.3 79.4 - - - +
810C GLN* 1.3 61.2 + - + +
812C LEU* 3.4 3.5 + - - +
813C LYS* 3.1 54.9 + - + +
873C GLN* 3.7 48.5 - - + -
874C ILE* 4.2 13.7 - - + -
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Residues in contact with GLN 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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806C VAL 5.4 0.4 + - - -
807C ARG 3.3 7.5 + - - +
808C ASN 3.3 0.2 - - - -
809C PHE* 1.3 78.9 - - + +
811C VAL* 1.3 61.5 + - - +
813C LYS* 2.9 40.9 - - - +
814C GLU* 2.8 47.5 + - + +
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Residues in contact with VAL 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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712C GLU* 3.7 32.3 - - + +
713C TRP* 4.0 14.1 - - + +
716C LEU* 4.2 5.6 - - + -
807C ARG* 3.3 27.0 + - + +
808C ASN* 3.2 10.5 + - - +
810C GLN* 1.3 77.3 - - + +
812C LEU* 1.3 56.7 + - - +
814C GLU* 3.3 16.1 + - - +
815C MET* 2.8 54.7 + - + +
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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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716C LEU* 3.8 15.7 - - + -
720C MET* 3.9 24.7 - - + -
798C PHE 4.6 1.1 - - - +
801C ALA* 4.0 21.8 - - + -
802C ILE* 4.1 16.8 - - + -
808C ASN 2.9 19.0 + - - +
809C PHE* 3.6 6.1 - - - +
811C VAL* 1.3 73.5 - - - +
813C LYS* 1.3 64.2 + - - +
815C MET* 3.1 26.9 + - - +
816C TYR* 2.9 22.9 + - - +
822C PHE* 4.0 10.6 - - + -
874C ILE* 3.8 34.5 - - + +
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Residues in contact with LYS 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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809C PHE* 3.1 42.2 + - + +
810C GLN* 2.9 50.4 - - - +
812C LEU* 1.3 74.3 - - - +
814C GLU* 1.3 64.0 + - + +
816C TYR* 3.2 4.2 + - - +
817C ASN* 3.1 32.2 + - - +
873C GLN 4.1 13.5 - - - +
874C ILE* 3.4 26.8 - - - +
876C GLY* 5.6 4.5 - - - +
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Residues in contact with GLU 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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710C LYS* 5.1 8.4 + - - +
713C TRP* 4.9 7.7 + - + +
810C GLN* 2.8 40.2 + - + +
811C VAL* 3.5 18.2 - - - +
813C LYS* 1.3 73.6 - - + +
815C MET* 1.3 58.6 + - - +
817C ASN* 3.2 6.2 + - - +
818C GLU* 2.9 55.3 + - - +
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Residues in contact with MET 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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713C TRP* 3.4 61.0 - - + +
716C LEU* 3.6 26.7 - - + -
717C MET* 5.4 3.1 - - - +
720C MET* 6.2 0.2 - - - +
811C VAL* 2.8 34.9 + - + +
812C LEU* 3.1 23.8 + - + +
814C GLU* 1.3 77.0 - - - +
816C TYR* 1.3 58.4 + - - +
819C TRP* 2.8 50.6 + - + +
822C PHE* 3.8 24.0 - - + +
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Residues in contact with TYR 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 2.9 12.7 + - - +
813C LYS 3.2 7.2 + - - +
815C MET* 1.3 76.3 - - - +
817C ASN* 1.3 70.4 + - - +
822C PHE* 3.7 8.2 - - + -
823C ARG* 3.0 70.9 + - - +
826C LEU* 3.7 37.2 - - + -
827C ASP* 3.3 17.5 + - - -
830C GLU* 3.8 3.0 + - - -
871C LEU* 5.8 0.4 - - + -
874C ILE* 4.0 12.1 - - + +
875C ALA* 3.4 42.2 - - + +
877C HIS* 3.3 25.4 - - - -
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Residues in contact with ASN 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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131C PHE* 3.2 18.0 - - - -
813C LYS* 3.1 22.2 + - - +
814C GLU* 3.2 6.4 + - - +
816C TYR* 1.3 94.5 - - - +
818C GLU* 1.3 62.5 + - + +
819C TRP 3.9 0.2 - - - -
823C ARG* 4.2 9.9 + - - +
875C ALA 5.3 2.6 + - - -
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Residues in contact with GLU 818 (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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131C PHE* 3.7 12.3 - - - -
707C VAL* 3.6 16.5 - - + +
710C LYS* 3.9 13.8 + - - -
713C TRP* 3.8 24.2 - - + -
814C GLU* 2.9 37.3 + - - +
817C ASN* 1.3 87.2 - - + +
819C TRP* 1.3 58.8 + - - +
820C PRO* 3.5 9.4 - - - +
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Residues in contact with TRP 819 (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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131C PHE* 4.5 2.5 - - - -
615C TRP* 3.6 31.4 - + - -
618C TYR* 4.5 7.7 + + - -
706C PRO* 5.8 1.5 - - + +
707C VAL* 4.1 17.4 + - + -
709C PRO* 3.4 37.6 - - + +
713C TRP* 3.6 41.5 - + + -
717C MET* 3.9 21.1 - - + -
815C MET* 2.8 25.0 + - + +
817C ASN 3.9 0.4 - - - -
818C GLU* 1.3 78.1 - - - +
820C PRO* 1.3 77.2 - - + +
821C PHE* 3.7 35.7 - + + +
822C PHE* 3.0 15.7 + - + -
823C ARG* 3.0 19.4 + - - +
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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