Contacts of the helix formed by residues 816 - 824 (chain C) in PDB entry 6VSB
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 SER 816 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804C GLN 4.1 1.3 - - - -
805C ILE 3.0 28.9 - - - -
806C LEU 3.4 16.2 - - - -
807C PRO* 3.6 4.0 - - - +
808C ASP 4.5 0.2 - - - +
811C LYS* 5.6 0.7 - - - -
815C ARG* 1.3 77.2 - - - +
817C PHE* 1.3 64.0 + - - +
818C ILE 3.6 0.2 + - - -
819C GLU* 2.8 46.7 + - - +
820C ASP* 3.1 25.0 + - - -
1054C GLN* 3.1 7.0 + - - -
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Residues in contact with PHE 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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803C SER 5.0 0.4 - - - +
804C GLN* 3.9 28.5 + - + +
806C LEU 4.3 2.8 + - - -
808C ASP* 4.4 16.9 + - - +
811C LYS* 4.6 14.8 - - - +
815C ARG 4.0 0.2 + - - -
816C SER* 1.3 73.4 - - - +
818C ILE* 1.3 70.2 + - + +
820C ASP* 3.2 10.7 + - + +
821C LEU* 3.1 28.9 + - + +
935C GLN* 3.3 34.5 - - + -
2R NAG 6.1 5.2 - - + -
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Residues in contact with ILE 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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804C GLN* 3.1 34.1 + - + +
805C ILE* 3.8 22.7 - - + -
816C SER* 3.4 0.4 + - - -
817C PHE* 1.3 78.5 - - + +
819C GLU* 1.3 64.2 + - - +
821C LEU* 3.0 11.0 + - + +
822C LEU* 2.9 38.8 + - + +
931C ILE* 4.6 8.5 - - + +
934C ILE* 5.2 8.3 - - + -
935C GLN* 5.3 8.5 - - + +
938C LEU* 4.3 15.0 - - + -
1054C GLN* 3.6 20.0 - - + +
1061C VAL* 6.2 1.3 - - + -
1063C LEU* 4.2 17.9 - - + -
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Residues in contact with GLU 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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805C ILE 4.7 0.2 - - - +
807C PRO* 5.6 0.2 - - - +
815C ARG* 3.2 22.3 - - + +
816C SER* 2.8 39.3 + - - +
818C ILE* 1.3 76.1 - - - +
820C ASP* 1.3 63.7 + - - +
822C LEU* 3.0 10.2 + - - +
823C PHE* 3.0 30.2 + - + -
871C ALA* 4.5 4.7 - - - +
874C THR* 3.2 23.0 + - - +
1054C GLN* 3.1 26.6 + - + +
1055C SER* 3.3 37.5 + - - +
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Residues in contact with ASP 820 (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 LYS* 3.2 42.8 + - - +
815C ARG* 3.0 35.6 + - - +
816C SER 3.1 13.2 + - - +
817C PHE* 3.6 9.4 - - + +
819C GLU* 1.3 74.7 - - - +
821C LEU* 1.3 63.3 + - - +
823C PHE* 3.3 7.2 + - - +
824C ASN* 3.2 31.0 + - - +
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Residues in contact with LEU 821 (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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817C PHE* 3.1 21.4 + - + +
818C ILE* 3.0 12.7 + - - +
820C ASP* 1.3 78.1 - - - +
822C LEU* 1.3 63.0 + - + +
824C ASN* 3.2 21.1 + - + +
825C LYS* 3.2 21.0 + - + +
935C GLN* 3.2 38.8 - - + +
938C LEU* 3.6 28.3 - - + -
939C SER* 3.5 24.5 - - - +
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Residues in contact with LEU 822 (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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818C ILE* 2.9 32.8 + - + +
819C GLU* 3.0 10.7 + - - +
821C LEU* 1.3 76.4 - - - +
823C PHE* 1.3 62.8 + - + +
825C LYS* 3.1 19.8 + - + +
826C VAL* 4.0 4.3 + - - +
938C LEU* 3.6 30.3 - - + -
945C LEU* 3.5 40.1 - - + +
1054C GLN* 4.3 4.7 - - + -
1055C SER 3.2 26.7 - - - +
1056C ALA* 5.2 4.9 - - - -
1057C PRO* 5.5 2.4 - - + +
1061C VAL* 4.0 22.9 - - + -
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Residues in contact with PHE 823 (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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815C ARG* 3.1 39.3 - - - +
819C GLU* 3.0 26.1 + - + -
820C ASP* 3.3 6.5 + - - +
822C LEU* 1.3 78.0 - - + +
824C ASN* 1.3 64.4 + - - +
825C LYS 3.1 1.1 + - - -
826C VAL* 3.4 25.9 + - + +
828C LEU* 5.4 4.7 - - + -
867C ASP* 3.4 33.9 - - + -
871C ALA* 6.3 0.2 - - + -
1055C SER* 3.9 19.5 - - - -
1056C ALA* 3.8 9.0 - - - -
1057C PRO* 3.5 42.2 - - + -
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Residues in contact with ASN 824 (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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820C ASP* 3.2 19.5 + - - +
821C LEU* 3.5 19.0 - - + +
822C LEU 3.2 1.0 - - - -
823C PHE* 1.3 77.5 - - - +
825C LYS* 1.3 63.6 + - + +
826C VAL 3.4 3.8 + - - +
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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