Contacts of the helix formed by residues 816 - 824 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A GLN 4.3 0.7 - - - -
805A ILE 3.1 26.9 - - - -
806A LEU 3.6 12.3 - - - -
807A PRO* 3.7 12.2 - - - +
808A ASP 4.7 0.2 - - - +
811A LYS* 5.4 0.7 - - - -
815A ARG* 1.3 77.9 - - - +
817A PHE* 1.3 65.7 + - - +
818A ILE 3.7 1.8 + - - -
819A GLU* 2.7 39.0 + - - -
820A ASP* 2.9 22.2 + - - +
1054A GLN* 3.2 9.5 + - - -
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Residues in contact with PHE 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A SER 5.2 1.8 - - - +
804A GLN* 4.5 21.9 + - + +
806A LEU 4.5 3.4 + - - -
808A ASP* 5.6 2.4 - - - +
811A LYS* 4.4 22.9 - - - +
815A ARG 4.0 0.2 + - - -
816A SER* 1.3 73.5 - - - +
818A ILE* 1.3 63.0 + - + +
820A ASP* 3.2 8.4 + - + +
821A LEU* 2.9 38.8 + - + +
935A GLN* 3.0 44.0 - - + -
2E NAG 6.1 5.4 - - + -
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Residues in contact with ILE 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A GLN* 2.8 40.8 + - + +
805A ILE* 4.2 3.1 - - + -
816A SER 3.3 0.4 - - - -
817A PHE* 1.3 81.7 - - + +
819A GLU* 1.3 52.8 + - - +
821A LEU* 3.1 9.8 + - + +
822A LEU* 2.7 52.3 + - + +
931A ILE* 4.6 10.5 - - + +
934A ILE* 4.9 10.3 - - + -
935A GLN* 5.2 9.9 - - - +
938A LEU* 4.7 13.9 - - + -
1054A GLN* 3.5 22.9 - - + +
1061A VAL* 6.3 0.2 - - + -
1063A LEU* 4.1 22.9 - - + -
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Residues in contact with GLU 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805A ILE 3.8 1.9 - - - +
807A PRO* 5.4 2.4 - - - +
815A ARG* 4.1 10.3 - - + -
816A SER* 2.7 40.4 + - - +
818A ILE* 1.3 76.4 - - - +
820A ASP* 1.3 62.9 + - - +
822A LEU* 3.1 9.3 + - - +
823A PHE* 3.0 31.6 + - + -
871A ALA* 3.6 27.9 - - - +
874A THR* 3.7 10.8 + - - -
875A SER* 5.5 1.9 + - - -
878A LEU* 5.2 0.7 - - - +
1054A GLN* 3.3 19.7 + - + +
1055A SER* 3.5 36.3 - - - +
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Residues in contact with ASP 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A LYS* 3.1 43.9 - - - +
815A ARG* 2.8 43.0 + - - +
816A SER 2.9 13.8 + - - +
817A PHE* 3.5 9.6 - - + +
819A GLU* 1.3 76.0 - - - +
821A LEU* 1.3 63.5 + - - +
823A PHE* 3.4 4.3 + - - +
824A ASN* 3.3 32.5 + - - +
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Residues in contact with LEU 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A PHE* 2.9 33.6 + - + +
818A ILE* 3.4 11.4 - - + +
820A ASP* 1.3 75.8 - - - +
822A LEU* 1.3 66.1 + - + +
824A ASN* 3.4 8.2 + - - +
825A LYS* 3.3 22.2 + - + +
934A ILE 5.6 0.2 - - - +
935A GLN* 3.4 27.4 - - + +
938A LEU* 3.5 43.1 - - + +
939A SER* 3.8 17.0 - - - +
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Residues in contact with LEU 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818A ILE* 2.7 38.6 + - + +
819A GLU* 3.1 11.2 + - - +
821A LEU* 1.3 73.6 - - + +
823A PHE* 1.3 67.3 + - + +
825A LYS* 3.0 20.7 + - + +
826A VAL* 4.0 2.6 + - - +
938A LEU* 4.3 17.9 - - + -
945A LEU* 3.6 44.6 - - + +
1054A GLN* 4.1 12.3 - - + -
1055A SER 3.3 25.6 - - - +
1056A ALA* 5.4 4.3 - - + -
1057A PRO* 5.2 1.7 - - - +
1061A VAL* 4.0 19.3 - - + -
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Residues in contact with PHE 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A ARG* 3.2 46.9 - - - +
819A GLU* 3.0 28.5 + - - +
820A ASP 3.4 4.9 + - - +
822A LEU* 1.3 77.3 - - - +
824A ASN* 1.3 66.0 + - - +
825A LYS 3.2 1.4 + - - -
826A VAL* 3.3 21.5 + - - +
828A LEU* 5.3 4.1 - - + +
867A ASP* 3.5 39.7 - - + -
1055A SER* 3.9 21.8 - - - -
1056A ALA* 3.9 10.1 - - - -
1057A PRO* 3.9 37.0 - - + -
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Residues in contact with ASN 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A ASP* 3.3 20.7 + - - +
821A LEU* 3.9 6.6 - - - +
822A LEU 3.2 1.0 - - - -
823A PHE* 1.3 79.8 - - - +
825A LYS* 1.3 61.2 + - - +
826A VAL 3.4 4.8 - - - +
827A THR* 5.8 0.9 - - - +
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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