Contacts of the helix formed by residues 976 - 983 (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 VAL 976 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571B ASP* 3.3 29.0 + - + +
974C SER* 3.9 12.9 + - - -
975C SER* 1.3 76.7 - - - +
977C LEU* 1.3 65.1 + - - +
978C ASN* 3.7 19.7 - - + +
979C ASP* 3.1 41.4 + - + +
980C ILE* 3.4 13.5 + - - +
1000C ARG* 4.8 1.3 - - - +
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Residues in contact with LEU 977 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742C ILE 4.0 4.5 - - - +
743C CYS* 3.3 38.1 - - - +
746C SER* 3.7 24.0 - - - +
749C CYS* 3.8 11.0 - - + -
975C SER 3.5 5.4 + - - -
976C VAL* 1.3 72.2 - - - +
978C ASN* 1.3 66.9 + - - +
980C ILE* 3.1 28.5 - - + +
981C LEU* 3.1 13.4 + - + +
993C ILE* 4.2 30.1 - - + -
996C LEU* 4.7 10.5 - - + -
1000C ARG* 4.3 16.3 - - - +
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Residues in contact with ASN 978 (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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547B THR* 3.6 33.1 + - + +
548B GLY* 4.0 13.7 - - - -
743C CYS 5.6 0.9 - - - +
744C GLY 5.3 5.0 - - - +
746C SER* 5.5 4.3 - - - -
976C VAL* 3.2 12.4 - - + +
977C LEU* 1.3 83.9 - - - +
979C ASP* 1.3 60.0 + - - +
981C LEU* 4.4 6.5 - - - +
982C SER* 3.0 28.4 + - - -
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Residues in contact with ASP 979 (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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517B LEU* 6.6 0.2 - - - -
518B LEU* 4.7 14.7 - - - +
545B GLY 4.2 15.3 - - - +
546B LEU* 4.9 6.1 - - - +
547B THR* 5.1 4.5 + - - +
974C SER* 4.2 6.1 - - - +
976C VAL* 3.1 36.6 + - + +
978C ASN* 1.3 80.1 - - - +
980C ILE* 1.3 68.9 + - - +
982C SER* 3.2 4.6 + - - -
983C ARG* 3.1 37.2 + - - +
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Residues in contact with ILE 980 (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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972C ALA* 6.0 0.7 - - + -
973C ILE* 3.4 26.0 - - + -
974C SER* 3.8 13.9 + - - +
976C VAL 3.4 11.7 + - - +
977C LEU* 3.1 36.6 - - + +
979C ASP* 1.3 75.9 - - - +
981C LEU* 1.3 63.1 + - - +
982C SER 3.3 0.2 + - - -
983C ARG* 3.5 6.0 + - - +
984C LEU* 3.4 42.9 - - + +
989C ALA* 4.9 3.1 - - + +
992C GLN* 3.5 32.1 - - + -
993C ILE* 4.4 12.1 - - + -
996C LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 981 (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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386B LYS* 3.8 6.3 + - - +
746C SER* 3.3 29.2 - - - +
748C GLU* 3.9 35.4 - - + +
977C LEU* 3.1 18.5 + - + +
978C ASN* 4.4 5.8 - - - +
980C ILE* 1.3 84.9 - - - +
982C SER* 1.3 66.0 + - - +
983C ARG 3.6 0.2 + - - -
984C LEU 3.6 13.4 - - - +
986C PRO* 5.8 4.3 - - + -
989C ALA* 4.8 8.5 - - + -
993C ILE* 3.8 27.1 - - + -
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Residues in contact with SER 982 (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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386B LYS* 3.1 29.4 + - - +
389B ASP* 5.8 1.4 + - - +
390B LEU* 4.8 8.6 - - - +
542B ASN* 5.1 5.5 + - - -
547B THR* 4.2 18.9 - - - +
978C ASN 3.0 23.3 + - - -
979C ASP* 3.2 6.5 + - - -
981C LEU* 1.3 80.2 - - - +
983C ARG* 1.3 58.3 + - - +
984C LEU 3.3 0.2 - - - -
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Residues in contact with ARG 983 (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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381B GLY 3.4 20.4 + - - +
382B VAL* 3.9 7.2 - - - +
383B SER* 3.3 22.2 + - - -
386B LYS* 4.7 0.9 - - - -
390B LEU* 3.5 41.3 - - + +
392B PHE* 6.3 0.7 - - - -
429B PHE* 5.9 5.1 - - - +
517B LEU* 3.7 33.9 - - - +
973C ILE* 3.3 50.9 + - - +
974C SER* 4.2 10.7 + - - -
979C ASP* 3.1 23.9 + - - +
980C ILE* 4.3 2.9 - - - +
982C SER* 1.3 76.4 - - - +
984C LEU* 1.3 65.6 + - + +
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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