Contacts of the helix formed by residues 972 - 982 (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 GLN 972 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LYS* 4.8 9.0 - - - +
590C HIS* 6.2 0.9 - - - -
949C LYS* 4.3 24.9 + - - +
970C GLY 3.8 9.0 + - - +
971C ALA* 1.3 78.6 - - - +
973C GLU* 1.3 68.4 + - - +
974C GLY 3.3 3.1 - - - +
975C GLU* 3.0 30.7 + - + +
976C LEU* 3.0 25.4 + - - +
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Residues in contact with GLU 973 (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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590C HIS* 6.1 3.1 - - + -
923C LEU* 6.2 1.6 - - - -
972C GLN* 1.3 73.8 - - - +
974C GLY* 1.3 66.0 + - - +
976C LEU* 3.0 14.3 + - - +
977C ALA* 3.2 12.5 + - - +
732D MET* 3.9 24.7 - - + +
736D LEU* 6.4 2.5 - - + -
737D VAL* 6.6 0.4 - - + -
840D ARG 5.2 9.6 - - - +
841D GLU* 6.4 0.9 - - - -
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Residues in contact with GLY 974 (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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946C TRP* 3.9 21.8 - - - +
972C GLN* 3.3 2.4 - - - +
973C GLU* 1.3 79.0 - - - +
975C GLU* 1.3 63.2 + - - +
977C ALA* 3.4 6.0 + - - +
978C GLY 3.2 16.1 + - - -
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Residues in contact with GLU 975 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 3.8 9.8 - - + -
34C LYS* 3.0 39.3 + - - -
946C TRP* 3.7 28.2 + - + +
949C LYS* 3.9 12.0 - - + +
950C LEU* 3.7 29.0 - - + +
971C ALA* 3.6 4.0 - - - -
972C GLN* 3.0 36.2 + - + +
974C GLY* 1.3 76.2 - - - +
976C LEU* 1.3 65.3 + - + +
978C GLY* 3.3 2.4 + - - -
979C LEU* 3.0 25.0 + - - +
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Residues in contact with LEU 976 (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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587C PHE* 4.7 9.0 - - + -
923C LEU* 4.6 13.2 - - + +
926C HIS* 4.7 3.6 - - + -
927C LEU* 4.1 35.0 - - + +
930C VAL* 5.3 2.5 - - + -
971C ALA* 3.5 29.4 - - + -
972C GLN 3.0 25.9 + - - +
973C GLU* 3.2 10.3 - - - +
975C GLU* 1.3 75.4 - - - +
977C ALA* 1.3 57.7 + - - +
979C LEU* 2.7 33.2 + - + +
980C LEU* 2.8 27.3 + - + +
732D MET* 3.8 21.1 - - + -
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Residues in contact with ALA 977 (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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973C GLU 3.2 7.2 + - - +
974C GLY* 4.0 8.1 - - - +
976C LEU* 1.3 77.2 - - - +
978C GLY* 1.3 61.8 + - - +
980C LEU* 3.1 16.0 + - - +
981C GLY* 3.0 18.9 + - - -
995C ALA* 4.9 7.4 - - + +
732D MET* 4.7 7.5 - - + -
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Residues in contact with GLY 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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937C ILE* 5.5 3.3 - - - +
946C TRP* 3.3 47.2 - - - -
974C GLY 3.2 8.3 + - - -
975C GLU 3.7 0.4 - - - -
976C LEU 3.0 1.4 - - - -
977C ALA* 1.3 78.1 - - - +
979C LEU* 1.3 61.8 + - - +
981C GLY* 3.0 12.4 + - - -
982C SER* 3.3 11.3 + - - -
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Residues in contact with LEU 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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32C PHE* 3.7 33.7 - - + -
927C LEU* 4.8 8.3 - - + -
930C VAL* 3.7 31.5 - - + +
935C TRP* 3.3 43.6 - - + +
937C ILE* 5.9 5.2 - - + -
946C TRP* 4.7 1.3 - - - +
950C LEU* 5.4 8.7 - - + -
954C LEU* 4.4 2.7 - - + +
975C GLU* 3.0 17.6 + - + +
976C LEU* 2.7 18.4 + - + +
978C GLY* 1.3 69.2 - - - -
980C LEU* 1.3 59.7 + - - +
982C SER* 2.6 32.7 + - - +
983C THR* 4.1 0.9 + - - -
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Residues in contact with LEU 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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926C HIS* 4.3 22.0 - - + +
929C TRP* 5.3 5.2 - - + -
930C VAL* 4.4 15.0 - - + -
976C LEU* 2.8 54.4 + - + +
977C ALA* 3.1 13.9 + - - +
979C LEU* 1.3 78.0 - - - +
981C GLY* 1.3 60.2 + - - +
982C SER 3.3 0.2 + - - -
983C THR* 3.4 14.8 + - - -
993C VAL* 5.0 5.8 - - + +
994C ASP 4.1 14.3 - - - +
995C ALA* 3.5 26.6 - - - +
996C ASP 5.3 0.4 - - - -
997C GLY* 4.3 23.8 - - - +
732D MET* 4.8 5.6 - - - -
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Residues in contact with GLY 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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977C ALA 3.0 12.7 + - - -
978C GLY 3.0 6.5 + - - -
980C LEU* 1.3 78.9 - - - +
982C SER* 1.3 56.9 + - - +
983C THR* 3.6 3.8 + - - -
995C ALA* 4.6 12.3 - - - +
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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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930C VAL* 5.2 0.5 - - - +
934C GLY 3.7 1.6 - - - +
935C TRP* 3.0 17.5 - - - +
936C ASN* 2.1 57.8 + - - +
937C ILE* 4.2 6.5 - - - -
978C GLY 3.3 8.4 + - - -
979C LEU* 2.6 23.2 + - - +
981C GLY* 1.3 73.2 - - - +
983C THR* 1.3 64.0 + - - +
984C LEU* 4.8 0.7 - - - +
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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