Contacts of the helix formed by residues 974 - 985 (chain C) in PDB entry 3H2V
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 ASP 974 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972C CYS* 3.4 11.6 - - - -
973C THR* 1.3 80.5 - - - +
975C LYS* 1.3 56.3 + - - +
976C ARG* 3.1 17.1 + - - +
977C ILE* 3.0 29.5 + - + +
978C ARG* 2.6 38.0 + - - +
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Residues in contact with LYS 975 (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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973C THR 3.9 2.8 + - - -
974C ASP* 1.3 73.8 + - - +
976C ARG* 1.3 63.9 + - - +
978C ARG* 3.4 27.7 - - - +
979C THR* 2.8 39.6 + - - +
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Residues in contact with ARG 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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974C ASP* 3.1 16.6 + - - +
975C LYS* 1.3 82.1 - - - +
977C ILE* 1.3 80.2 + - - +
979C THR* 3.3 2.4 - - - -
980C ASN* 3.2 38.3 + - - +
1040C GLU* 5.8 1.0 + - - -
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Residues in contact with ILE 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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972C CYS* 4.4 3.1 - - - -
974C ASP* 3.0 28.6 + - + +
976C ARG* 1.3 100.0 - - - +
978C ARG* 1.3 60.9 + - - +
979C THR 2.8 5.6 + - - -
980C ASN* 3.3 5.0 + - - +
981C LEU* 2.9 24.6 + - - +
1040C GLU* 3.1 38.4 - - - +
1043C ALA* 4.3 11.0 - - + +
1044C ALA* 3.7 32.3 - - + +
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Residues in contact with ARG 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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969C ALA* 3.1 33.8 + - + +
970C LYS* 5.5 1.3 - - - +
972C CYS* 2.9 38.0 + - + -
973C THR* 4.2 6.9 - - - +
974C ASP 2.6 17.1 + - - +
975C LYS* 3.4 40.0 + - - +
977C ILE* 1.3 71.8 - - - +
979C THR* 1.3 61.3 + - - +
981C LEU* 4.1 5.8 - - - +
982C LEU* 3.4 37.4 + - - +
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Residues in contact with THR 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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975C LYS* 2.8 33.0 + - - +
976C ARG* 3.3 4.7 - - - -
977C ILE 2.8 0.8 - - - -
978C ARG* 1.3 78.4 + - - +
980C ASN* 1.3 78.2 + - - +
981C LEU 3.1 0.7 - - - -
982C LEU* 3.0 7.6 + - - +
983C GLN* 2.9 24.3 + - + +
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Residues in contact with ASN 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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976C ARG* 3.2 32.3 + - - +
977C ILE* 3.3 9.8 + - - +
979C THR* 1.3 82.2 - - - +
981C LEU* 1.3 64.8 + - - +
983C GLN* 3.2 20.1 + - - +
984C VAL* 3.1 28.0 + - + +
1040C GLU* 3.7 31.8 - - + +
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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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965C ALA* 3.3 37.9 - - + +
968C VAL* 3.6 26.0 - - + -
969C ALA* 3.7 12.8 - - + -
977C ILE 2.9 18.4 + - - +
978C ARG* 4.1 5.6 - - - +
980C ASN* 1.3 78.5 - - - +
982C LEU* 1.3 64.0 + - - +
984C VAL* 3.3 10.9 - - + +
985C CYS* 3.2 23.3 + - - -
1037C THR* 4.1 8.7 - - + +
1040C GLU* 4.1 13.8 + - + +
1041C ALA* 3.9 25.8 - - + +
1044C ALA* 4.1 11.2 - - + -
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Residues in contact with LEU 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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966C LYS* 3.8 37.7 - - + +
969C ALA* 3.9 21.5 - - + -
978C ARG* 3.4 25.7 + - - +
979C THR* 3.0 8.7 + - - +
981C LEU* 1.3 76.9 - - - +
983C GLN* 1.3 68.0 + - - +
985C CYS* 3.3 5.3 + - - -
986C GLU* 2.8 36.0 + - + +
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Residues in contact with GLN 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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979C THR* 2.9 16.5 + - + +
980C ASN* 3.4 22.3 + - - +
982C LEU* 1.3 81.3 - - - +
984C VAL* 1.3 80.6 + - - +
986C GLU* 2.9 24.5 + - - +
987C ARG* 3.6 21.5 + - - +
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Residues in contact with VAL 984 (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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980C ASN* 3.2 14.6 - - + +
981C LEU* 3.3 13.5 - - + +
983C GLN* 1.3 90.0 - - - +
985C CYS* 1.3 60.5 + - - +
986C GLU 3.2 1.4 + - - -
987C ARG* 3.4 42.7 + - - +
988C ILE* 3.7 13.0 - - - +
1033C SER* 4.3 4.3 - - - +
1036C GLU* 4.4 25.8 - - + +
1037C THR* 3.9 25.8 + - - +
1040C GLU* 4.8 6.7 - - + -
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Residues in contact with CYS 985 (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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962C THR* 3.3 28.8 - - + +
965C ALA* 4.1 25.6 - - + -
966C LYS* 3.2 26.9 - - - -
981C LEU* 3.2 21.5 + - + +
982C LEU* 3.8 13.5 - - - -
983C GLN 3.0 1.6 + - - -
984C VAL* 1.3 79.5 - - + +
986C GLU* 1.3 62.1 + - - +
987C ARG 3.4 0.9 - - - -
988C ILE* 3.8 12.7 + - + +
989C PRO* 3.7 3.6 - - - +
1037C THR* 3.7 15.0 - - + +
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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