Contacts of the helix formed by residues 976 - 984 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A THR 6.0 0.2 - - - +
571A ASP* 6.1 1.1 - - - +
974B SER* 3.3 15.9 - - - +
975B SER* 1.3 80.2 + - - +
977B LEU* 1.3 64.7 + - - +
978B ASN* 3.6 20.6 - - + +
979B ASP* 3.2 27.4 + - + +
980B ILE* 3.4 15.0 + - - +
996B LEU* 4.7 0.2 - - - -
1000B ARG* 5.0 0.9 - - - +
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Residues in contact with LEU 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B ILE 4.1 6.1 - - - +
743B CYS* 3.7 22.9 - - - +
746B SER* 4.3 7.9 - - - +
748B GLU* 6.2 0.9 - - + -
749B CYS* 3.5 35.4 - - + -
975B SER 3.8 3.2 + - - -
976B VAL* 1.3 74.3 - - - +
978B ASN* 1.3 62.2 + - - +
980B ILE* 3.2 40.8 - - + +
981B LEU* 3.4 12.6 + - + +
993B ILE* 3.8 27.4 - - + -
996B LEU* 4.2 12.7 - - + +
997B ILE* 5.8 0.4 - - + -
1000B ARG* 4.7 13.3 - - - +
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Residues in contact with ASN 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A THR* 3.2 57.2 + - - +
976B VAL* 3.2 13.7 - - + +
977B LEU* 1.3 80.1 - - - +
979B ASP* 1.3 61.3 + - - +
981B LEU* 4.5 2.4 - - - +
982B SER* 3.1 28.3 + - - -
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Residues in contact with ASP 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A GLY 5.7 1.2 - - - +
974B SER* 4.6 6.5 - - - +
976B VAL* 3.2 27.7 + - + +
978B ASN* 1.3 80.4 - - - +
980B ILE* 1.3 68.0 + - - +
981B LEU 3.2 1.8 - - - -
982B SER* 3.2 13.1 + - - -
983B ARG* 3.2 37.3 + - - +
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Residues in contact with ILE 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972B ALA* 5.5 0.4 - - + -
973B ILE* 3.5 26.5 - - + -
974B SER* 3.4 30.1 - - - +
976B VAL 3.4 6.9 + - - +
977B LEU* 3.2 16.8 - - + +
979B ASP* 1.3 77.8 + - - +
981B LEU* 1.3 73.4 + - - +
983B ARG* 5.0 2.7 - - - +
984B LEU* 3.1 37.2 + - + +
989B ALA* 5.2 1.6 - - - +
992B GLN* 4.3 5.4 - - + -
993B ILE* 3.5 37.0 - - + +
996B LEU* 3.5 26.0 - - + -
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Residues in contact with LEU 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B GLU* 3.0 43.7 - - + +
977B LEU* 3.4 13.8 + - + +
978B ASN* 4.5 2.7 - - - +
979B ASP 3.2 0.6 - - - -
980B ILE* 1.3 83.1 - - - +
982B SER* 1.3 65.4 + - - +
983B ARG 3.0 2.1 + - - -
984B LEU 3.2 18.4 - - - +
986B PRO* 5.3 8.3 - - + -
989B ALA* 4.0 17.5 - - + -
993B ILE* 4.0 24.9 - - + -
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Residues in contact with SER 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978B ASN* 3.1 25.3 + - - -
979B ASP* 3.2 9.0 + - - -
981B LEU* 1.3 79.9 - - - +
983B ARG* 1.3 58.4 + - - +
984B LEU 3.8 0.2 - - - -
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Residues in contact with ARG 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973B ILE* 3.2 45.2 + - - +
974B SER* 4.9 7.7 - - - -
979B ASP* 3.2 31.1 + - - +
980B ILE* 5.5 1.1 - - - +
981B LEU 3.1 0.6 - - - -
982B SER* 1.3 79.0 - - - +
984B LEU* 1.3 80.8 + - + +
985B ASP 4.5 0.2 + - - -
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Residues in contact with LEU 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973B ILE* 4.1 27.1 - - + -
980B ILE* 3.1 27.6 - - + +
981B LEU* 3.2 15.4 + - - +
983B ARG* 1.3 105.4 - - + +
985B ASP* 1.3 61.7 + - - +
986B PRO* 3.7 2.3 - - - +
988B GLU* 3.0 39.9 - - - +
989B ALA* 3.8 14.7 - - + +
992B GLN* 4.5 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