Contacts of the helix formed by residues 976 - 991 (chain B) in PDB entry 1VDV
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 976 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972B LEU 3.1 1.9 + - - -
973B LYS* 3.0 20.4 + - - +
974B SER 4.4 5.2 - - - +
975B SER* 1.3 79.9 - - - +
977B TYR* 1.3 64.9 + - - +
978B TYR 3.3 2.7 - - - -
979B ALA* 3.1 19.5 + - + +
980B ARG* 3.0 27.4 + - + +
1175B ARG* 4.8 12.4 - - - +
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Residues in contact with TYR 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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938B ALA* 5.4 2.6 - - - +
939B GLU* 2.9 46.5 + - + +
972B LEU* 3.1 37.9 + - + +
975B SER* 3.0 12.7 - - - +
976B GLN* 1.3 75.8 - - - +
978B TYR* 1.3 72.0 + + + +
980B ARG* 3.4 4.4 + - - +
981B LYS* 3.0 42.8 + - + +
998B LEU* 3.7 30.4 + - + +
999B CYS* 4.7 2.0 - - - -
1000B ILE* 3.8 31.3 + - + +
1159B CYS* 3.9 19.3 - - - -
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Residues in contact with TYR 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B GLU* 3.4 35.5 - - - +
972B LEU* 4.1 29.6 - - + +
976B GLN 3.2 1.2 + - - -
977B TYR* 1.3 91.8 - + + +
979B ALA* 1.3 67.6 + - - +
981B LYS* 3.2 26.4 + - - +
982B SER* 3.5 13.0 + - - -
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Residues in contact with ALA 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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976B GLN* 3.1 24.4 + - + +
978B TYR* 1.3 77.5 - - - +
980B ARG* 1.3 63.0 + - + +
982B SER* 3.3 20.7 + - - -
983B GLU* 3.4 6.1 + - - +
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Residues in contact with ARG 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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975B SER* 2.8 35.7 + - - +
976B GLN* 3.0 21.5 + - + +
977B TYR* 3.9 3.8 - - - +
979B ALA* 1.3 75.1 - - + +
981B LYS* 1.3 61.0 + - - +
982B SER 3.0 2.2 - - - -
983B GLU* 3.0 18.2 + - + +
984B VAL* 2.8 32.3 + - + +
998B LEU* 4.1 15.4 - - + +
1159B CYS* 3.9 12.5 + - - -
1160B SER 5.3 0.2 - - - -
1161B GLU* 3.0 42.4 + - - +
1175B ARG* 3.5 35.1 + - - +
1177B ASP* 3.2 21.0 + - - -
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Residues in contact with LYS 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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937B PRO* 4.3 12.5 - - - +
939B GLU* 2.9 29.2 + - - +
977B TYR* 3.0 34.1 + - + +
978B TYR* 3.2 22.7 + - - +
980B ARG* 1.3 75.6 - - - +
982B SER* 1.3 60.0 + - - +
984B VAL* 3.5 4.6 + - + +
985B ASP* 3.0 40.6 + - - +
998B LEU* 3.8 15.0 - - + +
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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 TYR 3.5 8.9 + - - -
979B ALA* 3.3 12.4 + - - -
980B ARG 3.0 0.4 - - - -
981B LYS* 1.3 77.8 - - - +
983B GLU* 1.3 63.9 + - - +
985B ASP* 3.4 7.7 + - - +
986B LYS* 3.1 23.6 + - - +
989B LYS* 5.2 0.5 + - - -
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Residues in contact with GLU 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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979B ALA 3.4 4.4 + - - +
980B ARG* 3.0 26.8 + - + +
982B SER* 1.3 79.0 - - - +
984B VAL* 1.3 64.2 + - - +
986B LYS* 3.2 10.3 + - - +
987B PHE* 2.9 24.3 + - + +
996B ARG* 3.3 26.5 + - - -
1161B GLU* 3.2 33.8 - - - +
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Residues in contact with VAL 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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980B ARG 2.8 20.6 + - - +
981B LYS* 3.7 7.4 - - + +
983B GLU* 1.3 80.6 - - - +
985B ASP* 1.3 67.2 + - - +
987B PHE* 3.2 6.2 + - - +
988B ASN* 3.0 29.5 + - - +
996B ARG* 3.3 33.4 - - + +
997B GLY* 4.2 4.9 - - - +
998B LEU* 4.2 20.6 - - + +
1161B GLU* 3.8 30.5 - - + +
1276B ASP* 5.0 3.8 - - - +
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Residues in contact with ASP 985 (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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981B LYS* 3.0 29.2 + - - +
982B SER* 3.8 6.9 - - - +
983B GLU 3.3 0.2 - - - -
984B VAL* 1.3 81.1 - - - +
986B LYS* 1.3 62.9 + - - +
988B ASN* 3.3 10.6 + - - +
989B LYS* 3.0 40.0 + - - +
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Residues in contact with LYS 986 (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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982B SER 3.1 14.0 + - - +
983B GLU* 3.2 12.8 + - - +
985B ASP* 1.3 76.1 - - - +
987B PHE* 1.3 63.6 + - - +
989B LYS* 3.0 28.7 + - - +
990B GLU* 2.6 57.4 + - - +
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Residues in contact with PHE 987 (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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544B SER* 5.9 0.2 - - - -
983B GLU* 2.9 16.0 + - + +
984B VAL 3.4 9.2 - - - +
986B LYS* 1.3 75.8 - - - +
988B ASN* 1.3 64.9 + - - +
990B GLU* 3.0 6.7 + - - -
991B ASN* 2.9 64.0 + - - +
994B LYS* 3.7 30.7 - - + -
995B LYS 4.1 0.4 - - - -
996B ARG* 3.4 52.5 - - + -
1163B GLU* 3.1 24.2 - - + -
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Residues in contact with ASN 988 (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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984B VAL* 3.0 27.0 + - - +
985B ASP* 3.7 10.6 + - - +
987B PHE* 1.3 77.9 - - - +
989B LYS* 1.3 61.6 + - + +
991B ASN 3.1 4.6 - - - +
995B LYS* 2.7 48.3 + - + +
996B ARG 2.7 44.7 + - - -
1280B ALA* 3.6 18.1 - - + +
1284B GLN* 4.2 1.9 + - - -
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Residues in contact with LYS 989 (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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541B THR* 4.2 10.4 - - - +
982B SER 5.2 0.2 + - - -
985B ASP* 3.0 39.8 + - - +
986B LYS* 3.0 20.0 + - - +
988B ASN* 1.3 78.0 - - - +
990B GLU* 1.3 62.8 + - + +
991B ASN 3.7 0.9 + - - -
1284B GLN* 5.6 1.7 + - - -
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Residues in contact with GLU 990 (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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540B PRO 3.8 5.5 - - - +
541B THR* 3.3 28.0 - - - +
986B LYS* 2.6 56.9 + - - +
987B PHE* 3.0 9.5 + - - +
989B LYS* 1.3 81.1 - - + +
991B ASN* 1.3 67.9 + - - +
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Residues in contact with ASN 991 (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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540B PRO 5.3 1.7 - - - +
541B THR* 3.9 3.3 - - - +
544B SER* 2.9 33.0 + - - +
987B PHE* 2.9 59.2 + - + +
988B ASN 3.1 2.2 - - - +
989B LYS 3.4 1.3 - - - -
990B GLU* 1.3 89.9 + - - +
992B CYS* 1.3 55.3 + - - +
993B TRP 3.6 0.2 - - - -
994B LYS* 3.2 19.8 - - + +
995B LYS* 2.7 35.2 + - - -
1284B GLN* 4.2 1.1 - - - -
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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