Contacts of the helix formed by residues 963 - 975 (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 SER 963 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961B GLY 3.1 7.5 + - - -
962B PHE* 1.3 70.5 - - - +
964B VAL* 1.3 65.8 + - - +
965B PRO* 3.2 4.0 - - - -
966B ARG* 2.9 22.6 + - - +
967B CYS* 3.1 11.7 + - - -
1155B TYR* 3.3 12.3 - - - +
1181B ASP* 2.7 35.8 + - - +
1244B LEU* 3.8 19.3 - - - -
1247B CYS* 5.7 2.2 - - - -
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Residues in contact with VAL 964 (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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888B CYS* 3.8 13.0 - - - -
946B MET* 3.6 32.1 - - + -
962B PHE* 3.4 19.7 - - + -
963B SER* 1.3 77.4 + - - +
965B PRO* 1.3 64.1 - - + +
967B CYS* 3.1 8.1 + - - +
968B TRP* 2.7 28.9 + - + +
1002B PRO* 4.0 17.3 - - + -
1003B THR 4.2 2.0 - - - +
1155B TYR* 3.3 36.8 - - + -
1156B GLY 5.3 0.9 - - - +
1157B VAL* 4.5 5.6 - - + -
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Residues in contact with PRO 965 (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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943B TRP* 4.1 26.2 - - + -
946B MET* 4.5 7.6 - - - -
947B TYR 4.9 3.8 - - - +
948B LYS* 6.0 1.3 - - - -
949B GLU 6.2 0.2 - - - +
962B PHE* 3.6 30.1 - - + +
963B SER 3.3 4.3 - - - -
964B VAL* 1.3 95.5 - - + +
966B ARG* 1.3 58.3 + - + +
968B TRP* 3.4 2.6 - - + +
969B ASP* 2.9 38.1 + - - +
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Residues in contact with ARG 966 (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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963B SER* 2.9 14.6 + - - +
965B PRO* 1.3 76.8 - - + +
967B CYS* 1.3 67.2 + - - +
969B ASP* 3.3 4.5 + - - +
970B GLU* 2.9 31.5 + - - +
1244B LEU* 3.6 34.2 - - + +
1245B ARG* 3.0 35.5 + - - +
1246B ASP* 3.2 17.2 + - - +
1247B CYS* 4.2 3.4 - - - +
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Residues in contact with CYS 967 (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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963B SER* 3.1 17.3 + - - -
964B VAL* 3.6 5.4 - - - +
966B ARG* 1.3 78.2 - - - +
968B TRP* 1.3 57.1 + - - +
971B CYS* 2.9 32.7 + - - +
1155B TYR 4.5 0.4 - - - -
1156B GLY* 4.4 7.2 - - - -
1157B VAL* 3.6 20.4 - - + +
1179B VAL* 3.8 35.4 - - + +
1181B ASP* 4.0 29.4 - - - -
1244B LEU* 4.0 10.5 - - - +
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Residues in contact with TRP 968 (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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939B GLU* 3.6 33.1 + - + +
942B ARG* 4.1 18.4 - - + -
943B TRP* 3.5 38.7 - + + +
946B MET* 3.9 14.1 - - + -
964B VAL* 2.7 19.2 + - + +
965B PRO* 3.4 8.1 - - + +
967B CYS* 1.3 75.1 - - - +
969B ASP* 1.3 70.1 + - - +
971B CYS* 3.3 2.3 + - - +
972B LEU* 2.9 52.9 + - + +
1000B ILE* 3.8 34.0 - - + +
1002B PRO* 3.8 32.5 - - + -
1157B VAL* 3.6 23.1 - - + +
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Residues in contact with ASP 969 (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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943B TRP* 4.5 13.6 - - - -
965B PRO* 2.9 26.8 + - - +
966B ARG* 4.0 4.2 - - - +
968B TRP* 1.3 84.8 - - - +
970B GLU* 1.3 65.6 + - - +
972B LEU* 3.1 13.3 + - - +
973B LYS* 3.0 24.4 + - - +
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Residues in contact with GLU 970 (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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559B LEU* 5.6 3.1 - - - +
966B ARG* 2.9 19.3 + - - +
967B CYS 4.1 2.2 - - - +
969B ASP* 1.3 77.5 - - - +
971B CYS* 1.3 57.6 + - - +
973B LYS* 3.2 10.2 + - + +
974B SER* 2.8 36.6 + - - +
1179B VAL* 3.8 17.3 - - + -
1242B SER* 4.0 19.4 + - - -
1243B LEU 5.4 2.4 - - - +
1244B LEU* 3.3 27.6 - - - +
1245B ARG* 5.2 3.1 + - - +
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Residues in contact with CYS 971 (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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967B CYS 2.9 21.8 + - - +
968B TRP 3.8 2.9 - - - +
970B GLU* 1.3 74.3 - - - +
972B LEU* 1.3 58.9 + - - +
974B SER* 3.4 6.7 + - - -
975B SER* 2.7 38.7 + - - -
1000B ILE* 4.1 2.0 - - + -
1157B VAL* 3.8 23.1 - - + -
1159B CYS* 3.9 22.4 - - - -
1177B ASP* 3.6 31.4 - - - -
1179B VAL* 3.5 12.3 - - + +
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Residues in contact with LEU 972 (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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939B GLU* 5.0 2.7 - - + -
968B TRP* 2.9 46.5 + - + +
969B ASP* 3.4 14.6 - - - +
971B CYS* 1.3 76.1 - - - +
973B LYS* 1.3 62.3 + - - +
975B SER* 3.9 3.1 - - - -
976B GLN* 3.1 2.9 + - - -
977B TYR* 3.1 58.2 + - + +
978B TYR* 4.1 28.5 - - + +
1000B ILE* 3.6 26.4 - - + +
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Residues in contact with LYS 973 (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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969B ASP 3.0 12.4 + - - +
970B GLU* 3.6 12.1 - - + +
972B LEU* 1.3 75.1 - - - +
974B SER* 1.3 69.0 + - - +
976B GLN* 3.0 20.5 + - - +
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Residues in contact with SER 974 (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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559B LEU* 6.2 3.8 - - - -
970B GLU* 2.8 29.7 + - - +
971B CYS* 3.4 10.4 + - - -
973B LYS* 1.3 77.8 - - - +
975B SER* 1.3 60.5 + - - +
976B GLN* 3.6 4.9 + - - +
1175B ARG* 3.1 16.9 + - - -
1177B ASP* 3.8 8.5 + - - +
1179B VAL* 4.5 6.6 - - - +
1240B ARG* 4.0 12.9 + - - +
1242B SER* 5.4 5.1 + - - -
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Residues in contact with SER 975 (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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971B CYS 2.7 24.6 + - - -
972B LEU* 3.3 5.9 + - - -
974B SER* 1.3 76.9 + - - +
976B GLN* 1.3 67.0 + - - +
977B TYR* 3.4 13.9 + - - +
980B ARG* 2.8 42.2 + - - -
1159B CYS* 3.9 12.3 - - - +
1175B ARG* 3.7 4.4 - - - +
1177B ASP* 3.4 26.2 - - - -
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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