Contacts of the helix formed by residues 976 - 991 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972A LEU 3.1 4.8 + - - -
973A LYS* 3.1 16.2 + - - +
974A SER 4.4 4.3 - - - +
975A SER* 1.3 80.6 - - - +
977A TYR* 1.3 65.4 + - - +
978A TYR 3.4 2.2 - - - -
979A ALA* 3.2 18.3 + - + +
980A ARG* 3.0 25.9 + - + +
1175A ARG* 4.5 12.6 + - - -
1240A ARG* 5.7 1.0 + - - -
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Residues in contact with TYR 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A ALA* 5.3 3.3 - - - +
939A GLU* 2.7 44.3 + - + +
972A LEU* 3.2 33.8 + - + +
975A SER* 3.1 15.8 - - - +
976A GLN* 1.3 75.5 - - - +
978A TYR* 1.3 71.0 + + + +
980A ARG* 3.3 3.0 + - - +
981A LYS* 2.8 52.6 + - + +
998A LEU* 3.5 38.5 + - + +
999A CYS* 4.6 1.6 - - - -
1000A ILE* 3.9 29.6 + - + +
1159A CYS* 3.7 15.3 - - - -
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Residues in contact with TYR 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A GLU* 3.8 28.6 - - - +
972A LEU* 4.0 34.9 - - + +
976A GLN 3.4 0.8 - - - -
977A TYR* 1.3 89.2 - + + +
979A ALA* 1.3 64.1 + - - +
981A LYS* 3.1 35.6 + - - +
982A SER* 3.4 10.2 + - - -
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Residues in contact with ALA 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976A GLN* 3.2 24.2 + - + +
978A TYR* 1.3 78.6 - - - +
980A ARG* 1.3 63.4 + - + +
982A SER* 3.3 20.8 + - - -
983A GLU* 3.4 5.7 + - - +
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Residues in contact with ARG 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A SER* 2.7 46.4 + - - +
976A GLN* 3.0 19.2 + - + +
977A TYR* 3.9 4.1 - - - +
979A ALA* 1.3 73.5 - - + +
981A LYS* 1.3 59.6 + - - +
982A SER 3.0 2.2 - - - -
983A GLU* 3.1 14.3 + - + +
984A VAL* 2.9 32.7 + - - +
998A LEU* 4.1 11.7 - - + +
1159A CYS* 3.9 15.0 + - - -
1161A GLU* 2.9 41.2 + - - +
1175A ARG* 3.5 36.3 + - - +
1177A ASP* 3.4 10.3 + - - -
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Residues in contact with LYS 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937A PRO* 4.6 8.9 - - - +
939A GLU* 3.1 29.6 + - - +
977A TYR* 2.8 31.7 + - + +
978A TYR* 3.1 31.7 + - - +
980A ARG* 1.3 77.0 - - - +
982A SER* 1.3 60.3 + - - +
984A VAL* 3.7 5.5 + - + +
985A ASP* 2.9 35.5 + - - +
998A LEU* 3.8 14.8 - - + +
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Residues in contact with SER 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A TYR 3.4 10.1 + - - -
979A ALA* 3.3 11.0 + - - -
980A ARG 3.0 0.2 - - - -
981A LYS* 1.3 77.8 - - - +
983A GLU* 1.3 66.2 + - - +
984A VAL 3.2 0.2 - - - -
985A ASP* 3.3 9.5 + - - +
986A LYS* 3.1 23.1 + - - +
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Residues in contact with GLU 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979A ALA 3.4 4.4 + - - +
980A ARG* 3.1 22.4 + - + +
982A SER* 1.3 79.7 - - - +
984A VAL* 1.3 65.6 + - - +
986A LYS* 3.3 9.5 + - + +
987A PHE* 2.9 31.9 + - - +
996A ARG* 3.3 26.1 + - - -
1161A GLU* 3.1 26.3 - - - +
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Residues in contact with VAL 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980A ARG 2.9 20.2 + - - +
981A LYS* 3.8 7.2 - - + +
983A GLU* 1.3 81.2 - - - +
985A ASP* 1.3 66.6 + - - +
987A PHE* 3.2 5.5 + - - +
988A ASN* 3.0 28.6 + - - +
996A ARG* 3.3 33.9 - - + +
997A GLY* 4.3 4.9 - - - +
998A LEU* 4.2 20.4 - - + +
1161A GLU* 3.9 30.1 - - + +
1276A ASP* 4.9 4.0 - - - +
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Residues in contact with ASP 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A LYS* 2.9 23.8 + - - +
982A SER* 3.3 10.3 + - - +
984A VAL* 1.3 80.7 - - - +
986A LYS* 1.3 63.8 + - - +
988A ASN* 3.2 10.8 + - - +
989A LYS* 3.1 42.9 + - - +
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Residues in contact with LYS 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982A SER 3.1 13.2 + - - +
983A GLU* 3.6 11.2 - - + +
985A ASP* 1.3 78.0 - - - +
987A PHE* 1.3 62.8 + - - +
989A LYS* 3.0 14.2 + - + +
990A GLU* 3.0 56.8 + - + +
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Residues in contact with PHE 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A SER* 5.9 0.4 - - - -
983A GLU* 2.9 22.1 + - - +
984A VAL 3.5 7.9 - - - +
986A LYS* 1.3 76.2 - - - +
988A ASN* 1.3 66.0 + - - +
990A GLU* 3.2 7.8 + - - -
991A ASN* 2.8 64.8 + - - +
994A LYS* 3.7 31.4 - - + -
995A LYS 4.1 0.4 - - - -
996A ARG* 3.4 48.0 - - + -
1163A GLU* 3.2 23.6 - - + -
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Residues in contact with ASN 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984A VAL* 3.0 21.1 + - - +
985A ASP* 3.6 12.1 + - - +
986A LYS 3.2 0.2 - - - -
987A PHE* 1.3 79.8 - - - +
989A LYS* 1.3 60.6 + - + +
991A ASN 3.1 6.2 - - - +
995A LYS* 2.7 47.9 + - + +
996A ARG 2.8 43.7 + - - -
1280A ALA* 3.6 16.8 - - + +
1284A GLN* 4.2 1.9 + - - -
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Residues in contact with LYS 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A THR* 3.9 11.6 - - - +
985A ASP* 3.1 35.8 + - - +
986A LYS* 3.0 13.1 + - + +
988A ASN* 1.3 78.2 - - + +
990A GLU* 1.3 64.9 + - + +
991A ASN 3.6 1.2 + - - -
1284A GLN* 5.5 2.1 + - - -
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Residues in contact with GLU 990 (chain A).
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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540A PRO 4.0 4.5 - - - +
541A THR* 3.4 26.0 - - - +
986A LYS* 3.0 50.1 + - + +
987A PHE* 3.2 7.7 + - - +
989A LYS* 1.3 82.1 - - + +
991A ASN* 1.3 68.8 + - - +
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Residues in contact with ASN 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A PRO 5.6 1.0 - - - +
541A THR* 3.9 3.1 - - - -
544A SER* 3.0 31.1 + - - +
987A PHE* 2.8 58.1 + - + +
988A ASN 3.1 1.7 - - - +
989A LYS 3.3 1.4 - - - -
990A GLU* 1.3 92.0 + - - +
992A CYS* 1.3 54.5 + - - +
993A TRP 3.6 0.2 - - - -
994A LYS* 3.3 19.9 - - + +
995A LYS* 2.7 35.2 + - - -
1284A GLN* 3.6 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