Contacts of the helix formed by residues 982 - 994 (chain A) in PDB entry 2NVX
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 THR 982 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A LEU* 5.0 3.8 - - - -
915A SER* 5.6 4.0 - - - +
919A ILE* 5.1 11.2 - - + -
925A LEU* 5.8 3.4 - - + -
980A ASP 5.0 0.5 + - - -
981A LEU* 1.3 79.6 - - - +
983A ILE* 1.3 72.0 + - + +
984A LYS* 3.8 15.7 - - + +
985A ASP* 2.7 44.5 + - - +
986A ILE* 3.5 9.8 + - - +
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Residues in contact with ILE 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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901A LEU* 5.2 1.8 - - + -
908A LEU* 3.8 19.1 - - + -
913A LEU* 5.4 6.0 - - + +
919A ILE* 4.2 28.0 - - + +
925A LEU* 4.0 28.5 - - + -
928A LEU* 5.3 3.6 - - + -
929A LEU* 3.4 30.5 - - + -
982A THR* 1.3 78.2 - - - +
984A LYS* 1.3 62.4 + - - +
986A ILE* 3.8 3.2 + - + +
987A VAL* 3.3 24.0 + - + +
1028A THR* 3.8 28.9 - - + -
1032A LEU* 4.4 9.6 - - + -
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Residues in contact with LYS 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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925A LEU* 4.4 16.4 - - + +
928A LEU* 4.3 18.6 - - + -
982A THR* 3.2 10.5 - - + +
983A ILE* 1.3 77.9 - - - +
985A ASP* 1.3 68.1 + - - +
986A ILE 3.2 0.2 - - - -
987A VAL* 4.9 1.1 - - - -
988A LEU* 2.7 59.9 + - + +
989A GLY 3.7 0.2 + - - -
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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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980A ASP 4.5 2.1 - - - +
981A LEU* 3.6 21.9 - - + -
982A THR* 2.7 45.6 + - - +
984A LYS* 1.3 75.0 - - - +
986A ILE* 1.3 64.8 + - - +
989A GLY* 3.1 18.7 + - - -
1039A LYS* 3.9 30.7 + - - +
1042A PHE* 3.9 9.1 - - + -
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Residues in contact with ILE 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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932A GLU* 4.7 2.7 - - - +
981A LEU* 3.6 41.5 - - + -
982A THR 3.5 6.3 + - - +
983A ILE* 4.1 7.9 - - + +
984A LYS 3.2 0.6 - - - -
985A ASP* 1.3 75.5 - - - +
987A VAL* 1.3 60.8 - - + +
989A GLY* 2.8 17.8 + - - -
990A VAL* 3.0 25.0 + - + +
1027A ALA 5.2 0.9 - - - +
1028A THR* 3.5 33.9 - - + +
1031A VAL* 4.4 14.8 - - + -
1032A LEU* 3.6 32.5 - - + -
1042A PHE* 4.2 14.3 - - + -
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Residues in contact with VAL 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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928A LEU* 3.9 40.6 - - + +
929A LEU* 4.3 16.8 - - + -
931A GLU* 5.8 2.5 - - + -
932A GLU* 4.1 20.0 - - + +
983A ILE 3.3 18.3 + - - +
984A LYS* 4.4 1.8 - - - +
986A ILE* 1.3 78.9 - - - +
988A LEU* 1.3 61.4 + - + +
989A GLY 3.4 0.9 + - - -
990A VAL* 3.9 4.0 + - - +
991A LYS* 3.5 22.8 + - + +
1028A THR* 3.5 24.0 - - - +
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Residues in contact with LEU 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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928A LEU* 4.9 19.7 - - + -
984A LYS* 2.7 45.9 + - + +
985A ASP* 5.6 0.2 - - - -
987A VAL* 1.3 74.9 - - + +
989A GLY* 1.3 61.6 + - - +
991A LYS* 4.2 22.7 - - + +
992A ASP* 3.2 36.0 - - - +
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Residues in contact with GLY 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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985A ASP 3.1 19.8 + - - -
986A ILE 2.8 6.4 + - - -
988A LEU* 1.3 77.0 - - - +
990A VAL* 1.3 62.9 + - - -
992A ASP* 3.0 14.5 + - - +
993A LEU 3.0 10.9 + - - -
1042A PHE* 4.6 0.9 - - - -
1046A LEU* 3.6 25.1 - - - +
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Residues in contact with VAL 990 (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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932A GLU* 5.6 4.9 - - - +
986A ILE* 3.0 21.9 + - + +
987A VAL* 4.4 4.0 - - - +
989A GLY* 1.3 73.9 - - - +
991A LYS* 1.3 61.6 + - - +
993A LEU* 3.6 8.1 + - - +
994A GLN* 3.2 23.4 + - - +
1022A LEU* 3.6 31.9 - - + +
1023A ARG* 4.2 14.4 - - + +
1026A LEU* 3.2 30.5 - - + -
1027A ALA 5.8 1.3 - - - +
1042A PHE* 4.1 10.1 - - + -
1046A LEU* 4.3 1.8 - - - +
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Residues in contact with LYS 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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931A GLU* 5.2 17.0 + - + +
987A VAL* 3.5 17.4 + - + +
988A LEU* 4.6 19.8 - - + +
989A GLY 3.2 0.8 - - - -
990A VAL* 1.3 79.1 - - - +
992A ASP* 1.3 64.6 + - - +
994A GLN* 3.8 25.8 - - - +
995A GLU* 3.9 12.0 - - - +
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Residues in contact with ASP 992 (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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988A LEU* 3.2 30.8 + - - +
989A GLY* 3.0 5.9 + - - +
991A LYS* 1.3 84.0 - - - +
993A LEU* 1.3 64.2 + - - +
994A GLN 3.4 0.4 - - - -
995A GLU* 3.5 23.6 - - - +
996A ASN* 3.8 13.5 + - - +
1046A LEU* 6.0 0.2 - - - -
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Residues in contact with LEU 993 (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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989A GLY 3.0 14.0 + - - +
990A VAL* 3.9 5.6 - - + +
992A ASP* 1.3 73.6 - - - +
994A GLN* 1.3 57.7 + - - +
995A GLU 3.0 1.8 - - - -
996A ASN* 2.7 30.4 + - + +
997A LEU* 3.3 25.0 + - + +
1022A LEU* 3.2 30.5 - - + -
1026A LEU* 5.9 2.9 - - + -
1046A LEU* 3.7 45.7 - - + +
1049A ILE* 4.3 11.7 - - + -
1050A GLU* 3.8 24.9 - - + +
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Residues in contact with GLN 994 (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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935A GLN* 5.4 3.4 + - - +
990A VAL 3.2 16.0 + - - +
991A LYS* 3.8 20.3 - - - +
993A LEU* 1.3 79.4 - - - +
995A GLU* 1.3 60.7 + - - +
996A ASN 3.4 0.3 + - - -
997A LEU* 3.7 23.0 + - - +
1011A GLN* 4.7 8.7 + - - -
1015A VAL* 5.4 0.7 - - - +
1019A CYS* 3.6 25.7 - - - +
1022A LEU* 4.3 9.3 - - + +
1023A ARG* 3.3 39.1 - - - +
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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