Contacts of the helix formed by residues 969 - 986 (chain A) in PDB entry 3NC0
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 ASN 969 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A ASN* 3.6 9.3 + - - +
967A PRO 4.0 1.6 + - - -
968A VAL* 1.3 74.9 - - - +
970A ASN* 1.3 66.1 + - - +
971A GLN* 4.0 17.7 - - + +
972A MET* 2.6 40.6 + - - +
973A PHE 3.1 5.7 + - - -
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Residues in contact with ASN 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A VAL* 4.2 13.7 - - + +
957A LYS* 2.8 45.6 - - + +
958A ILE* 4.5 0.2 - - - -
959A SER 2.9 17.5 + - - +
960A THR* 4.5 0.4 - - - +
961A PRO* 2.9 42.2 - - + +
968A VAL 4.2 3.0 + - - -
969A ASN* 1.3 72.3 - - - +
971A GLN* 1.3 56.4 + - - +
973A PHE* 4.0 1.8 - - - +
974A ILE* 2.8 37.0 + - + +
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Residues in contact with GLN 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A VAL* 3.8 12.6 + - + +
954A GLU* 4.5 23.1 + - - +
969A ASN* 2.8 17.4 + - - +
970A ASN* 1.3 78.5 - - - +
972A MET* 1.3 57.7 + - + +
974A ILE* 3.2 11.7 - - - +
975A GLN* 3.0 43.0 + - - +
1002A PHE* 3.7 31.6 - - + +
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Residues in contact with MET 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A VAL* 3.6 15.3 - - + -
969A ASN* 2.6 33.8 + - - +
971A GLN* 1.3 69.8 - - + +
973A PHE* 1.3 64.3 + - - +
974A ILE 3.2 1.6 - - - -
975A GLN* 3.4 4.0 + - - +
976A ASP* 2.8 52.5 + - - +
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Residues in contact with PHE 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A CYS* 3.9 24.2 - - - -
957A LYS* 4.8 2.2 - - - -
961A PRO* 3.3 43.1 - - + -
962A LEU* 3.1 38.6 - - + -
968A VAL* 3.2 25.4 - - + +
969A ASN 3.1 4.8 + - - +
970A ASN 4.0 3.6 - - - +
972A MET* 1.3 80.4 - - - +
974A ILE* 1.3 60.7 + - + +
976A ASP* 4.1 4.8 - - + +
977A TYR* 2.8 51.8 + + + +
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Residues in contact with ILE 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A PHE* 3.5 35.7 - - + -
920A CYS* 4.6 7.6 - - - -
923A LEU* 3.5 24.2 - - + -
950A PHE* 5.0 2.2 - - + -
953A VAL* 3.7 12.8 - - + -
957A LYS* 5.1 4.0 - - - +
970A ASN* 2.8 25.1 + - + +
971A GLN* 3.2 15.0 - - - +
973A PHE* 1.3 80.4 - - + +
975A GLN* 1.3 64.1 + - - +
977A TYR* 3.8 12.5 - - + +
978A VAL* 3.0 38.2 + - + +
1002A PHE* 3.3 23.3 - - + -
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Residues in contact with GLN 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A GLN* 3.0 37.6 + - - +
972A MET* 3.9 5.6 - - - +
974A ILE* 1.3 81.4 - - - +
976A ASP* 1.3 62.6 + - - +
978A VAL* 4.6 0.2 - - - -
979A ALA* 2.8 31.3 + - - +
998A VAL* 3.3 33.7 - - + +
999A THR* 4.1 11.1 + - - +
1002A PHE* 3.2 41.4 - - + +
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Residues in contact with ASP 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A MET* 2.8 48.1 + - - +
973A PHE* 4.1 5.6 - - + +
975A GLN* 1.3 78.8 - - - +
977A TYR* 1.3 59.3 + - - +
979A ALA* 3.8 6.6 - - - +
980A ASN* 2.8 39.9 + - - +
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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
----------------------------------------------------------
920A CYS* 3.4 43.0 + - + +
921A ASP* 5.3 0.7 + - - -
923A LEU* 4.5 7.4 - - + -
924A GLN* 3.1 29.5 + - - +
973A PHE* 2.8 48.1 + + + +
974A ILE* 3.8 19.1 - - + +
976A ASP* 1.3 74.0 - - - +
978A VAL* 1.3 62.1 + - + +
980A ASN* 3.6 6.9 + - + +
981A LEU* 3.0 43.0 + - + +
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Residues in contact with VAL 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A LEU* 3.7 31.0 - - + -
927A PHE* 4.1 17.3 - - + -
950A PHE* 4.5 12.3 - - + -
974A ILE 3.0 22.1 + - - +
975A GLN* 3.8 5.6 - - - +
977A TYR* 1.3 77.9 - - + +
979A ALA* 1.3 57.0 + - - +
981A LEU* 3.1 8.4 + - + +
982A LEU* 2.8 57.7 + - + +
998A VAL* 4.1 10.5 - - + -
1001A LEU* 4.4 6.5 - - + -
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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
----------------------------------------------------------
975A GLN 2.8 23.0 + - - +
976A ASP* 3.8 7.4 - - - +
978A VAL* 1.3 73.4 - - - +
980A ASN* 1.3 57.7 + - - +
983A LYS* 2.9 35.3 + - - +
994A VAL* 4.0 13.5 - - + +
995A LYS* 5.9 1.8 - - - +
998A VAL* 3.9 19.7 - - + +
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Residues in contact with ASN 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A ASP* 2.8 24.6 + - - +
977A TYR* 3.6 7.7 - - + +
979A ALA* 1.3 77.0 - - - +
981A LEU* 1.3 54.1 + - - +
983A LYS* 4.1 2.6 - - - +
984A SER* 2.8 42.9 + - - -
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Residues in contact with LEU 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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923A LEU* 5.1 1.3 - - + -
924A GLN* 3.6 60.8 - - + +
927A PHE* 4.9 12.6 - - + -
977A TYR* 3.0 33.3 + - + +
978A VAL* 3.1 9.6 + - + +
980A ASN* 1.3 75.4 - - - +
982A LEU* 1.3 63.2 + - + +
984A SER* 4.0 4.4 - - - -
985A ALA* 3.0 36.3 + - + +
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Residues in contact with LEU 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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927A PHE* 3.6 28.3 - - + -
931A THR* 4.8 6.7 - - + -
978A VAL* 2.8 41.5 + - + +
979A ALA 4.0 2.7 - - - +
981A LEU* 1.3 74.2 - - + +
983A LYS* 1.3 60.7 + - - +
985A ALA* 3.1 5.0 + - + -
986A PHE* 2.8 38.5 + - + +
989A LEU* 5.5 0.4 - - - -
994A VAL* 4.5 9.6 - - + -
997A PHE* 3.5 33.7 - - + -
998A VAL* 4.3 7.4 - - + -
1018A PHE* 4.1 27.4 - - + -
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Residues in contact with LYS 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 2.9 18.9 + - - +
980A ASN* 4.1 3.4 - - - +
982A LEU* 1.3 76.8 - - - +
984A SER* 1.3 61.3 + - - +
986A PHE 3.1 26.9 - - - +
987A PRO* 3.1 14.3 - - + +
989A LEU 5.0 9.0 - - - +
991A ASP* 3.1 43.8 + - - +
994A VAL* 4.3 20.1 - - + +
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Residues in contact with SER 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A ASN* 2.8 28.1 + - - -
981A LEU* 4.0 4.9 - - - -
983A LYS* 1.3 73.4 - - - +
985A ALA* 1.3 59.6 + - - +
987A PRO* 4.0 9.4 - - - +
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Residues in contact with ALA 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 LEU* 3.0 25.2 + - + +
982A LEU* 3.7 4.9 - - + +
984A SER* 1.3 77.8 - - - +
986A PHE* 1.3 84.8 + - + +
987A PRO* 3.6 6.5 - - - +
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Residues in contact with PHE 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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931A THR* 3.7 42.6 - - + -
982A LEU* 2.8 19.4 + - + +
983A LYS* 3.1 9.7 - - - +
985A ALA* 1.3 96.6 - - + +
987A PRO* 1.3 59.8 - - - +
988A HIS* 3.1 30.6 + + - +
989A LEU* 3.3 34.5 + - + +
1018A PHE* 4.9 6.3 - + - -
1022A ILE* 3.9 33.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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