Contacts of the helix formed by residues 961 - 980 (chain A) in PDB entry 3O37
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 LYS 961 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A VAL* 6.0 0.7 - - + -
900A LEU* 3.2 12.6 - - - +
960A SER* 1.3 83.8 + - - +
962A PRO* 1.3 67.2 - - + +
963A GLU* 3.5 33.0 - - - +
964A ASP* 2.8 55.5 + - - +
965A PHE 3.9 1.2 + - - -
872B ASP* 3.5 28.3 + - - +
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Residues in contact with PRO 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A LEU* 3.5 4.4 - - + -
904A ASP* 3.5 36.6 - - + +
961A LYS* 1.3 86.5 - - + +
963A GLU* 1.3 73.1 + - - +
964A ASP 2.8 1.6 + - - -
965A PHE* 2.9 30.2 + - + -
966A VAL* 3.0 17.9 + - + +
1005A TYR* 3.6 25.8 - - + +
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Residues in contact with GLU 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A LYS* 3.2 37.3 + - - +
962A PRO* 1.3 83.0 - - - +
964A ASP* 1.3 57.3 + - - +
966A VAL* 3.8 8.7 - - - +
967A ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A MET 5.1 2.0 - - - +
959A TYR* 3.6 29.6 - - + -
960A SER* 2.7 32.8 + - - -
961A LYS* 2.8 40.6 + - - +
963A GLU* 1.3 79.3 - - - +
965A PHE* 1.3 58.5 + - - +
967A ALA* 3.6 14.3 + - - +
968A ASP* 3.6 6.1 + - - -
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Residues in contact with PHE 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A LEU* 3.8 27.1 - - + -
904A ASP 3.7 15.3 - - - -
908A CYS* 3.5 35.2 - - + -
911A LEU* 3.7 23.8 - - + -
948A ILE* 4.6 1.1 - - + +
959A TYR* 3.8 27.8 - + + +
962A PRO* 2.9 33.1 + - + -
964A ASP* 1.3 73.1 - - - +
966A VAL* 1.3 89.8 + - + +
967A ALA 3.1 1.8 - - - -
968A ASP* 3.1 3.9 + - - +
969A PHE* 3.0 34.6 + + + -
1005A TYR* 3.5 25.6 - + - -
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Residues in contact with VAL 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A PRO* 3.0 23.3 + - + +
963A GLU* 3.8 8.1 - - - +
965A PHE* 1.3 88.9 - - + +
967A ALA* 1.3 63.4 + - - +
969A PHE* 3.1 7.9 + - - +
970A ARG* 2.9 59.7 + - + +
997A PHE* 4.4 3.1 - - + -
1001A LEU* 3.8 35.7 - - + -
1005A TYR* 5.6 1.1 - - + -
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Residues in contact with ALA 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A GLU 3.0 18.7 + - - +
964A ASP* 3.6 8.5 - - - +
965A PHE 3.1 0.2 - - - -
966A VAL* 1.3 78.0 - - - +
968A ASP* 1.3 58.6 + - - +
970A ARG* 3.3 8.3 + - - +
971A LEU* 2.9 27.4 + - - +
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Residues in contact with ASP 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A MET* 3.2 32.9 - - - +
948A ILE* 3.8 13.5 - - + -
951A ARG* 2.8 29.4 + - - -
958A MET* 5.1 0.2 - - - +
959A TYR* 2.4 39.5 + - - +
964A ASP 3.6 3.6 + - - +
965A PHE 3.1 8.5 + - - +
967A ALA* 1.3 78.1 - - - +
969A PHE* 1.3 66.0 + - - +
971A LEU* 3.2 18.4 + - - +
972A ILE* 3.2 2.9 + - - +
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Residues in contact with PHE 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A CYS* 3.7 23.3 - - - -
911A LEU* 4.2 7.2 - - + -
912A LEU* 3.5 46.4 - - + -
915A LEU* 3.4 33.9 - - + -
945A LEU* 3.9 4.9 - - + -
948A ILE* 3.6 17.3 - - + -
965A PHE* 3.0 35.5 + + - -
966A VAL 3.1 5.8 + - - +
968A ASP* 1.3 75.2 - - - +
970A ARG* 1.3 63.6 + - - +
972A ILE* 3.1 22.6 + - + +
973A PHE* 3.3 15.9 - + + -
997A PHE* 3.5 32.3 - + + -
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Residues in contact with ARG 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A VAL* 2.9 37.1 + - - +
967A ALA* 3.8 6.3 - - - +
969A PHE* 1.3 74.2 - - - +
971A LEU* 1.3 60.6 + - - +
973A PHE* 3.2 12.4 + - + +
974A GLN* 2.8 31.6 + - - +
994A GLU* 5.7 3.1 - - - +
997A PHE* 4.4 5.6 - - + -
998A GLU* 3.1 41.5 + - - +
1001A LEU* 3.5 16.2 - - - +
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Residues in contact with LEU 971 (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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941A ASN* 3.3 39.5 - - + +
943A MET* 3.7 26.2 - - + -
967A ALA 2.9 13.2 + - - +
968A ASP* 3.3 17.7 - - - +
970A ARG* 1.3 76.2 - - - +
972A ILE* 1.3 58.3 + - - +
974A GLN* 4.3 8.5 - - + -
975A ASN* 2.8 51.4 + - - +
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Residues in contact with ILE 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A PHE* 4.0 32.4 - - + -
943A MET* 3.6 28.9 - - + +
944A ASP 3.5 26.7 - - - -
945A LEU* 3.6 23.8 - - + +
948A ILE* 3.8 13.2 - - + -
968A ASP 3.6 9.4 - - - +
969A PHE* 3.1 11.4 + - + +
971A LEU* 1.3 79.5 - - - +
973A PHE* 1.3 70.7 + - + +
975A ASN* 3.3 4.1 + - - +
976A CYS* 3.0 26.3 + - - +
993A LEU* 5.8 0.4 - - + -
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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
----------------------------------------------------------
915A LEU* 4.7 9.0 - - + -
924A PHE* 6.0 0.7 - + - -
945A LEU* 6.3 0.4 - - + -
969A PHE* 3.3 23.1 - + + -
970A ARG* 3.2 14.0 + - + +
972A ILE* 1.3 84.2 - - + +
974A GLN* 1.3 66.1 - - - +
976A CYS* 3.3 6.7 + - + +
977A ALA* 3.0 24.3 + - - +
990A GLY* 3.8 12.9 - - - +
993A LEU* 3.8 26.7 - - + -
994A GLU* 3.6 56.3 - - + +
997A PHE* 3.6 46.9 - + + -
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Residues in contact with GLN 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A ARG 2.8 20.7 + - - +
971A LEU* 3.8 10.8 - - + +
973A PHE* 1.3 71.6 + - - +
975A ASN* 1.3 68.9 + - - +
977A ALA* 3.5 7.6 + - - +
978A GLU* 3.0 57.4 + - - +
994A GLU* 5.8 1.8 + - - -
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Residues in contact with ASN 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A TYR* 3.2 19.3 + - - +
939A ILE* 3.4 31.6 - - + +
941A ASN* 2.9 24.7 + - - +
942A PRO* 3.7 0.2 - - - +
943A MET* 3.5 18.9 + - - +
971A LEU* 2.8 38.0 + - - +
972A ILE* 3.6 5.2 - - - +
974A GLN* 1.3 77.5 - - - +
976A CYS* 1.3 63.7 + - - +
978A GLU* 3.4 1.0 + - - -
979A PHE* 3.0 28.8 + - - +
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Residues in contact with CYS 976 (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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924A PHE* 3.5 28.7 - - + -
935A TYR* 5.4 1.8 - - - -
972A ILE 3.0 13.3 + - - +
973A PHE* 3.5 11.7 - - + +
975A ASN* 1.3 77.1 - - - +
977A ALA* 1.3 57.9 + - - +
979A PHE* 5.1 0.2 - - - -
980A ASN* 3.0 51.0 + - - +
986A VAL 3.4 25.8 - - - -
987A ALA* 3.9 8.4 - - - -
990A GLY* 3.7 11.7 - - - -
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Residues in contact with ALA 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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973A PHE 3.0 16.1 + - - +
974A GLN* 4.0 12.6 - - - +
976A CYS* 1.3 78.5 - - - +
978A GLU* 1.3 63.5 + - + +
980A ASN 3.4 15.3 - - - +
982A PRO* 5.9 1.4 - - - +
987A ALA* 5.6 5.4 - - - +
991A ILE* 5.5 11.4 - - + -
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Residues in contact with GLU 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A ILE* 4.9 8.7 - - + +
939A ILE* 4.6 10.8 - - + -
974A GLN* 3.0 52.3 + - - +
975A ASN* 4.1 2.5 - - - +
977A ALA* 1.3 78.3 - - + +
979A PHE* 1.3 60.2 + - - +
980A ASN 4.8 0.2 - - - -
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Residues in contact with PHE 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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932A VAL* 3.9 26.5 - - + -
934A ASP* 4.0 7.0 - - + -
935A TYR* 3.5 49.8 - + + -
938A ILE* 4.0 29.7 - - + +
939A ILE* 3.9 11.2 - - + -
975A ASN 3.0 17.4 + - - +
976A CYS 4.3 0.7 - - - +
978A GLU* 1.3 80.6 - - - +
980A ASN* 1.3 85.4 + - - +
981A GLU* 3.9 5.5 + - - +
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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
----------------------------------------------------------
924A PHE* 5.4 0.2 - - - -
935A TYR* 5.4 2.2 - - - -
976A CYS* 3.0 33.5 + - - +
977A ALA 3.4 16.1 - - - +
978A GLU 4.8 0.2 - - - -
979A PHE* 1.3 101.2 - - - +
981A GLU* 1.3 66.3 + - - +
982A PRO* 3.6 3.6 - - - +
984A SER* 3.6 15.0 + - - +
986A VAL* 3.2 37.9 - - - +
987A ALA* 4.1 10.8 - - + +
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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
------------------------------------------------------------
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