Contacts of the helix formed by residues 968 - 988 (chain A) in PDB entry 5I4E
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 PHE 968 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A TRP* 3.6 33.8 - + + -
965A LEU 2.8 26.5 + - - +
966A GLU* 3.1 30.0 - - + -
967A ALA* 1.4 72.7 - - - +
969A ASP* 1.3 82.6 + - - +
970A GLY 3.1 2.0 - - - -
971A GLU* 3.0 31.3 + - - +
972A CYS* 3.4 14.6 + - - -
1006A ASP* 4.8 13.2 - - - -
1010A ALA* 5.1 9.0 - - + -
1013A TRP* 3.6 40.2 - + - -
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Residues in contact with ASP 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A GLU* 3.1 19.8 - - - +
967A ALA* 3.2 0.8 - - - -
968A PHE* 1.3 102.4 - - - +
970A GLY* 1.3 52.7 + - - +
971A GLU 3.1 1.1 - - - -
972A CYS* 3.1 13.7 + - + +
973A GLN* 2.8 36.2 + - - +
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Residues in contact with GLY 970 (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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967A ALA* 3.2 13.5 + - - -
968A PHE 3.1 1.0 - - - -
969A ASP* 1.3 78.7 - - - +
971A GLU* 1.3 57.7 + - - +
973A GLN* 4.0 13.2 - - - +
974A SER* 3.5 22.3 + - - -
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Residues in contact with GLU 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A LYS 5.3 0.9 - - - +
935A LEU* 4.8 8.3 - - - +
938A TRP* 3.7 49.2 + - + +
967A ALA 4.3 1.0 + - - -
968A PHE* 3.0 15.2 + - - +
970A GLY* 1.3 73.6 - - - +
972A CYS* 1.4 51.4 + - - +
973A GLN 3.1 3.8 - - - -
974A SER* 2.8 10.7 + - - -
975A LEU* 2.8 62.7 + - + +
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Residues in contact with CYS 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A TRP* 6.4 0.9 - - - -
968A PHE* 3.4 18.5 + - - -
969A ASP* 3.1 17.6 + - + +
971A GLU* 1.4 77.9 - - - +
973A GLN* 1.3 56.7 + - - +
975A LEU* 3.9 10.7 - - - +
976A GLU* 3.2 29.5 + - - +
1003A GLU* 6.1 0.7 - - - +
1006A ASP* 3.6 30.7 - - - -
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Residues in contact with GLN 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A ASP 2.8 19.1 + - - +
970A GLY* 4.0 13.3 - - - +
971A GLU 3.0 0.2 + - - -
972A CYS* 1.3 73.9 - - - +
974A SER* 1.3 58.3 - - - +
976A GLU* 4.5 4.5 - - - +
977A GLY* 3.2 22.7 + - - -
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Residues in contact with SER 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A GLY 3.5 12.4 + - - -
971A GLU* 2.8 10.2 + - - -
973A GLN* 1.3 77.9 - - - +
975A LEU* 1.3 54.0 + - - -
977A GLY* 3.3 2.3 + - - -
978A GLN* 2.8 50.5 + - - +
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Residues in contact with LEU 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931A ILE* 3.9 15.8 - - + +
934A LYS* 6.3 0.4 - - + -
935A LEU* 3.5 46.0 - - + -
971A GLU* 2.8 59.3 + - + +
972A CYS* 3.9 8.7 - - - +
974A SER* 1.3 69.1 - - - +
976A GLU* 1.4 55.1 + - - +
977A GLY 3.1 0.9 - - - -
978A GLN* 3.0 17.5 + - - +
979A SER* 2.8 38.8 + - - +
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Residues in contact with GLU 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A CYS 3.2 20.8 + - - +
973A GLN* 4.5 4.0 - - - +
975A LEU* 1.4 77.8 - - - +
977A GLY* 1.3 59.8 + - - +
979A SER* 4.7 4.7 - - - +
980A ASN* 3.2 57.3 + - - +
1003A GLU* 4.3 22.2 - - - +
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Residues in contact with GLY 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A GLN 3.2 17.4 + - - -
974A SER* 3.5 6.1 - - - -
975A LEU 3.1 0.6 - - - -
976A GLU* 1.3 83.1 + - - +
978A GLN* 1.4 56.2 + - - +
980A ASN* 4.4 3.3 - - - +
981A SER* 3.5 21.5 + - - -
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Residues in contact with GLN 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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930A ARG* 4.6 11.8 + - - -
931A ILE* 3.7 24.4 - - + +
974A SER* 2.8 41.5 + - - +
975A LEU* 3.0 19.6 + - - +
977A GLY* 1.4 78.1 - - - +
979A SER* 1.4 54.6 + - - +
981A SER* 3.2 6.4 + - - -
982A ASP* 2.8 41.5 + - - +
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Residues in contact with SER 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A TYR* 4.4 14.1 - - - -
931A ILE* 4.2 10.4 - - - +
932A LEU* 4.2 19.2 - - - +
935A LEU* 6.0 0.5 - - - +
975A LEU 2.8 20.9 + - - -
976A GLU* 4.4 4.5 - - - -
978A GLN* 1.4 70.5 - - - +
980A ASN* 1.4 55.8 + - - +
982A ASP* 3.2 8.9 + - - +
983A LEU* 2.8 45.3 + - - +
999A PRO* 5.7 6.8 - - - +
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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
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976A GLU* 3.2 42.0 + - - +
977A GLY* 4.6 4.5 - - - +
979A SER* 1.4 79.6 - - - +
981A SER* 1.4 51.5 + - - +
983A LEU* 3.7 10.2 - - - +
984A LEU* 2.8 34.9 + - - +
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Residues in contact with SER 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A GLY 3.5 15.9 + - - -
978A GLN* 3.2 11.1 + - - -
980A ASN* 1.4 75.4 - - - +
982A ASP* 1.4 65.1 + - - +
984A LEU* 3.7 11.9 - - - +
985A SER* 3.1 28.2 + - - -
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Residues in contact with ASP 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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924A LEU* 4.0 35.6 - - + +
927A LYS* 4.0 22.3 - - - +
928A TYR* 4.4 15.3 - - + -
931A ILE* 4.0 16.6 - - - +
978A GLN* 2.8 25.7 + - - +
979A SER* 3.5 9.1 - - - +
981A SER* 1.4 74.8 - - - +
983A LEU* 1.3 56.8 + - - +
985A SER* 3.3 5.9 + - - -
986A ILE* 3.0 35.7 + - + +
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Residues in contact with LEU 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A TYR* 4.0 28.0 - - + -
979A SER* 2.8 31.4 + - - +
980A ASN* 4.1 9.6 - - - +
982A ASP* 1.3 69.4 - - - +
984A LEU* 1.4 58.8 + - - +
986A ILE* 3.7 19.0 - - + +
987A LEU* 3.0 36.2 + - + +
993A LEU* 4.0 22.9 - - + -
995A TYR* 4.4 8.7 - - + -
996A ASN* 3.4 32.5 - - - +
999A PRO* 5.3 4.3 - - + -
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Residues in contact with LEU 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 ASN 2.8 22.7 + - - +
981A SER* 3.7 11.9 - - - +
982A ASP 3.3 0.6 - - - -
983A LEU* 1.4 70.0 - - - +
985A SER* 1.4 65.9 + - - +
987A LEU* 3.5 21.6 + - + +
988A ALA* 3.8 11.6 + - - +
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Residues in contact with SER 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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924A LEU* 3.8 23.7 - - - +
981A SER* 3.1 16.1 + - - -
982A ASP 3.6 8.7 - - - -
984A LEU* 1.4 74.5 - - - +
986A ILE* 1.4 63.5 + - - +
988A ALA* 3.6 10.5 - - - +
989A GLN* 3.4 24.2 + - - +
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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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921A ILE* 5.6 8.5 - - + +
924A LEU* 3.7 36.8 - - + +
925A LEU* 4.7 15.7 - - + -
928A TYR* 5.6 3.1 - - + -
982A ASP* 3.0 28.8 + - + +
983A LEU* 3.7 23.1 - - + +
985A SER* 1.4 74.4 - - - +
987A LEU* 1.3 53.3 + - - +
989A GLN* 2.7 28.8 + - - +
990A LEU 2.8 34.7 + - - +
991A THR* 4.6 0.7 - - - -
992A GLU* 4.5 11.7 - - - +
993A LEU* 4.5 17.0 - - + -
995A TYR* 6.2 1.1 - - + -
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Residues in contact with LEU 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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983A LEU* 3.0 25.7 + - + +
984A LEU* 3.9 14.6 - - + +
985A SER 3.5 0.6 - - - -
986A ILE* 1.3 75.7 - - - +
988A ALA* 1.3 57.8 - - - +
989A GLN 3.0 9.9 + - - +
990A LEU 4.2 2.9 - - - -
991A THR* 4.1 17.7 - - + +
993A LEU* 2.6 44.9 - - + -
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Residues in contact with ALA 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 LEU 3.8 8.9 + - - +
985A SER* 3.6 14.4 - - - +
987A LEU* 1.3 77.4 - - - +
989A GLN* 1.3 62.1 + - + +
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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
------------------------------------------------------------
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