Contacts of the helix formed by residues 968 - 985 (chain A) in PDB entry 5J68
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 ASP 968 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834A THR* 3.1 19.9 + - - -
966A ILE* 3.2 21.1 - - - +
967A GLN* 1.3 78.7 - - - +
969A ASN* 1.3 63.9 + - - +
970A GLY* 3.2 3.5 + - - +
971A THR* 2.5 38.6 + - - -
972A LYS* 3.1 26.6 - - - +
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Residues in contact with ASN 969 (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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968A ASP* 1.3 77.0 - - - +
970A GLY* 1.3 64.9 + - - +
972A LYS* 4.2 13.7 + - - +
973A GLU* 3.5 23.0 + - - +
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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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968A ASP* 3.2 4.1 + - - +
969A ASN* 1.3 81.5 - - - +
971A THR* 1.3 60.6 + - - +
973A GLU* 4.3 2.1 - - - +
974A ALA* 3.7 16.8 + - - +
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Residues in contact with THR 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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830A LEU* 6.2 1.8 - - + -
833A LEU* 4.6 4.5 - - + +
834A THR* 2.6 55.2 + - - +
837A SER* 6.1 0.9 - - - -
842A LEU* 5.5 7.4 - - + -
966A ILE* 3.8 17.0 - - + -
968A ASP* 2.5 22.9 + - - -
970A GLY* 1.3 70.6 - - - -
972A LYS* 1.3 52.7 + - - +
973A GLU 3.1 2.5 - - - -
974A ALA* 3.0 7.7 + - + +
975A PHE* 2.7 36.9 + - + +
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Residues in contact with LYS 972 (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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963A TYR* 3.4 43.0 + - + +
964A THR* 3.9 10.9 + - - +
966A ILE* 3.5 18.3 - - + +
967A GLN* 3.8 19.8 - - - +
968A ASP 3.1 36.2 + - - +
969A ASN* 4.2 13.8 + - - +
971A THR* 1.3 77.5 - - - +
973A GLU* 1.3 63.1 + - - +
975A PHE* 4.1 1.3 - - - -
976A LYS* 3.4 21.3 + - - +
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Residues in contact with GLU 973 (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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969A ASN 3.5 16.0 + - - +
970A GLY 4.3 2.9 - - - +
971A THR 3.1 0.8 - - - -
972A LYS* 1.3 83.5 - - - +
974A ALA* 1.3 61.8 + - - +
975A PHE 3.4 0.4 - - - -
976A LYS* 3.5 24.2 + - - +
977A SER* 3.4 21.1 + - - -
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Residues in contact with ALA 974 (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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837A SER* 4.9 16.8 - - - +
839A ARG* 5.5 0.2 + - - -
842A LEU* 3.6 18.7 - - + +
970A GLY 3.7 11.3 + - - +
971A THR* 3.0 11.0 + - + +
973A GLU* 1.3 77.4 - - - +
975A PHE* 1.3 62.7 + - - +
977A SER* 2.9 20.4 + - - -
978A ALA* 3.4 5.5 + - - +
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Residues in contact with PHE 975 (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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830A LEU* 6.3 1.6 - - + -
842A LEU* 3.7 31.5 - - + +
845A PHE* 3.4 39.3 - + - -
846A ILE* 4.0 22.7 - - + -
850A GLY 4.9 3.4 - - - -
851A SER 5.1 2.5 - - - -
962A LEU* 4.5 13.0 - - + -
963A TYR* 3.7 33.7 - + + -
966A ILE* 3.7 19.5 - - + -
971A THR* 2.7 21.4 + - + +
972A LYS* 4.3 1.1 - - - -
974A ALA* 1.3 72.6 - - - +
976A LYS* 1.3 67.9 + - - +
978A ALA* 3.1 4.3 + - - +
979A LEU* 2.9 32.8 + - + -
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Residues in contact with LYS 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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963A TYR* 2.9 52.4 + - + -
972A LYS 3.4 17.8 + - - +
973A GLU* 3.7 24.9 - - - +
974A ALA 3.3 0.4 - - - -
975A PHE* 1.3 79.2 - - - +
977A SER* 1.3 61.9 + - - +
979A LEU* 3.2 5.3 + - + +
980A MET* 3.1 41.1 + - - +
2B NAG 3.9 20.2 - - + +
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Residues in contact with SER 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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839A ARG* 3.9 15.4 + - - -
973A GLU 3.4 8.1 + - - -
974A ALA* 2.9 23.0 + - - -
976A LYS* 1.3 78.7 - - - +
978A ALA* 1.3 60.6 + - - +
980A MET* 3.5 12.1 + - - +
981A SER* 3.2 22.2 + - - -
990A ASP* 5.8 0.7 - - - -
991A VAL* 4.7 7.7 + - - +
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Residues in contact with ALA 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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839A ARG* 3.8 26.2 - - - +
842A LEU* 3.8 37.2 - - + -
843A LEU* 3.6 14.0 - - + +
846A ILE* 4.2 6.1 - - + -
974A ALA 3.4 1.1 + - - +
975A PHE* 3.1 9.7 + - + +
977A SER* 1.3 78.8 + - - +
979A LEU* 1.3 65.0 + - - +
981A SER* 3.4 3.5 + - - -
982A SER* 3.2 16.8 + - - -
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Residues in contact with LEU 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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846A ILE* 3.7 26.4 - - + +
851A SER* 3.6 33.2 - - - +
852A HIS* 5.2 1.6 - - + -
961A PRO* 6.5 0.9 - - + -
963A TYR* 5.6 7.4 - - + -
975A PHE* 2.9 22.8 + - + +
976A LYS* 3.5 11.7 - - - +
978A ALA* 1.3 74.7 - - - +
980A MET* 1.3 67.3 + - - +
982A SER* 2.8 24.5 + - - +
983A TYR* 3.1 16.4 + - + +
1B NAG 4.6 20.0 - - - +
2B NAG 4.6 17.5 - - + +
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Residues in contact with MET 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 LYS* 3.1 31.0 + - - +
977A SER* 3.9 6.1 - - - +
979A LEU* 1.3 78.3 - - - +
981A SER* 1.3 56.6 + - - +
983A TYR* 4.7 0.2 - - - -
984A TRP* 3.0 42.6 + - + +
985A CYS* 3.7 1.9 + - - -
991A VAL* 3.4 41.2 - - + +
1043A ILE* 4.4 13.9 - - + -
2B NAG 3.5 44.4 - - + +
4B MAN 6.5 1.1 - - - -
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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
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839A ARG* 3.2 27.6 + - - -
843A LEU* 5.0 0.8 - - - +
977A SER 3.2 11.1 + - - -
978A ALA 3.5 8.7 - - - -
979A LEU 3.1 0.6 - - - -
980A MET* 1.3 78.3 - - - +
982A SER* 1.3 55.5 + - - +
985A CYS* 3.2 17.2 + - - -
987A GLY* 2.6 41.0 + - - -
989A GLY 2.7 27.8 + - - -
990A ASP* 4.9 1.6 - - - -
991A VAL* 4.7 1.5 - - - +
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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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733A ARG* 3.7 18.4 + - - -
843A LEU* 3.8 21.3 - - - +
846A ILE* 4.1 12.8 - - - +
978A ALA 3.2 2.7 + - - -
979A LEU* 2.8 32.8 + - - +
981A SER* 1.3 80.1 - - - +
983A TYR* 1.3 61.7 + - - +
986A SER* 4.1 6.9 - - - -
987A GLY* 3.7 15.9 + - - +
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Residues in contact with TYR 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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732A ASN* 4.1 3.8 + - + -
733A ARG* 3.6 52.3 - - + +
979A LEU* 3.1 23.7 + - + +
980A MET* 4.2 2.2 - - - +
982A SER* 1.3 82.0 + - - +
984A TRP* 1.3 111.5 + + + +
986A SER* 4.5 2.0 + - - -
1013A PRO* 5.7 2.3 - - - +
1B NAG 3.1 53.3 + - - -
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Residues in contact with TRP 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 MET* 3.0 27.5 + - + +
983A TYR* 1.3 108.1 - + + +
985A CYS* 1.3 67.4 + - - +
986A SER 3.5 0.9 - - - -
991A VAL* 5.4 0.4 - - + -
996A CYS* 3.8 1.3 - - - -
1012A SER* 3.7 18.5 + - - -
1013A PRO* 3.7 12.4 - - - +
1041A PRO* 4.2 8.3 - - + -
1042A ALA* 3.9 16.2 - - + -
1043A ILE* 3.2 69.4 - - + +
1B NAG 3.7 6.7 - - - -
2B NAG 2.8 64.0 + - - -
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Residues in contact with CYS 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 MET 4.3 3.4 - - - -
981A SER 3.2 5.4 + - - +
984A TRP* 1.3 78.6 - - - +
986A SER* 1.3 66.8 + - - +
987A GLY 2.9 6.4 + - - -
988A LYS 3.0 10.6 + - - -
989A GLY 3.4 28.5 - - - +
990A ASP 4.1 1.8 - - - -
991A VAL* 4.0 18.6 - - - -
996A CYS* 2.0 52.5 - - + -
1011A CYS* 3.2 21.6 - - - +
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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