Contacts of the helix formed by residues 968 - 986 (chain A) in PDB entry 5UAK
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 968 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ASN 4.9 2.2 - - - -
966A THR 3.5 5.4 + - - +
967A LEU* 1.3 86.5 - - + +
969A ALA* 1.3 63.5 + - - +
970A GLY* 4.4 4.0 - - - +
971A GLY* 3.5 25.1 + - - +
972A ILE* 3.5 12.0 + - - +
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Residues in contact with ALA 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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266A ILE* 3.9 21.3 - - + +
267A GLU* 4.1 17.5 - - - +
967A LEU 3.8 1.0 + - - -
968A LYS* 1.3 72.0 - - - +
970A GLY* 1.3 56.7 + - - +
972A ILE* 2.9 15.3 + - - +
973A LEU* 2.8 36.7 + - + +
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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 LYS* 3.4 5.7 - - - +
969A ALA* 1.3 77.4 - - - +
971A GLY* 1.3 56.1 + - - +
973A LEU* 4.3 4.2 - - - +
974A ASN* 3.1 32.7 + - - +
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Residues in contact with GLY 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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967A LEU* 5.6 7.0 - - - -
968A LYS* 3.5 24.2 + - - +
969A ALA 3.2 1.2 - - - -
970A GLY* 1.3 71.3 - - - +
972A ILE* 1.3 60.8 + - - +
974A ASN* 4.7 2.5 - - - -
975A ARG* 3.0 40.3 + - - +
1166A PHE* 5.3 1.3 - - - -
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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
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266A ILE* 3.5 34.1 - - + -
956A VAL* 4.8 8.3 - - + -
964A LEU* 4.0 27.1 - - + -
967A LEU* 3.5 42.2 - - + +
968A LYS 3.5 16.5 + - - +
969A ALA* 2.9 9.9 + - - +
971A GLY* 1.3 72.8 - - - +
973A LEU* 1.3 59.9 + - - +
975A ARG* 3.9 1.2 - - - +
976A PHE* 2.9 37.2 + - + +
1166A PHE* 3.7 24.4 - - + -
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Residues in contact with LEU 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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259A LEU* 3.9 21.8 - - + -
262A THR* 4.8 4.7 - - - +
263A SER* 3.7 39.7 - - - +
266A ILE* 4.9 13.2 - - + +
267A GLU* 5.8 3.8 - - + +
969A ALA* 2.8 21.6 + - + +
970A GLY* 4.3 4.0 - - - +
972A ILE* 1.3 74.2 - - - +
974A ASN* 1.3 51.8 + - - +
976A PHE* 3.4 5.2 + - - +
977A SER* 2.7 49.8 + - - +
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Residues in contact with ASN 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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970A GLY 3.1 22.2 + - - +
971A GLY* 4.1 3.4 - - - +
973A LEU* 1.3 80.2 - - - +
975A ARG* 1.3 58.6 + - - +
977A SER* 3.6 5.3 + - - -
978A LYS* 2.8 63.3 + - - +
979A ASP 3.8 0.3 + - - -
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Residues in contact with ARG 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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952A MET* 4.5 8.2 - - + +
967A LEU* 5.3 11.1 - - - +
971A GLY* 3.0 23.0 + - - +
972A ILE 4.1 1.3 - - - +
974A ASN* 1.3 79.1 + - - +
976A PHE* 1.3 59.8 + - - +
979A ASP* 3.5 26.5 - - + +
980A ILE* 4.1 4.0 + - - +
1162A ARG* 3.4 72.8 + - + +
1163A VAL* 4.7 3.0 - - + +
1165A LYS* 4.6 17.8 - - - +
1166A PHE* 3.4 34.1 - - + -
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Residues in contact with PHE 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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258A ARG* 5.3 5.0 + - - -
262A THR* 3.9 32.1 - - + -
266A ILE* 6.2 1.1 - - + -
285A ILE* 5.9 0.2 - - + -
949A HIS* 3.4 33.7 - + - -
952A MET* 3.7 38.1 - - + +
953A LEU* 3.8 41.1 - - + -
956A VAL* 4.4 11.2 - - + -
972A ILE* 2.9 24.3 + - + +
973A LEU* 3.8 5.6 - - - +
975A ARG* 1.3 79.6 - - - +
977A SER* 1.3 59.2 + - - +
980A ILE* 3.1 25.2 - - - +
1166A PHE* 6.4 0.7 - + + -
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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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258A ARG* 4.6 11.2 + - - +
259A LEU* 3.6 27.1 - - - -
262A THR* 5.6 0.2 - - - -
973A LEU* 2.7 32.0 + - - +
974A ASN* 3.4 8.0 + - - -
976A PHE* 1.3 78.9 - - - +
978A LYS* 1.3 72.9 + - - +
979A ASP 3.6 0.4 - - - -
980A ILE* 4.1 2.3 - - - +
981A ALA* 3.7 19.1 + - - +
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Residues in contact with LYS 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A ASN* 2.8 42.2 + - - +
977A SER* 1.3 80.7 + - - +
979A ASP* 1.3 63.9 + - + +
981A ALA* 3.7 5.5 - - - +
982A ILE* 3.5 36.3 + - + +
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Residues in contact with ASP 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A ASN 3.8 1.8 + - - -
975A ARG* 3.5 22.7 + - + +
977A SER 3.6 0.2 - - - -
978A LYS* 1.3 76.2 - - - +
980A ILE* 1.3 60.2 + - - +
981A ALA 3.2 1.8 - - - -
982A ILE* 2.9 18.8 + - - +
983A LEU* 2.8 28.8 + - - +
1159A SER* 2.7 51.7 + - - +
1162A ARG* 4.1 9.1 - - - +
1163A VAL* 3.8 13.0 - - - +
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Residues in contact with ILE 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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258A ARG* 4.8 10.8 - - - +
289A ARG* 4.9 6.3 - - - +
945A SER* 4.5 5.2 - - - +
948A LEU* 5.0 2.9 - - + -
949A HIS* 3.5 52.3 - - + +
952A MET* 4.3 18.6 - - - -
975A ARG 4.1 4.2 + - - +
976A PHE* 3.1 28.3 - - + +
977A SER 4.1 4.7 - - - +
979A ASP* 1.3 78.6 - - - +
981A ALA* 1.3 55.6 + - - +
983A LEU* 3.6 20.8 - - + +
984A ASP* 2.8 33.4 + - + +
1163A VAL* 5.5 8.9 - - + +
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Residues in contact with ALA 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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255A ILE* 6.5 1.6 - - + -
258A ARG* 5.4 6.7 - - - +
977A SER 3.7 11.6 + - - +
978A LYS* 3.7 11.2 + - - +
979A ASP 3.2 0.2 - - - -
980A ILE* 1.3 81.3 - - + +
982A ILE* 1.3 56.3 + - + +
984A ASP* 4.3 4.7 - - - -
985A ASP* 2.8 46.7 + - - +
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Residues in contact with ILE 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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978A LYS* 3.5 39.2 + - + +
979A ASP* 2.9 16.8 + - - +
981A ALA* 1.3 76.3 - - + +
983A LEU* 1.3 61.1 + - - +
986A LEU* 2.9 47.7 + - + +
987A LEU* 3.3 6.4 + - - +
1156A LEU* 3.6 30.7 - - + -
1159A SER* 5.8 1.3 - - - +
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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
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852A TYR* 4.6 14.6 + - + +
941A LEU 5.7 0.2 - - - +
945A SER* 3.8 30.0 - - - -
948A LEU* 4.6 21.8 - - + -
979A ASP* 2.8 15.0 + - - +
980A ILE* 3.6 19.7 - - + +
982A ILE* 1.3 79.1 - - - +
984A ASP* 1.3 57.7 + - - +
987A LEU* 3.5 31.7 - - + +
988A PRO* 3.5 6.9 - - - +
1159A SER* 5.1 4.9 - - - +
1160A VAL* 3.8 35.2 - - + -
1163A VAL* 5.0 12.6 - - + -
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Residues in contact with ASP 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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251A ARG* 5.5 1.0 + - - -
289A ARG* 3.9 20.5 + - - +
292A GLU* 5.3 2.4 - - - +
293A LEU* 4.3 7.4 - - - +
296A THR* 3.6 26.5 + - - +
942A ILE* 4.4 10.9 - - - +
945A SER* 2.9 30.7 + - - +
980A ILE* 2.8 21.4 + - + +
981A ALA* 3.7 3.8 - - - +
982A ILE 3.3 0.2 - - - -
983A LEU* 1.3 75.8 - - - +
985A ASP* 1.3 69.7 + - - +
988A PRO* 3.4 19.1 - - - +
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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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251A ARG* 3.3 33.9 + - - -
296A THR* 4.3 6.5 - - - +
981A ALA* 2.8 27.4 + - - +
984A ASP* 1.3 90.7 - - - +
986A LEU* 1.3 77.1 + - + +
987A LEU 3.6 0.2 - - - -
988A PRO* 3.6 8.1 - - - +
989A LEU* 4.1 16.6 - - - +
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Residues in contact with LEU 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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982A ILE* 2.9 39.3 + - + +
985A ASP* 1.3 90.2 - - + +
987A LEU* 1.3 64.4 + - - +
988A PRO 3.5 0.4 - - - -
989A LEU* 3.6 16.8 + - + +
990A THR* 3.5 17.9 + - + +
1156A LEU* 4.7 13.2 - - + -
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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