Contacts of the helix formed by residues 970 - 980 (chain A) in PDB entry 1KEK
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 GLY 970 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A GLU 3.5 19.9 - - - +
874A GLU* 5.0 0.5 - - - +
965A TRP* 2.8 36.1 + - - -
969A ILE* 1.3 76.3 - - - +
971A TYR* 1.3 58.8 + - - +
972A GLY 3.4 2.0 - - - -
973A GLY* 3.3 4.7 + - - -
974A LEU* 2.8 30.2 + - - +
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Residues in contact with TYR 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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965A TRP 3.5 1.8 + - - -
966A ALA 3.3 24.2 - - - +
967A TYR 3.8 6.7 - - - +
968A ASP 3.1 15.2 + - - +
969A ILE 3.3 0.6 - - - -
970A GLY* 1.3 78.4 - - - +
972A GLY* 1.3 55.5 + - - +
974A LEU* 3.4 5.6 - - + +
975A ASP* 2.7 44.8 + - + +
1023A LYS* 3.1 24.9 - - - -
1025A LEU* 3.5 25.8 - - + -
1028A MET* 2.9 12.2 - - + +
1029A VAL* 5.4 2.7 - - + -
971B TYR* 2.7 47.1 + + - -
972B GLY* 4.6 6.7 - - - -
975B ASP* 3.5 17.9 - - + -
1028B MET* 2.9 18.6 - - + +
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Residues in contact with GLY 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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968A ASP 4.7 0.8 + - - -
969A ILE 4.8 2.6 + - - -
970A GLY 3.4 0.4 - - - -
971A TYR* 1.3 79.3 - - - +
973A GLY* 1.3 55.8 + - - +
975A ASP* 3.6 6.1 + - - +
976A HIS* 3.0 27.5 + - - +
62B GLN* 3.9 13.8 - - - +
968B ASP 5.3 4.6 - - - +
971B TYR* 4.7 7.4 - - - -
972B GLY* 4.6 20.1 - - - -
1003B LYS* 5.0 1.0 + - - -
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Residues in contact with GLY 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A GLU 5.6 0.4 + - - -
873A ALA* 4.1 5.8 - - - -
874A GLU* 3.5 16.8 - - - -
969A ILE 5.6 0.4 + - - -
970A GLY* 3.3 5.5 + - - -
971A TYR 3.3 0.2 - - - -
972A GLY* 1.3 73.9 - - - +
974A LEU* 1.3 66.9 + - - +
976A HIS* 3.3 0.5 + - - +
977A VAL* 2.9 29.6 + - - +
62B GLN* 3.3 28.0 - - - +
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Residues in contact with LEU 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A ALA* 3.7 15.0 - - + +
965A TRP* 4.2 12.8 - - + -
966A ALA* 3.7 38.8 - - + +
970A GLY 2.8 22.0 + - - +
971A TYR* 3.4 7.0 - - + +
973A GLY* 1.3 72.4 - - - +
975A ASP* 1.3 58.5 + - - +
977A VAL* 3.3 1.5 + - + +
978A LEU* 2.9 53.0 + - + +
986A VAL* 3.8 29.8 - - + -
1025A LEU* 4.6 16.2 - - + -
1064A LEU* 5.0 3.1 - - + -
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Residues in contact with ASP 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A TYR* 2.7 29.0 + - + +
972A GLY 3.9 3.2 - - - +
974A LEU* 1.3 75.4 - - - +
976A HIS* 1.3 57.5 + - - +
978A LEU* 3.5 7.8 + - - +
979A ALA* 2.9 30.3 + - - +
1029A VAL* 5.7 2.6 - - + +
1032A TYR* 2.6 33.7 + - - -
971B TYR* 3.6 20.1 - - + -
1003B LYS* 3.3 12.1 + - - -
1023B LYS* 2.9 24.1 + - - -
1028B MET* 3.4 14.4 - - - +
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Residues in contact with HIS 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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877A PHE* 6.1 0.6 - + - -
972A GLY 3.0 18.6 + - - +
973A GLY 3.7 4.3 - - - +
974A LEU 3.3 0.2 - - - -
975A ASP* 1.3 77.9 + - - +
977A VAL* 1.3 58.6 + - + +
979A ALA* 3.2 3.8 + - - +
980A SER* 3.0 30.8 + - - -
60B GLU* 3.0 29.5 + - - +
61B MET* 3.3 30.9 + - - +
62B GLN* 3.5 30.2 + - + +
968B ASP* 4.6 2.7 + - - -
1003B LYS* 3.0 45.8 - - + +
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Residues in contact with VAL 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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873A ALA* 3.6 36.1 - - + +
874A GLU* 4.0 5.4 - - + +
877A PHE* 3.8 26.5 - - + -
959A ILE* 4.3 7.0 - - + -
973A GLY 2.9 20.0 + - - +
974A LEU 3.8 2.9 - - - +
976A HIS* 1.3 77.8 - - + +
978A LEU* 1.3 65.6 + - + +
980A SER* 2.6 29.3 + - - -
981A GLY 4.1 0.2 + - - -
984A VAL* 3.8 26.8 - - + +
986A VAL* 5.6 0.9 - - + -
1062A PRO* 4.6 3.3 - - - +
61B MET* 4.3 10.8 - - + -
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Residues in contact with LEU 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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974A LEU* 2.9 42.6 + - + +
975A ASP* 4.0 5.2 - - - +
977A VAL* 1.3 78.6 - - + +
979A ALA* 1.3 60.8 + - - +
980A SER 3.0 0.2 - - - -
981A GLY 3.3 0.9 + - - -
984A VAL* 5.3 3.1 - - + -
986A VAL* 3.6 25.6 - - + -
1029A VAL* 4.0 33.0 - - + -
1032A TYR* 5.2 3.1 - - + -
1034A TYR* 3.8 1.0 - - - -
1035A VAL* 3.6 22.0 - - + +
1062A PRO* 3.0 42.9 - - + +
1063A SER 4.0 14.1 - - - +
1064A LEU* 4.1 9.0 - - + -
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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
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975A ASP 2.9 18.6 + - - +
976A HIS 3.2 2.4 + - - +
978A LEU* 1.3 77.2 - - - +
980A SER* 1.3 61.9 + - - +
981A GLY 3.1 1.2 + - - -
1032A TYR* 3.6 24.8 - - + -
1034A TYR* 2.7 28.7 + - - +
1003B LYS* 3.5 27.6 - - + -
1020B THR* 3.5 9.2 + - - +
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Residues in contact with SER 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A PHE* 3.1 37.1 - - - -
976A HIS* 3.0 16.7 + - - -
977A VAL* 2.6 20.5 + - - -
978A LEU 3.0 1.2 - - - -
979A ALA* 1.3 78.8 - - - +
981A GLY* 1.3 60.9 + - - +
982A GLU* 3.1 17.8 + - - +
984A VAL* 5.8 0.2 - - - +
1020B THR* 4.1 11.0 - - - +
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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