Contacts of the helix formed by residues 1024 - 1031 (chain B) 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 ASP1024 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031A THR* 4.2 25.1 + - - +
1032A TYR* 5.1 2.8 - - - +
1022B LYS* 3.5 4.5 + - - +
1023B LYS* 1.3 74.1 - - - +
1025B LEU* 1.3 64.1 + - - +
1026B ALA* 3.8 1.9 + - - +
1027B ARG* 2.7 48.0 + - - +
1028B MET* 3.1 25.1 + - - +
1159B ARG* 2.9 42.9 + - - +
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Residues in contact with LEU1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966B ALA* 4.2 17.3 - - + +
967B TYR* 3.8 46.7 + - + +
971B TYR* 3.4 38.4 - - + +
974B LEU* 4.6 7.6 - - + -
988B VAL* 4.9 0.4 - - + -
1023B LYS* 3.1 15.3 + - + -
1024B ASP* 1.3 71.7 - - - +
1026B ALA* 1.3 58.8 + - - +
1028B MET* 3.2 5.2 + - + +
1029B VAL* 3.0 40.9 + - + +
1064B LEU* 4.2 11.2 - - + -
1066B ILE* 3.9 17.9 - - + -
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Residues in contact with ALA1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024B ASP* 3.3 6.3 - - - +
1025B LEU* 1.3 80.2 - - - +
1027B ARG* 1.3 56.7 + - - +
1029B VAL* 3.3 1.4 + - - -
1030B MET* 3.1 34.7 + - - +
1037B VAL* 3.9 14.5 - - + +
1039B THR* 4.5 3.4 - - + -
1064B LEU* 4.9 1.1 - - - -
1066B ILE* 4.1 19.3 - - + +
1099B PHE* 3.7 33.4 - - + -
1159B ARG* 4.3 3.4 - - - +
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Residues in contact with ARG1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A MET 5.0 0.2 + - - -
1031A THR* 3.6 38.6 + - + +
1173A GLU* 3.4 29.9 + - - -
1024B ASP* 2.7 33.9 + - - +
1026B ALA* 1.3 72.9 - - - +
1028B MET* 1.3 65.6 + - - +
1030B MET* 3.4 28.4 + - + +
1031B THR* 3.3 17.8 + - - +
1159B ARG* 4.6 10.9 - - - +
1162B GLU* 3.9 24.1 + - - +
1163B LEU* 4.4 12.3 - - + -
1166B MET* 4.4 19.9 - - - -
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Residues in contact with MET1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A TYR* 2.9 30.3 - - + +
975A ASP* 3.4 19.7 - - - +
1028A MET* 3.5 55.7 - - + +
1029A VAL* 5.0 2.0 - - + +
1031A THR* 3.6 8.1 - - + +
1032A TYR* 4.6 5.2 - - + -
971B TYR* 3.0 14.6 - - + +
1023B LYS* 3.8 24.5 - - - -
1024B ASP 3.1 16.4 + - - +
1025B LEU* 3.6 7.0 - - + +
1027B ARG* 1.3 79.3 - - - +
1029B VAL* 1.3 61.1 + - + +
1031B THR* 2.8 28.8 + - - -
1032B TYR* 4.6 1.2 - - - -
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Residues in contact with VAL1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A MET* 5.3 1.6 - - + -
971B TYR* 5.3 4.5 - - + -
974B LEU* 6.0 0.2 - - + -
975B ASP* 5.9 3.1 - - - +
978B LEU* 3.9 19.3 - - + -
1025B LEU* 3.0 29.8 + - + +
1026B ALA 3.3 0.6 + - - -
1028B MET* 1.3 76.9 - - + +
1030B MET* 1.3 62.2 + - - +
1031B THR 3.2 1.0 + - - -
1032B TYR* 3.2 32.5 + - + +
1033B GLY 4.5 0.2 + - - -
1035B VAL* 3.5 25.6 - - + +
1037B VAL* 3.2 25.4 - - + -
1064B LEU* 3.7 20.2 - - + -
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Residues in contact with MET1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B ALA 3.1 16.4 + - - +
1027B ARG* 3.8 36.6 - - + +
1028B MET 3.2 0.4 - - - -
1029B VAL* 1.3 77.3 - - - +
1031B THR* 1.3 60.6 + - - +
1032B TYR 3.1 1.3 + - - -
1033B GLY* 3.3 11.8 + - - +
1035B VAL 5.5 0.2 - - - -
1037B VAL* 3.9 20.4 - - + -
1099B PHE* 3.7 28.5 - - + -
1101B TYR* 3.7 45.6 - - + -
1113B PHE* 3.9 20.2 - - + -
1163B LEU* 4.9 0.9 - - + -
1166B MET* 4.0 15.0 - - + -
1173B GLU* 3.4 8.5 - - - +
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Residues in contact with THR1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A ASP* 4.3 19.3 + - - +
1027A ARG* 3.8 46.6 + - + +
1028A MET* 3.3 26.9 - - + +
1031A THR* 5.3 2.0 - - + -
1027B ARG 3.3 17.5 - - - +
1028B MET* 2.8 16.8 + - - +
1029B VAL 3.2 0.4 + - - -
1030B MET* 1.3 74.9 - - - +
1032B TYR* 1.4 66.1 + - - +
1173B GLU* 3.2 15.1 - - - +
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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