Contacts of the helix formed by residues 1024 - 1031 (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 ASP1024 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1022A LYS 3.6 3.7 + - - +
1023A LYS* 1.3 72.0 - - - +
1025A LEU* 1.3 64.8 + - - +
1026A ALA* 3.8 1.9 + - - +
1027A ARG* 2.9 43.2 + - + +
1028A MET* 3.1 25.4 + - - +
1159A ARG* 2.6 48.6 + - - -
1031B THR* 4.3 24.1 + - - +
1032B TYR* 5.2 2.4 - - - -
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Residues in contact with LEU1025 (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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966A ALA* 4.2 18.2 - - + +
967A TYR* 3.8 45.0 + - + +
971A TYR* 3.5 36.8 - - + +
974A LEU* 4.6 8.1 - - + -
988A VAL* 4.9 2.7 - - + -
1023A LYS* 3.2 11.0 + - - +
1024A ASP* 1.3 73.8 - - - +
1026A ALA* 1.3 64.4 + - - +
1028A MET* 3.2 8.9 + - + +
1029A VAL* 2.9 38.7 + - + +
1064A LEU* 4.2 13.7 - - + -
1066A ILE* 4.1 13.7 - - + -
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Residues in contact with ALA1026 (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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1024A ASP* 3.2 6.5 - - - +
1025A LEU* 1.3 80.3 - - - +
1027A ARG* 1.3 57.6 + - - +
1029A VAL* 3.2 1.6 + - - -
1030A MET* 3.0 35.6 + - + +
1037A VAL* 3.9 13.2 - - + +
1039A THR* 4.6 3.4 - - + -
1064A LEU* 4.9 1.6 - - - -
1066A ILE* 4.1 19.7 - - + +
1099A PHE* 3.8 31.2 - - + -
1159A ARG* 4.3 3.8 - - - +
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Residues in contact with ARG1027 (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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1024A ASP* 2.9 36.5 + - - +
1026A ALA* 1.3 73.1 - - - +
1028A MET* 1.4 65.4 + - - +
1030A MET* 3.4 24.4 + - + +
1031A THR* 3.3 18.9 + - - +
1159A ARG* 4.5 9.7 - - - +
1162A GLU* 3.7 33.0 + - - +
1163A LEU* 4.3 21.5 - - + -
1166A MET* 4.3 14.8 - - + -
1031B THR* 3.8 42.7 + - + +
1173B GLU* 3.8 14.5 + - - -
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Residues in contact with MET1028 (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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971A TYR* 2.9 15.9 - - + +
1023A LYS* 3.9 27.4 - - - -
1024A ASP 3.1 10.9 + - - +
1025A LEU* 3.4 9.6 - - - +
1027A ARG* 1.4 77.2 - - - +
1029A VAL* 1.3 60.0 + - + +
1031A THR* 2.8 28.3 + - - +
1032A TYR* 4.6 0.7 - - - -
971B TYR* 2.9 29.6 - - - +
975B ASP* 3.9 15.0 - - - +
1028B MET* 3.5 45.3 - - + +
1029B VAL* 4.8 1.6 - - + +
1031B THR* 3.3 24.0 - - + +
1032B TYR* 4.7 5.4 - - + -
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Residues in contact with VAL1029 (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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971A TYR* 5.4 3.8 - - + -
974A LEU* 6.1 0.2 - - + -
975A ASP* 5.7 2.9 - - - +
978A LEU* 4.0 20.2 - - + -
1025A LEU* 2.9 29.6 + - + +
1026A ALA 3.2 1.1 + - - +
1028A MET* 1.3 73.3 - - + +
1030A MET* 1.3 58.6 + - - +
1031A THR 3.0 10.2 + - - -
1032A TYR* 3.0 33.5 + - + +
1033A GLY 4.4 0.5 + - - -
1035A VAL* 3.6 23.8 - - + +
1037A VAL* 3.4 24.7 - - + -
1064A LEU* 3.8 19.3 - - + -
1028B MET* 5.6 2.0 - - + -
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Residues in contact with MET1030 (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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1026A ALA* 3.0 33.1 + - + +
1027A ARG* 3.9 17.7 - - + +
1028A MET 3.4 0.6 - - - -
1029A VAL* 1.3 75.1 - - - +
1031A THR* 1.3 60.1 + - - +
1032A TYR 3.2 0.7 + - - -
1033A GLY* 3.3 13.5 + - - +
1035A VAL 5.5 0.7 - - - -
1037A VAL* 3.8 16.8 - - + -
1099A PHE* 3.1 37.9 - - + -
1101A TYR* 3.6 54.9 + - + -
1113A PHE* 3.8 16.2 - - + -
1163A LEU* 5.5 0.4 - - + -
1166A MET* 4.0 12.6 - - + -
1173A GLU* 4.3 2.8 - - - +
1027B ARG* 5.0 0.2 + - - -
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Residues in contact with THR1031 (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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1027A ARG 3.3 17.9 - - - +
1028A MET* 2.8 19.2 + - - +
1029A VAL 3.0 0.4 + - - -
1030A MET* 1.3 78.5 - - - +
1032A TYR* 1.3 66.0 + - - +
1033A GLY 3.3 0.2 - - - -
1173A GLU* 3.2 12.5 - - - +
1024B ASP* 4.2 20.6 + - - +
1027B ARG* 3.6 51.4 + - + +
1028B MET* 3.6 17.1 - - + +
1031B THR* 5.3 1.6 - - + -
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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