Contacts of the helix formed by residues 919 - 934 (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 ASP 919 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916B GLY* 3.0 15.1 + - - +
917B LYS 3.4 0.4 - - - -
918B ASN* 1.3 77.0 - - - +
920B PRO* 1.3 69.9 - - - +
921B ILE* 3.1 15.2 + - - +
922B LYS* 2.7 39.3 + - + +
923B SER* 2.8 31.9 + - - -
954B LYS* 4.3 0.7 - - - -
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Residues in contact with PRO 920 (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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831B ARG* 3.5 47.3 - - - +
918B ASN 3.7 7.6 - - - +
919B ASP* 1.3 93.4 - - - +
921B ILE* 1.3 65.4 + - + +
923B SER* 3.4 7.6 + - - +
924B LYS* 3.3 21.0 - - - +
953B THR* 4.5 3.3 + - - -
954B LYS* 4.3 11.4 - - + +
1057B GLU* 4.7 6.3 - - - +
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Residues in contact with ILE 921 (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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919B ASP* 3.1 11.1 + - - +
920B PRO* 1.3 80.3 - - + +
922B LYS* 1.3 76.2 + - + +
924B LYS* 3.3 5.1 + - - +
925B GLU* 3.0 30.7 + - + +
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Residues in contact with LYS 922 (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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912B GLY 4.8 0.5 - - - +
916B GLY* 4.0 21.8 - - - -
919B ASP* 2.7 24.6 + - + +
921B ILE* 1.3 79.5 - - + +
923B SER* 1.4 64.4 + - - +
925B GLU* 3.5 24.2 - - - +
926B TYR* 3.1 48.5 + - + +
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Residues in contact with SER 923 (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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913B TRP* 3.4 13.9 - - - -
916B GLY 3.3 15.5 + - - -
917B LYS* 3.6 15.3 - - - -
919B ASP 2.8 24.3 + - - -
920B PRO 3.4 4.3 + - - -
922B LYS* 1.4 78.3 - - - +
924B LYS* 1.4 58.9 + - - +
927B GLY* 2.9 26.0 + - - -
952B TYR 3.5 20.1 - - - +
953B THR* 3.5 0.4 - - - -
954B LYS* 2.8 21.0 + - - +
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Residues in contact with LYS 924 (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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830B GLU* 6.1 3.8 - - + +
831B ARG* 6.5 1.1 - - - -
858B LEU* 5.9 4.8 - - - +
860B GLN* 5.2 7.7 + - - +
920B PRO 3.3 17.9 + - - +
921B ILE* 3.3 4.0 + - - +
922B LYS 3.2 0.2 - - - -
923B SER* 1.4 80.2 + - - +
925B GLU* 1.3 58.6 + - - +
928B ASP* 2.7 66.7 + - - +
953B THR* 3.7 28.5 - - + +
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Residues in contact with GLU 925 (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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921B ILE* 3.0 21.7 + - + +
922B LYS* 3.5 30.5 - - - +
924B LYS* 1.3 78.7 - - - +
926B TYR* 1.3 78.1 + - + +
928B ASP* 3.5 5.9 + - - +
929B LYS* 3.3 44.6 + - - +
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Residues in contact with TYR 926 (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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908B GLU* 4.3 9.9 - - - -
909B ALA* 3.6 18.5 - - - +
912B GLY* 3.5 36.6 - - - -
913B TRP* 3.5 19.1 - - - +
922B LYS* 3.1 48.7 + - + +
925B GLU* 1.3 89.8 + - + +
927B GLY* 1.3 66.7 + - - +
929B LYS* 3.0 35.0 + - + +
930B LEU* 2.9 28.7 + - - +
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Residues in contact with GLY 927 (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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913B TRP* 4.1 2.8 - - - -
923B SER 2.9 21.2 + - - -
924B LYS* 3.8 0.9 - - - -
926B TYR* 1.3 77.3 - - - +
928B ASP* 1.3 59.0 + - - +
930B LEU* 3.2 6.4 + - - -
931B LYS* 2.9 26.2 + - - +
952B TYR* 3.3 36.9 - - - -
953B THR* 6.0 0.4 - - - -
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Residues in contact with ASP 928 (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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924B LYS* 2.7 61.3 + - - +
925B GLU* 3.9 5.5 - - - +
927B GLY* 1.3 73.4 - - - +
929B LYS* 1.3 62.4 + - + +
931B LYS* 3.2 34.1 + - - +
932B LYS* 3.3 21.8 + - + +
953B THR* 4.8 2.4 - - - +
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Residues in contact with LYS 929 (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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908B GLU* 5.4 4.9 + - - -
909B ALA* 4.0 14.8 - - + -
925B GLU* 3.3 31.2 + - - +
926B TYR* 3.0 43.8 + - + +
928B ASP* 1.3 75.2 - - + +
930B LEU* 1.4 60.5 - - - +
932B LYS* 3.0 14.2 + - + +
933B LEU* 2.8 38.4 + - + +
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Residues in contact with LEU 930 (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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906B VAL* 4.1 10.1 - - + +
909B ALA* 3.6 35.0 - - + +
910B LEU* 3.8 28.7 - - + -
913B TRP* 4.1 17.3 - - + -
926B TYR 2.9 20.0 + - - +
927B GLY* 3.4 10.3 - - - +
929B LYS* 1.4 79.9 - - - +
931B LYS* 1.4 56.0 + - - +
933B LEU* 4.4 5.8 - - + +
934B LEU* 2.9 52.2 + - + +
945B ILE* 5.0 0.7 - - + -
952B TYR* 3.6 23.2 + - + +
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Residues in contact with LYS 931 (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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211A GLU* 2.8 36.0 + - - -
860B GLN* 5.8 0.6 + - - -
927B GLY 2.9 13.2 + - - +
928B ASP* 3.2 32.0 + - + +
930B LEU* 1.4 77.2 - - - +
932B LYS* 1.3 63.4 + - + +
934B LEU* 4.3 0.4 - - - -
935B ALA* 3.5 19.8 + - - +
949B SER* 3.5 34.7 + - - -
952B TYR* 3.9 16.4 - - + -
953B THR* 4.7 4.4 - - - +
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Residues in contact with LYS 932 (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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928B ASP* 3.3 15.9 + - + +
929B LYS* 3.0 13.5 + - + +
931B LYS* 1.3 77.6 - - + +
933B LEU* 1.3 66.5 + - + +
935B ALA* 3.2 19.6 + - - +
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Residues in contact with LEU 933 (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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903B SER* 5.5 0.7 - - - +
905B ASP* 3.5 50.0 - - + +
906B VAL* 3.8 21.8 - - + +
909B ALA* 4.0 14.1 - - + -
929B LYS* 2.8 27.9 + - + +
930B LEU* 4.3 4.7 - - + +
932B LYS* 1.3 75.6 - - + +
934B LEU* 1.3 62.5 + - + +
935B ALA 3.4 2.0 + - - +
937B GLN* 4.9 5.0 - - - +
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Residues in contact with LEU 934 (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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906B VAL* 3.9 26.9 - - + -
910B LEU* 5.5 0.7 - - + -
930B LEU* 2.9 36.5 + - + +
931B LYS* 4.3 0.7 - - - -
933B LEU* 1.3 73.4 - - - +
935B ALA* 1.3 59.2 + - - +
936B GLY 3.1 0.7 + - - -
937B GLN* 2.8 39.6 + - + +
942B LEU* 3.6 40.6 - - + +
945B ILE* 3.8 30.1 - - + -
946B ALA* 4.0 16.3 - - + +
952B TYR* 4.0 9.9 - - - +
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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