Contacts of the helix formed by residues 920 - 929 (chain B) in PDB entry 5KKR
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 THR 920 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778B HIS* 3.8 27.4 - - + +
853B LYS* 5.5 5.2 - - + -
854B HIS* 4.9 15.3 - - + +
857B VAL* 4.7 1.3 - - - -
918B ARG 5.2 0.7 - - - +
919B PRO* 1.3 74.6 - - - +
921B PHE* 1.3 55.0 + - - +
922B THR* 3.1 16.9 + - - -
923B LYS* 3.0 16.7 + - + +
924B LEU* 2.5 37.5 + - - +
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Residues in contact with PHE 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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771B VAL* 3.2 41.3 - - + +
774B MET* 3.6 29.2 - - + -
775B GLY* 4.2 10.3 - - - -
778B HIS* 4.5 4.7 - - + -
853B LYS* 3.5 39.9 - - + -
856B ASP* 3.5 39.0 - - + -
857B VAL* 3.5 17.9 - - + +
860B LEU* 3.5 26.5 - - + -
920B THR* 1.3 73.8 - - - +
922B THR* 1.3 58.4 + - - +
924B LEU* 3.8 6.5 - - + -
925B MET* 3.0 26.7 + - - +
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Residues in contact with THR 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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775B GLY* 5.0 11.9 - - - +
778B HIS* 3.6 23.1 + - + -
920B THR* 3.1 13.7 + - - -
921B PHE* 1.3 78.3 - - - +
923B LYS* 1.3 62.4 + - - +
925B MET* 3.7 15.2 + - - +
926B ASP* 4.2 3.6 + - - +
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Residues in contact with LYS 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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909B PHE* 5.3 5.3 - - - -
917B GLU 5.3 4.0 + - - -
918B ARG 5.5 0.2 - - - -
919B PRO* 3.7 27.1 - - + +
920B THR* 3.0 19.4 + - + +
922B THR* 1.3 79.5 + - - +
924B LEU* 1.3 65.6 + - - +
926B ASP* 3.4 18.5 + - - +
927B MET* 3.8 29.4 + - + +
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Residues in contact with LEU 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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771B VAL* 3.8 19.5 - - + -
857B VAL* 4.2 12.6 - - + -
860B LEU* 3.6 30.3 - - + -
906B ILE* 3.8 19.3 - - + -
910B CYS* 3.7 23.3 - - - -
919B PRO* 4.5 12.1 - - + -
920B THR 2.5 21.0 + - - +
921B PHE* 3.2 9.2 + - + +
923B LYS* 1.3 73.3 - - - +
925B MET* 1.3 58.6 + - - +
927B MET* 2.9 32.2 + - - +
928B LEU* 3.2 24.1 - - + +
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Residues in contact with MET 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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768B GLN* 4.0 34.3 - - - +
771B VAL* 3.7 31.2 - - + +
772B LYS* 4.7 14.8 - - + -
921B PHE 3.0 14.1 + - - +
922B THR* 3.7 11.0 - - - +
923B LYS 3.3 0.2 - - - -
924B LEU* 1.3 76.9 - - - +
926B ASP* 1.3 59.6 + - - +
928B LEU* 3.4 4.7 + - - -
929B GLU* 3.1 36.4 + - - +
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Residues in contact with ASP 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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922B THR 4.2 3.3 + - - +
923B LYS* 3.4 13.5 + - - +
924B LEU 3.1 0.6 - - - -
925B MET* 1.3 78.7 - - - +
927B MET* 1.3 62.3 + - + +
928B LEU 3.5 0.3 + - - -
929B GLU* 3.7 13.5 + - - +
930B LYS* 2.7 63.5 + - - +
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Residues in contact with MET 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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906B ILE* 3.6 31.5 - - + +
909B PHE* 4.1 26.5 - - + -
919B PRO* 3.8 33.2 - - + -
923B LYS* 3.8 29.4 - - + +
924B LEU* 2.9 21.4 + - + +
926B ASP* 1.3 78.4 - - + +
928B LEU* 1.3 62.3 + - + +
930B LYS* 4.0 14.0 - - - +
931B LEU 5.2 1.9 + - - +
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Residues in contact with LEU 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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764B ARG* 3.2 34.2 - - + +
767B ALA* 4.1 14.8 - - + +
768B GLN* 3.8 24.9 - - + -
771B VAL* 3.6 33.9 - - + -
860B LEU* 6.1 1.8 - - + -
864B TRP* 5.1 11.2 - - + +
906B ILE* 3.9 24.0 - - + -
924B LEU* 3.2 35.0 - - + +
925B MET* 3.4 6.5 + - - +
926B ASP 3.2 0.2 - - - -
927B MET* 1.3 77.7 - - - +
929B GLU* 1.3 60.2 - - - +
930B LYS 3.1 5.8 + - - -
931B LEU 3.5 2.8 + - - -
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Residues in contact with GLU 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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764B ARG* 4.4 3.4 - - - +
768B GLN* 3.9 17.9 - - - +
925B MET* 3.1 30.0 + - + +
926B ASP* 3.7 16.8 + - - +
928B LEU* 1.3 72.5 - - - +
930B LYS* 1.3 58.8 + - + +
931B LEU* 3.1 23.2 + - - +
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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
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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