Contacts of the helix formed by residues 928 - 938 (chain A) in PDB entry 3IKM
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 928 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922A GLN* 4.9 6.1 - - - -
923A GLY* 3.6 10.9 + - - -
927A ARG* 1.3 85.5 - - - +
929A THR* 1.3 52.8 + - - -
930A ASP 2.7 5.6 - - - -
931A LEU* 2.3 42.8 + - - +
932A HIS* 2.9 13.4 + - - -
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Residues in contact with THR 929 (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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926A SER* 6.2 0.2 - - - -
927A ARG* 3.2 24.4 + - - +
928A GLY* 1.3 76.0 - - - +
930A ASP* 1.3 50.5 + - - +
932A HIS* 3.0 14.1 + - - +
933A SER* 2.5 35.8 + - - -
943A ARG* 4.5 6.5 - - + +
947A LYS* 3.0 47.3 + - + +
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Residues in contact with ASP 930 (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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922A GLN* 2.9 21.5 - - - +
923A GLY 4.6 0.4 - - - -
924A ARG* 4.0 13.3 - - - +
925A LYS* 5.1 5.9 - - - +
926A SER* 4.4 11.9 + - - +
927A ARG 2.6 24.2 + - - +
929A THR* 1.3 80.4 - - - +
931A LEU* 1.3 52.7 + - - -
933A SER* 2.4 31.7 + - - +
934A LYS* 2.9 13.2 + - - +
943A ARG* 4.1 7.6 - - - +
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Residues in contact with LEU 931 (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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918A TRP* 3.6 36.6 - - + +
919A MET* 3.8 28.0 - - + +
922A GLN* 4.3 6.0 + - + +
927A ARG 3.8 0.6 + - - -
928A GLY* 2.3 36.5 + - - +
930A ASP* 1.3 65.8 + - - +
932A HIS* 1.3 99.3 + - + +
933A SER 2.8 0.9 - - - -
934A LYS* 2.5 52.6 + - + +
935A THR* 2.9 8.4 + - - +
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Residues in contact with HIS 932 (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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896A LEU* 4.8 10.9 - - + +
919A MET* 6.5 0.9 - - - -
927A ARG* 6.1 1.1 - - - -
928A GLY* 2.9 29.4 + - - -
929A THR* 3.3 14.6 - - - +
931A LEU* 1.3 95.6 - - + +
933A SER* 1.3 55.6 + - - +
935A THR* 2.6 38.6 + - - +
936A ALA* 3.2 4.7 + - - +
943A ARG* 4.9 1.1 - - - -
946A ALA* 4.9 1.6 - - - +
947A LYS* 3.3 49.1 - - + -
950A ASN* 5.3 7.0 - - + +
951A TYR* 3.5 29.2 + + - -
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Residues in contact with SER 933 (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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929A THR 2.5 19.1 + - - -
930A ASP* 2.4 26.2 + - - -
932A HIS* 1.3 73.3 - - - +
934A LYS* 1.3 49.5 + - - -
936A ALA* 3.3 1.4 + - - +
937A THR* 2.6 42.4 + - - -
943A ARG* 2.9 59.5 + - - +
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Residues in contact with LYS 934 (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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918A TRP* 5.0 15.6 - - + +
920A THR* 4.9 6.7 - - - +
922A GLN* 3.2 36.6 - - - +
924A ARG* 5.3 3.4 - - - +
930A ASP* 2.9 13.4 + - - +
931A LEU* 2.5 43.3 + - + +
933A SER* 1.3 72.5 - - - +
935A THR* 1.3 56.8 + - - +
937A THR* 4.5 5.2 - - - -
938A THR* 2.8 38.3 + - + +
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Residues in contact with THR 935 (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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931A LEU* 2.9 10.8 + - - +
932A HIS* 2.6 22.7 + - - +
934A LYS* 1.3 72.2 - - - +
936A ALA* 1.3 54.3 + - - +
938A THR* 2.6 25.4 + - - +
939A VAL* 3.9 6.9 - - - +
946A ALA* 4.3 11.2 - - + +
950A ASN* 3.5 31.9 + - - +
953A ARG* 4.9 7.6 - - - +
985A MET* 6.6 0.2 - - + -
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Residues in contact with ALA 936 (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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932A HIS 3.2 3.0 + - - +
933A SER 4.0 4.3 - - - +
935A THR* 1.3 77.9 - - - +
937A THR* 1.3 51.5 + - - +
938A THR 3.1 2.9 - - - -
939A VAL* 2.5 40.9 - - - +
940A GLY 2.6 1.9 + - - -
941A ILE* 2.8 18.0 + - + +
942A SER 3.2 28.5 - - - +
943A ARG* 4.1 5.6 - - + -
946A ALA* 3.3 17.3 - - + -
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Residues in contact with THR 937 (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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933A SER* 2.6 35.8 + - - -
934A LYS* 4.2 4.9 - - - -
936A ALA* 1.3 68.4 - - - +
938A THR* 1.3 59.8 + - + +
939A VAL 2.8 0.5 + - - -
940A GLY* 2.3 32.3 + - - -
941A ILE 4.2 2.8 + - - +
943A ARG* 4.0 12.8 + - - -
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Residues in contact with THR 938 (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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934A LYS* 2.8 29.2 + - + +
935A THR* 2.6 18.7 + - - +
936A ALA 2.9 1.6 - - - +
937A THR* 1.3 71.1 - - - +
939A VAL* 1.3 74.6 + - - +
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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