Contacts of the helix formed by residues 1046 - 1059 (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 GLU1046 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1042A GLU 4.1 2.0 + - - +
1043A VAL* 2.7 49.3 - - + +
1045A ALA* 1.3 67.3 - - - +
1047A ARG* 1.3 59.9 + - - +
1048A ALA 2.9 1.3 - - - -
1049A TRP* 2.3 90.4 + - + +
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Residues in contact with ARG1047 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A LEU* 3.7 41.0 - - + +
1043A VAL* 2.5 33.1 + - + +
1044A VAL* 4.4 5.6 - - - +
1046A GLU* 1.3 87.1 + - - +
1048A ALA* 1.3 58.2 + - - +
1049A TRP* 3.5 6.1 - - - +
1050A LYS* 2.9 58.9 + - - +
1051A GLY 3.8 4.9 + - - -
1090A GLU* 5.3 2.9 - - - +
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Residues in contact with ALA1048 (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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307A PHE* 4.2 12.1 - - - -
311A LEU* 5.4 0.4 - - - -
1044A VAL 3.3 14.6 + - - +
1045A ALA 3.1 3.7 + - - +
1047A ARG* 1.3 79.0 - - - +
1049A TRP* 1.3 62.9 + - - +
1050A LYS 3.1 0.6 + - - -
1051A GLY 3.6 8.3 + - - +
1052A GLY 4.7 1.0 + - - -
1090A GLU* 3.4 27.7 + - + +
1092A PHE* 3.0 37.5 - - + -
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Residues in contact with TRP1049 (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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964A ARG* 5.9 5.2 - - - -
1045A ALA 2.9 8.1 + - - +
1046A GLU* 2.3 71.8 + - + +
1047A ARG* 3.5 5.3 - - - +
1048A ALA* 1.3 77.6 - - - +
1050A LYS* 1.3 95.4 + - + +
1051A GLY 3.7 0.3 + - - -
1052A GLY* 4.5 4.9 + - - -
1092A PHE* 5.8 0.4 - - - -
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Residues in contact with LYS1050 (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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1046A GLU 3.3 0.2 + - - -
1047A ARG* 2.9 48.7 - - - +
1048A ALA 3.1 0.8 - - - -
1049A TRP* 1.3 111.8 - - + +
1051A GLY* 1.3 60.8 + - - +
1052A GLY 3.7 0.6 + - - -
1053A THR 5.3 0.5 + - - -
1054A GLU* 3.3 33.5 - - - +
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Residues in contact with GLY1051 (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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307A PHE* 3.4 25.8 - - - -
311A LEU* 5.9 3.1 - - - +
1047A ARG 3.8 5.8 + - - -
1048A ALA 3.6 5.3 + - - -
1049A TRP 3.6 1.6 - - - -
1050A LYS* 1.3 76.5 - - - +
1052A GLY* 1.3 53.9 + - - +
1053A THR 3.9 0.2 - - - -
1054A GLU* 3.6 6.7 + - - +
1055A SER* 2.8 41.7 + - - -
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Residues in contact with GLY1052 (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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307A PHE* 4.0 12.9 - - - -
961A PHE* 4.2 18.2 - - - -
1048A ALA 4.7 1.2 + - - -
1049A TRP 4.5 5.0 + - - -
1050A LYS 3.7 2.4 + - - -
1051A GLY* 1.3 75.2 - - - +
1053A THR* 1.3 63.9 + - - +
1055A SER* 3.0 6.9 + - - -
1056A GLU* 2.9 25.5 - - - +
1094A THR* 5.7 5.4 - - - -
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Residues in contact with THR1053 (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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755A LYS* 5.3 4.0 - - + -
756A ASP* 5.7 4.9 - - - +
960A PRO* 4.9 1.6 - - - +
961A PHE* 4.0 36.5 + - - -
964A ARG* 3.7 40.9 + - + +
965A LEU* 4.2 23.8 - - + +
968A GLN* 5.2 3.4 - - - +
1050A LYS 5.3 0.4 + - - -
1051A GLY 3.9 0.4 - - - -
1052A GLY* 1.3 68.2 - - - +
1054A GLU* 1.3 69.6 + - - +
1056A GLU* 2.8 19.3 + - - +
1057A MET* 3.2 10.7 + - + +
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Residues in contact with GLU1054 (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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732A TYR* 4.1 13.0 + - - -
755A LYS* 4.2 8.9 - - + +
758A ASN* 2.9 32.6 + - - +
964A ARG* 5.2 10.3 - - - +
1050A LYS* 3.3 37.8 - - - +
1051A GLY* 3.7 4.3 - - - +
1053A THR* 1.3 80.4 - - - +
1055A SER* 1.3 63.9 + - - +
1057A MET* 3.0 3.4 + - - -
1058A PHE* 2.6 45.5 + - + -
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Residues in contact with SER1055 (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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306A SER* 3.9 3.7 + - - -
307A PHE* 2.9 45.4 + - - +
1051A GLY 2.8 26.6 + - - -
1052A GLY 3.0 7.2 + - - -
1054A GLU* 1.3 72.9 - - - +
1056A GLU* 1.3 54.1 + - - +
1058A PHE* 3.5 6.5 - - - +
1059A ASN* 2.2 49.8 + - - +
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Residues in contact with GLU1056 (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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307A PHE* 5.5 2.4 - - - -
955A TYR* 5.8 0.5 - - - +
956A GLY* 5.3 3.8 + - - -
961A PHE* 5.2 8.0 - - - -
965A LEU* 5.9 10.3 - - + -
1052A GLY* 2.9 18.4 - - - +
1053A THR* 2.8 18.0 + - - +
1055A SER* 1.3 74.4 - - - +
1057A MET* 1.3 57.8 + - - +
1058A PHE 3.0 5.2 + - - -
1059A ASN* 2.7 26.3 + - - +
1060A LYS* 3.7 7.8 + - - -
1064A ILE* 3.5 9.5 - - - +
1065A ALA* 4.8 3.6 + - - +
1074A VAL* 4.6 9.3 - - + -
1094A THR* 4.8 13.4 - - - +
1098A ASN* 4.4 14.7 + - - -
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Residues in contact with MET1057 (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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756A ASP* 2.7 50.6 - - + +
769A ASP* 2.8 32.5 - - - +
770A PHE* 5.7 0.9 - - + -
773A LYS* 2.8 37.9 - - - +
965A LEU* 5.7 9.3 - - + +
969A PHE* 5.3 4.3 - - - -
1053A THR* 3.2 9.2 + - + +
1054A GLU* 3.0 7.8 + - - +
1056A GLU* 1.3 73.2 - - - +
1058A PHE* 1.3 57.4 + - - +
1064A ILE* 2.5 49.4 - - + +
1065A ALA* 4.2 13.9 - - - -
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Residues in contact with PHE1058 (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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755A LYS 3.4 12.3 - - - -
756A ASP* 3.4 21.5 - - - -
757A GLY 3.7 3.4 - - - -
758A ASN* 2.8 46.2 - - + -
1054A GLU* 2.6 33.3 + - + +
1055A SER* 3.5 7.9 - - - +
1057A MET* 1.3 87.8 - - + +
1059A ASN* 1.3 52.4 + - - +
1060A LYS 2.4 36.6 + - - +
1061A LEU* 4.7 0.2 - - - -
1064A ILE* 4.4 1.1 - - - -
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Residues in contact with ASN1059 (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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306A SER* 3.9 18.6 + - - -
1055A SER* 2.2 42.4 + - - +
1056A GLU* 2.7 36.4 + - - +
1058A PHE* 1.3 68.1 - - - +
1060A LYS* 1.3 66.6 + - + +
1061A LEU 4.0 1.6 + - - -
1074A VAL 3.1 39.4 - - - +
1099A TRP* 5.8 3.1 - - - -
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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
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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