Contacts of the helix formed by residues 912 - 925 (chain A) in PDB entry 6J8H
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 912 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASN* 3.0 23.7 + - - +
885A MET* 4.5 3.8 - - - -
909A HIS* 4.0 9.6 + - - -
911A ASN* 1.3 84.6 + - - +
913A PHE* 1.3 56.7 + - - +
914A PHE* 3.3 7.9 - - + +
915A HIS* 4.0 21.9 + - + +
916A SER* 2.6 39.2 + - - -
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Residues in contact with PHE 913 (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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144A THR* 3.4 39.7 + - + +
146A ASN* 5.2 1.0 - - - +
878A PHE* 3.7 38.8 - + - -
881A ALA* 3.8 26.2 - - + -
882A VAL* 4.4 5.8 - - + -
885A MET* 3.7 31.5 - - + +
912A ASP* 1.3 70.5 - - - +
914A PHE* 1.3 67.3 + + + +
916A SER* 3.7 1.1 - - - -
917A PHE* 2.7 41.0 + + + +
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Residues in contact with PHE 914 (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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912A ASP* 3.3 4.5 - - + +
913A PHE* 1.3 84.0 - + + +
915A HIS* 1.3 62.1 + - - +
917A PHE* 3.2 24.8 + + - +
918A LEU* 2.9 45.7 + - + +
1431A LEU* 3.4 42.6 - - + -
1432A TYR* 3.9 26.0 - + + +
1434A TYR* 4.1 10.5 - - + -
1435A ILE* 3.7 33.7 - - + -
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Residues in contact with HIS 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A ARG 3.7 19.6 + - - -
908A TRP* 5.1 2.2 - + - -
909A HIS* 3.3 59.0 + + + +
912A ASP* 3.3 19.7 + - + +
913A PHE 3.2 0.4 - - - -
914A PHE* 1.3 81.7 - + - +
916A SER* 1.3 65.5 + - - +
918A LEU* 3.2 25.9 + - + +
919A ILE* 3.2 10.7 + - - +
1428A GLU* 3.6 30.8 + - - -
1431A LEU* 4.2 23.9 - - + +
1434A TYR* 5.0 5.5 - + - -
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Residues in contact with SER 916 (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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881A ALA* 2.1 40.1 + - - +
884A GLY* 5.0 0.3 - - - -
885A MET* 4.0 13.9 + - - -
909A HIS 3.9 0.6 + - - -
910A MET* 4.0 26.8 - - - +
912A ASP 2.6 21.9 + - - -
913A PHE* 3.8 3.4 + - - -
915A HIS* 1.3 72.7 - - - +
917A PHE* 1.3 62.8 + - - +
919A ILE* 3.4 5.0 + - - +
920A VAL* 3.3 23.2 + - - +
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Residues in contact with PHE 917 (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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877A VAL* 3.6 30.5 - - + -
878A PHE* 6.3 0.2 - - - -
881A ALA* 3.7 15.7 - - + -
913A PHE* 2.7 32.0 + + + +
914A PHE* 3.4 27.6 - + - +
916A SER* 1.3 76.0 + - - +
918A LEU* 1.3 77.8 + - + +
920A VAL* 3.2 2.5 + - - +
921A PHE* 3.0 40.6 + + + +
1435A ILE* 5.7 3.4 - - + -
1438A VAL* 4.9 15.0 - - + -
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Residues in contact with LEU 918 (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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908A TRP* 3.8 26.4 - - + -
914A PHE* 2.9 40.9 + - + +
915A HIS* 3.2 19.7 + - + +
917A PHE* 1.3 90.4 - - + +
919A ILE* 1.3 61.4 + - - +
921A PHE* 3.3 8.7 + - + +
922A ARG* 3.0 23.0 + - - +
1412A MET* 6.0 0.2 - - + -
1434A TYR* 4.0 37.5 - - + -
1438A VAL* 4.3 23.8 - - + -
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Residues in contact with ILE 919 (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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892A TYR* 4.4 5.8 - - - +
908A TRP* 4.0 16.8 - - + +
909A HIS* 3.6 44.4 - - - +
910A MET* 3.7 27.1 - - + +
915A HIS 3.2 4.0 + - - +
916A SER 3.8 6.7 - - - +
918A LEU* 1.3 78.4 - - - +
920A VAL* 1.3 64.2 + - + +
922A ARG* 3.3 8.5 + - + +
923A VAL* 3.2 26.6 + - + +
931A THR* 3.5 29.6 + - + +
948A TYR* 3.8 15.0 - - + +
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Residues in contact with VAL 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A VAL* 4.2 23.8 - - + +
880A PHE* 4.0 24.9 - - + +
881A ALA* 3.8 23.1 - - - +
910A MET* 4.6 11.9 - - + -
916A SER 3.3 12.3 + - - +
917A PHE* 3.2 9.7 + - - +
919A ILE* 1.3 77.0 - - + +
921A PHE* 1.3 64.4 + - - +
923A VAL* 3.3 15.9 + - - +
924A LEU* 3.5 17.5 + - + +
951A VAL* 4.2 18.8 - - + -
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Residues in contact with PHE 921 (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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877A VAL* 5.6 3.4 - - + -
917A PHE* 3.0 32.9 + + + +
918A LEU* 3.7 12.8 - - + +
920A VAL* 1.3 76.9 - - - +
922A ARG* 1.3 67.2 + - - +
924A LEU* 3.1 34.2 + - + +
925A CYS* 3.7 13.0 - - - -
1408A TRP* 5.2 4.7 - + - -
1438A VAL* 4.1 41.3 - - + -
1441A ILE* 4.0 42.2 - - + -
1442A ILE* 4.4 15.0 - - + -
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Residues in contact with ARG 922 (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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908A TRP* 3.7 48.3 - - + +
918A LEU 3.0 12.6 + - - +
919A ILE* 3.5 11.0 - - - +
920A VAL 3.2 0.4 - - - -
921A PHE* 1.3 80.7 - - - +
923A VAL* 1.3 50.9 + - + +
925A CYS* 2.6 38.6 + - - +
927A GLU* 2.8 50.2 + - + +
930A GLU* 4.1 24.4 + - - +
931A THR* 3.4 27.1 + - - +
1408A TRP* 3.8 26.5 - - + -
1409A THR* 3.9 16.9 - - - +
2007A 9SL 4.4 1.4 + - - -
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Residues in contact with VAL 923 (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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919A ILE* 3.2 20.3 + - + +
920A VAL* 3.7 9.2 - - - +
921A PHE 3.2 0.6 - - - -
922A ARG* 1.3 72.4 - - + +
924A LEU* 1.3 59.2 + - + +
925A CYS 2.5 18.8 - - - +
926A GLY* 4.3 0.2 - - - -
927A GLU 4.5 4.7 + - - +
928A TRP* 3.9 31.6 - - + +
931A THR* 5.8 2.2 - - - +
948A TYR* 4.5 22.2 - - + +
951A VAL* 4.2 23.8 - - + -
952A MET* 3.9 30.5 - - + +
956A ASN* 4.0 1.7 + - - -
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Residues in contact with LEU 924 (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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873A LEU* 4.4 6.5 - - + -
877A VAL* 4.2 23.3 - - + -
920A VAL* 3.5 16.6 + - + +
921A PHE* 3.1 28.5 + - + +
923A VAL* 1.3 74.6 - - - +
925A CYS* 1.3 63.9 + - - +
926A GLY 3.8 0.5 + - - -
951A VAL* 4.7 11.2 - - + -
955A GLY* 4.5 15.3 - - - -
956A ASN* 3.9 28.7 + - - +
959A VAL* 3.8 34.3 - - + +
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Residues in contact with CYS 925 (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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921A PHE* 3.7 30.1 - - - -
922A ARG* 2.6 20.7 - - - +
923A VAL 2.5 18.4 - - - +
924A LEU* 1.3 77.4 - - - +
926A GLY* 1.3 57.8 + - - +
927A GLU* 2.8 8.8 + - + -
1405A PHE* 3.7 49.6 - - + -
1408A TRP* 4.5 5.4 - - - -
1441A ILE* 4.9 2.5 - - - -
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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