Contacts of the helix formed by residues 906 - 922 (chain A) in PDB entry 3G8O
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 PRO 906 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719A ASN* 3.8 18.8 - - + +
720A GLN* 4.2 19.1 - - - +
723A GLU* 3.1 42.0 - - + +
904A GLU* 3.8 4.5 - - + +
905A PHE* 1.3 84.4 - - - +
907A GLU* 1.3 57.6 + - - +
908A MET 3.6 0.6 + - - -
909A MET* 3.6 16.0 + - - +
910A SER* 2.6 34.7 + - - -
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Residues in contact with GLU 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A GLU* 3.7 3.4 + - - +
905A PHE 5.1 2.5 - - - +
906A PRO* 1.3 72.4 - - - +
908A MET* 1.3 69.5 + - + +
910A SER* 3.2 9.5 + - - -
911A GLU* 3.0 23.2 + - - +
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Residues in contact with MET 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A GLU* 2.9 56.4 + - + +
724A ARG* 5.8 0.2 - - - -
726A LEU* 3.7 15.3 - - + +
727A LEU* 4.2 31.2 - - + +
907A GLU* 1.3 76.2 - - + +
909A MET* 1.3 63.7 + - - +
911A GLU* 3.3 13.0 + - - +
912A VAL* 3.3 15.8 + - - +
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Residues in contact with MET 909 (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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1A 30X 3.7 21.8 - - + -
719A ASN* 3.1 42.4 - - + +
722A GLY* 4.8 3.6 - - - -
723A GLU* 2.8 23.3 + - - +
726A LEU* 3.8 11.4 - - + +
755A TRP* 4.1 17.7 - - + -
905A PHE* 3.8 19.3 - - + -
906A PRO* 3.6 31.0 - - - +
908A MET* 1.3 70.7 - - - +
910A SER* 1.3 66.2 + - - +
912A VAL* 3.0 6.9 + - - +
913A ILE* 3.0 33.7 + - + +
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Residues in contact with SER 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A PHE* 3.8 21.5 - - - -
905A PHE* 2.8 26.2 + - - +
906A PRO 2.6 25.4 + - - -
907A GLU* 3.2 13.2 + - - -
909A MET* 1.3 80.3 - - - +
911A GLU* 1.3 56.8 + - - +
913A ILE* 3.3 2.8 + - - +
914A ALA* 2.9 32.0 + - - +
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Residues in contact with GLU 911 (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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752A GLN* 4.8 9.2 + - - +
907A GLU 3.0 12.1 + - - +
908A MET* 3.6 10.8 - - - +
910A SER* 1.3 75.1 - - - +
912A VAL* 1.3 60.1 + - + +
914A ALA* 4.6 6.2 - - - +
915A ALA* 3.0 48.3 + - - +
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Residues in contact with VAL 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LEU* 3.7 26.2 - - + -
752A GLN* 3.9 50.3 - - + +
755A TRP* 3.8 27.8 - - + -
908A MET 3.3 13.7 + - - +
909A MET* 3.0 8.6 + - - +
911A GLU* 1.3 77.0 - - + +
913A ILE* 1.3 64.4 + - - +
915A ALA* 4.2 0.2 - - - +
916A GLN* 3.0 26.1 + - + +
917A LEU* 3.9 4.0 + - + +
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Residues in contact with ILE 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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755A TRP* 4.0 14.1 - - + -
891A CYS* 3.4 27.1 - - - -
892A LEU* 4.0 9.1 - - + +
895A PHE* 3.7 30.7 - - + -
905A PHE* 3.8 20.4 - - + -
909A MET* 3.0 38.4 + - + +
910A SER* 3.6 5.6 - - - +
912A VAL* 1.3 77.7 - - - +
914A ALA* 1.3 61.8 + - - +
917A LEU* 3.3 38.5 + - + +
918A PRO* 3.3 9.2 - - - +
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Residues in contact with ALA 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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895A PHE* 4.4 7.0 - - + -
910A SER 2.9 18.1 + - - +
911A GLU* 4.1 8.7 - - - +
913A ILE* 1.3 79.8 - - - +
915A ALA* 1.3 61.4 + - - +
918A PRO* 3.9 12.3 - - - +
893B ASN* 4.4 7.3 - - - +
896B ILE* 3.7 32.8 - - + +
897B GLN* 5.0 10.6 - - + +
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Residues in contact with ALA 915 (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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752A GLN* 4.5 8.7 - - - +
911A GLU* 3.0 34.4 + - - +
912A VAL 4.2 1.1 - - - +
914A ALA* 1.3 79.6 - - - +
916A GLN* 1.3 74.8 + - + +
918A PRO* 4.9 0.4 - - - -
919A LYS* 3.3 19.2 + - - -
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Residues in contact with GLN 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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749A THR* 5.5 6.0 + - - +
752A GLN* 3.2 47.3 + - + +
753A TYR* 3.5 23.3 - - + -
912A VAL* 3.0 10.2 + - + +
914A ALA 3.6 0.2 - - - -
915A ALA* 1.3 91.7 + - - +
917A LEU* 1.3 63.8 + - + +
918A PRO* 3.4 2.9 - - - -
919A LYS* 3.1 28.6 + - - +
920A ILE* 2.8 46.0 + - + +
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Residues in contact with LEU 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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752A GLN 5.8 1.1 - - - +
755A TRP* 5.1 7.9 - - + -
756A MET* 5.0 0.7 - - + -
888A HIS* 3.4 63.5 - - + +
891A CYS* 3.7 26.7 - - + -
892A LEU* 4.1 12.8 - - + +
912A VAL* 3.9 4.4 + - + +
913A ILE* 3.3 35.2 + - + +
916A GLN* 1.3 76.8 - - + +
918A PRO* 1.3 67.6 - - + +
920A ILE* 3.2 8.8 + - + +
921A LEU* 2.9 29.4 + - + +
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Residues in contact with PRO 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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892A LEU* 4.0 17.0 - - + -
913A ILE 3.3 13.9 - - - +
914A ALA 3.9 6.7 - - - +
915A ALA 4.9 0.4 - - - -
916A GLN* 3.6 3.6 - - - +
917A LEU* 1.3 90.6 - - + +
919A LYS* 1.3 60.3 + - - +
921A LEU* 4.0 3.3 - - + +
922A ALA* 3.1 24.4 + - - +
889B LEU* 3.9 14.7 - - + +
892B LEU* 4.3 13.2 - - + -
893B ASN* 3.7 20.4 - - - +
896B ILE* 3.5 30.5 - - + -
921B LEU* 4.6 4.7 - - + +
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Residues in contact with LYS 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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753A TYR* 4.5 5.6 - - - +
915A ALA 3.3 23.0 + - - -
916A GLN* 3.1 25.9 + - - +
918A PRO* 1.3 81.2 - - - +
920A ILE* 1.3 61.4 + - - +
922A ALA 3.3 5.7 + - - -
924A MET* 3.0 60.2 + - + +
925A VAL* 4.3 9.0 - - + -
889B LEU* 4.2 12.7 - - + +
893B ASN* 6.2 0.6 - - - +
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Residues in contact with ILE 920 (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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752A GLN 4.6 2.5 - - - +
753A TYR* 4.2 28.3 - - + +
829A THR* 6.3 0.9 - - + -
888A HIS* 3.7 36.8 - - + +
916A GLN* 2.8 41.4 + - + +
917A LEU* 3.7 10.8 - - + +
919A LYS* 1.3 74.2 - - + +
921A LEU* 1.3 63.6 + - + +
923A GLY* 3.0 14.0 + - - -
925A VAL* 4.2 32.7 - - + +
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Residues in contact with LEU 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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885A LYS* 3.7 37.5 + - + +
888A HIS* 3.7 21.3 - - + +
889A LEU* 3.8 30.3 - - + +
892A LEU* 3.6 30.5 - - + -
917A LEU* 2.9 20.7 + - + +
918A PRO* 4.0 3.6 - - + +
920A ILE* 1.3 75.0 - - + +
922A ALA* 1.3 57.5 + - - +
923A GLY* 3.0 4.2 + - - -
918B PRO 4.7 3.4 - - - +
921B LEU* 3.3 14.3 - - + +
922B ALA* 3.4 34.4 - - + +
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Residues in contact with ALA 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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918A PRO 3.1 19.6 + - - +
919A LYS* 3.7 6.1 - - - +
920A ILE 3.2 0.6 - - - -
921A LEU* 1.3 75.3 - - - +
923A GLY* 1.3 60.6 + - - +
924A MET* 3.6 15.3 + - + +
885B LYS* 2.7 39.7 + - - +
889B LEU* 4.7 8.5 - - + -
921B LEU* 3.5 27.5 + - + +
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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