Contacts of the helix formed by residues 906 - 922 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716B THR 5.7 0.2 - - - +
719B ASN* 3.7 32.3 - - + +
720B GLN* 4.3 8.1 - - + +
723B GLU* 3.2 32.8 - - + +
904B GLU* 3.7 20.4 - - + +
905B PHE* 1.3 87.1 - - - +
907B GLU* 1.3 59.2 + - - +
908B MET 3.8 0.2 - - - -
909B MET* 3.4 6.5 - - - +
910B SER* 2.8 26.0 + - - -
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Residues in contact with GLU 907 (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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723B GLU* 3.6 5.3 + - - +
906B PRO* 1.3 71.1 - - - +
908B MET* 1.3 88.6 + - - +
910B SER* 3.0 8.3 + - - -
911B GLU* 3.0 20.3 + - + +
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Residues in contact with MET 908 (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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723B GLU* 3.0 20.0 + - - +
726B LEU* 3.7 17.3 - - + -
727B LEU* 4.0 16.8 - - + -
907B GLU* 1.3 96.8 - - + +
909B MET* 1.3 61.5 + - - +
911B GLU* 3.2 36.8 + - - +
912B VAL* 3.1 27.7 + - - +
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Residues in contact with MET 909 (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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2B 30X 3.4 31.2 - - + -
719B ASN* 3.4 35.2 - - - +
722B GLY* 4.5 5.4 - - - +
723B GLU* 2.8 33.2 + - - +
726B LEU* 4.2 5.2 - - + -
755B TRP* 3.6 15.0 - - + -
905B PHE* 3.6 12.8 - - + -
906B PRO* 3.4 13.2 - - + +
908B MET* 1.3 77.3 - - - +
910B SER* 1.3 62.6 + - - +
912B VAL* 3.0 24.6 - - - +
913B ILE* 3.1 43.2 + - + +
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Residues in contact with SER 910 (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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895B PHE* 3.6 24.0 - - - -
905B PHE* 3.0 24.1 + - - +
906B PRO 2.8 22.1 + - - -
907B GLU* 3.0 5.8 + - - -
909B MET* 1.3 76.1 - - - +
911B GLU* 1.3 57.3 + - - +
913B ILE* 3.8 2.8 - - - +
914B ALA* 3.0 32.9 + - - +
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Residues in contact with GLU 911 (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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752B GLN* 4.5 13.5 - - - +
907B GLU* 3.0 12.4 + - + +
908B MET* 3.2 43.9 - - - +
909B MET 3.1 0.2 - - - -
910B SER* 1.3 77.9 - - - +
912B VAL* 1.3 62.7 + - + +
914B ALA* 4.2 3.0 - - - +
915B ALA* 3.0 29.6 + - + +
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Residues in contact with VAL 912 (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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726B LEU* 3.8 22.7 - - + -
751B ILE* 5.6 2.2 - - + -
752B GLN* 4.2 27.4 - - + +
755B TRP* 3.6 43.4 + - + +
908B MET 3.1 12.3 + - - +
909B MET* 3.0 20.4 - - - +
911B GLU* 1.3 78.1 - - - +
913B ILE* 1.3 70.0 + - - +
915B ALA* 3.7 6.0 - - - +
916B GLN* 3.1 23.6 + - - +
917B LEU* 4.0 2.4 + - - +
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Residues in contact with ILE 913 (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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896A ILE* 5.3 0.2 - - + -
755B TRP* 3.8 19.1 - - + -
891B CYS* 3.5 17.0 - - - -
892B LEU* 4.3 7.2 - - + -
895B PHE* 3.8 31.4 - - + -
905B PHE* 3.6 17.0 - - + -
909B MET* 3.1 44.3 + - + +
910B SER* 3.8 4.5 - - - +
912B VAL* 1.3 82.5 - - - +
914B ALA* 1.3 60.5 + - - +
917B LEU* 3.0 51.0 + - + +
918B PRO* 3.5 4.2 - - - +
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Residues in contact with ALA 914 (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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893A ASN* 4.5 5.4 - - - +
896A ILE* 3.6 32.2 - - + +
897A GLN* 3.8 27.1 - - + +
895B PHE* 5.1 2.7 - - + -
910B SER 3.0 18.3 + - - +
911B GLU* 4.2 3.6 - - - +
913B ILE* 1.3 77.1 - - - +
915B ALA* 1.3 63.0 + - - +
916B GLN 3.7 0.2 + - - -
918B PRO* 4.5 6.9 - - - +
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Residues in contact with ALA 915 (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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893A ASN* 5.7 0.6 - - - +
752B GLN* 3.7 30.3 - - - +
911B GLU* 3.0 21.9 + - + +
912B VAL 3.7 3.6 - - - +
913B ILE 3.2 0.4 - - - -
914B ALA* 1.3 80.1 - - - +
916B GLN* 1.3 73.4 + - + +
918B PRO* 5.3 0.4 - - - -
919B LYS* 5.4 1.4 - - - +
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Residues in contact with GLN 916 (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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749B THR* 5.0 8.9 + - - +
752B GLN* 3.1 43.6 + - + +
753B TYR* 3.7 23.5 + - + -
912B VAL 3.1 7.2 + - - +
914B ALA 3.5 0.2 - - - -
915B ALA* 1.3 94.7 + - + +
917B LEU* 1.3 61.8 + - - +
918B PRO* 3.4 4.3 - - - -
919B LYS* 3.1 25.5 + - - +
920B ILE* 2.8 48.9 + - + +
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Residues in contact with LEU 917 (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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755B TRP* 4.7 9.0 - - + +
888B HIS* 3.4 56.5 - - + +
891B CYS* 3.5 33.4 - - + -
892B LEU* 4.1 12.8 - - + +
912B VAL 4.0 1.8 + - - +
913B ILE* 3.0 40.0 + - + +
916B GLN* 1.3 75.9 - - - +
918B PRO* 1.3 60.4 - - + +
920B ILE* 3.3 7.0 + - + +
921B LEU* 2.9 33.8 + - + +
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Residues in contact with PRO 918 (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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889A LEU* 3.6 13.2 - - + +
892A LEU* 4.1 17.0 - - + -
893A ASN* 3.1 26.0 - - - +
896A ILE* 3.4 29.4 - - + -
921A LEU* 4.7 2.5 - - + +
892B LEU* 4.2 13.7 - - + -
913B ILE 3.5 8.5 - - - +
914B ALA 4.5 4.5 - - - +
916B GLN* 3.6 3.6 - - - -
917B LEU* 1.3 94.2 - - + +
919B LYS* 1.3 55.7 + - - +
921B LEU* 3.3 4.7 + - + +
922B ALA* 2.9 31.2 + - - +
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Residues in contact with LYS 919 (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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889A LEU* 3.7 18.5 - - + +
893A ASN* 4.5 5.3 + - - +
753B TYR* 4.1 9.8 + - - +
831B PRO* 5.3 1.2 - - - +
832B LEU* 5.7 1.3 - - - +
833B GLU* 4.7 16.3 + - - -
915B ALA 5.4 1.8 - - - +
916B GLN* 3.1 29.7 + - - +
918B PRO* 1.3 79.3 - - - +
920B ILE* 1.3 62.4 + - - +
922B ALA 3.4 1.2 + - - -
923B GLY 3.3 3.1 + - - -
924B MET* 2.9 63.9 + - + +
925B VAL* 4.1 10.1 - - + -
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Residues in contact with ILE 920 (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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752B GLN 4.2 4.0 - - - +
753B TYR* 3.9 38.6 - - + +
755B TRP* 5.7 0.7 - - - +
829B THR* 6.1 0.7 - - + -
888B HIS* 3.7 33.2 - - + +
916B GLN* 2.8 45.2 + - + +
917B LEU* 3.6 9.4 - - + +
919B LYS* 1.3 73.0 - - + +
921B LEU* 1.3 58.8 + - - +
923B GLY* 2.9 20.3 + - - -
925B VAL* 4.3 24.6 - - + +
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Residues in contact with LEU 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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918A PRO* 4.6 6.7 - - + +
921A LEU* 3.3 13.9 - - + +
922A ALA* 3.5 24.5 - - + +
885B LYS* 4.0 27.4 + - + +
888B HIS* 3.7 31.0 - - + +
889B LEU* 4.0 33.9 - - + +
892B LEU* 3.7 30.1 - - + -
917B LEU* 2.9 17.6 + - + +
918B PRO* 3.7 4.7 - - + +
920B ILE* 1.3 76.4 - - - +
922B ALA* 1.3 58.8 + - - +
923B GLY* 3.1 4.2 + - - -
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Residues in contact with ALA 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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885A LYS* 2.6 40.6 + - - -
889A LEU* 4.3 8.5 - - + -
921A LEU* 3.4 39.9 - - + +
918B PRO 2.9 16.9 + - - +
919B LYS 3.8 4.9 - - - +
920B ILE 3.2 0.4 - - - -
921B LEU* 1.3 75.3 - - - +
923B GLY* 1.3 59.0 + - - +
924B MET* 3.4 9.7 + - + -
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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