Contacts of the helix formed by residues 881 - 896 (chain B) in PDB entry 1OFD
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 SER 881 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B LEU* 1.3 76.0 - - - +
882B ARG* 1.3 59.1 + - - +
883B GLU* 3.7 3.5 + - - +
884B ALA* 3.1 15.8 + - - +
885B HIS* 3.0 25.7 + - - +
1151B GLY 2.8 26.1 + - - -
1152B VAL 2.8 11.8 + - - -
1154B THR 3.3 24.4 + - - +
1155B GLN* 3.7 6.4 - - - +
1160B ARG* 3.6 16.4 - - - +
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Residues in contact with ARG 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B LEU* 3.9 27.6 - - + +
880B LEU 3.9 0.6 + - - -
881B SER* 1.3 70.8 - - - +
883B GLU* 1.3 71.5 + - - +
885B HIS* 4.2 0.2 - - - -
886B GLU* 2.8 66.1 + - - +
907B ASP* 3.8 9.5 + - - +
909B VAL* 4.0 7.7 - - - +
925B THR 5.5 0.2 + - - -
926B LEU* 3.7 19.4 - - - +
928B HIS* 3.2 26.8 + - - +
987B TYR* 3.3 44.7 + - + -
1155B GLN* 4.7 3.6 + - - -
1160B ARG* 3.9 19.5 - - - +
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Residues in contact with GLU 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B SER* 3.7 4.3 - - - +
882B ARG* 1.3 73.6 - - - +
884B ALA* 1.3 58.5 + - - +
887B THR* 2.7 34.5 + - - -
928B HIS* 3.2 43.6 - - + +
929B LEU* 3.7 9.2 - - + +
1160B ARG* 2.6 73.5 + - - +
1163B PHE* 3.7 25.6 - - + +
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Residues in contact with ALA 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B LEU* 4.4 8.7 - - + -
881B SER* 3.1 18.7 + - - +
883B GLU* 1.3 78.8 - - - +
885B HIS* 1.3 62.4 + - - +
888B LEU* 3.4 9.6 + - - +
1135B GLU* 2.5 41.2 - - - +
1152B VAL* 3.7 27.4 - - + +
1163B PHE* 3.8 11.6 - - + -
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Residues in contact with HIS 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B MET 2.9 28.7 + - - -
876B SER 3.7 2.2 + - - -
877B LEU* 3.6 35.2 + - + +
880B LEU* 4.3 14.1 - - + +
881B SER 3.0 17.4 + - - +
882B ARG 3.9 0.7 - - - +
884B ALA* 1.3 74.9 - - - +
886B GLU* 1.3 64.1 + - - +
888B LEU* 3.5 7.7 + - - +
889B ALA* 3.3 16.0 + - + +
899B SER* 5.9 0.2 - - - -
900B ASN 4.1 11.0 + - - -
901B SER* 4.0 19.1 - - - -
902B GLY 4.4 0.7 - - - -
905B GLY 5.4 2.3 + - - -
906B GLU* 4.0 4.4 + - - -
910B ARG* 2.6 42.6 + - - -
940B SER* 4.0 2.2 + - - -
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Residues in contact with GLU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B LEU* 5.1 0.3 - - - +
882B ARG* 2.8 56.6 + - - +
885B HIS* 1.3 71.7 - - - +
887B THR* 1.3 64.9 + - - +
889B ALA* 3.2 2.6 + - - +
890B ILE* 3.0 30.3 + - - +
907B ASP* 5.6 0.7 - - - +
910B ARG* 3.4 39.8 + - - +
926B LEU* 3.7 8.9 - - - +
928B HIS* 2.6 31.7 + - - -
929B LEU* 3.6 20.1 - - + +
938B ALA* 4.1 4.9 - - + +
987B TYR* 4.7 1.4 + - - -
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Residues in contact with THR 887 (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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883B GLU 2.7 20.0 + - - -
886B GLU* 1.3 77.9 - - - +
888B LEU* 1.3 60.4 + - - +
890B ILE* 3.4 3.9 + - - +
891B ALA* 3.1 21.9 + - - +
929B LEU* 3.8 12.1 - - - +
930B HIS 5.7 0.3 + - - -
1135B GLU* 3.1 27.4 - - + +
1163B PHE* 3.4 18.3 - - + -
1165B GLY 4.3 4.5 + - - -
1166B VAL 3.7 9.2 - - - +
1167B PRO* 3.6 36.7 - - + +
1170B VAL* 4.6 2.2 - - + -
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Residues in contact with LEU 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872B THR* 4.0 21.8 - - + +
875B MET* 3.5 32.5 - - + -
880B LEU* 4.6 8.1 - - + -
884B ALA 3.4 15.5 + - - +
885B HIS* 3.7 6.7 - - - +
886B GLU 3.3 0.4 - - - -
887B THR* 1.3 75.3 - - - +
889B ALA* 1.3 66.5 + - - +
891B ALA* 3.2 5.7 + - - +
892B MET* 2.9 29.1 + - - +
899B SER* 4.4 0.9 - - - -
1131B ALA* 4.0 24.0 - - + +
1132B MET* 5.1 2.0 - - + -
1135B GLU* 3.4 31.0 - - + +
1170B VAL* 4.0 15.0 - - + -
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Residues in contact with ALA 889 (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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885B HIS 3.3 4.1 + - - +
886B GLU 3.2 9.3 + - - +
888B LEU* 1.3 79.4 - - - +
890B ILE* 1.3 63.1 + - - +
892B MET* 3.2 1.4 + - - +
893B ASN* 2.9 27.3 + - - -
899B SER* 3.3 24.3 + - - +
910B ARG* 3.7 12.3 - - - +
937B THR 4.0 2.5 - - - -
938B ALA 3.3 30.7 - - - +
939B ASN 4.5 3.1 - - - +
940B SER* 4.7 0.7 - - - +
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Residues in contact with ILE 890 (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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886B GLU 3.0 17.6 + - - +
889B ALA* 1.3 74.4 - - - +
891B ALA* 1.3 62.6 + - - +
893B ASN* 3.5 1.9 + - - +
894B ARG* 2.9 24.6 + - - +
914B LEU* 4.9 2.0 - - + -
926B LEU* 4.8 3.6 - - + -
929B LEU* 3.5 32.8 - - + -
932B LEU* 3.5 15.3 - - + -
936B ASP* 3.4 38.8 - - + +
937B THR 3.5 25.9 + - - +
938B ALA* 3.8 8.3 - - + +
1167B PRO* 3.5 25.1 - - + -
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Residues in contact with ALA 891 (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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887B THR 3.1 13.9 + - - +
888B LEU 3.4 7.9 - - - +
890B ILE* 1.3 77.9 - - - +
892B MET* 1.3 64.9 + - - +
894B ARG* 3.1 5.8 + - - +
895B LEU* 3.1 24.1 + - - +
1167B PRO* 3.5 25.5 - - + +
1170B VAL* 3.5 25.8 - - + -
1171B VAL* 3.8 13.3 - - + +
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Residues in contact with MET 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B PHE* 3.8 13.9 - - + +
872B THR* 3.8 24.9 - - - +
888B LEU* 2.9 23.2 + - - +
889B ALA 3.9 2.2 - - - +
891B ALA* 1.3 72.3 - - - +
893B ASN* 1.3 62.6 + - - +
895B LEU* 3.2 10.4 + - + +
896B GLY 3.1 2.9 + - - -
897B ALA* 2.9 49.0 + - + -
898B LYS 3.6 36.6 - - - +
899B SER* 3.6 7.4 - - - +
1170B VAL* 4.5 4.3 - - - -
1174B PHE* 3.4 42.4 - - + -
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Residues in contact with ASN 893 (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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889B ALA* 2.9 17.0 + - - +
890B ILE 3.9 1.6 - - - +
892B MET* 1.3 73.5 - - - +
894B ARG* 1.3 66.3 + - - +
896B GLY* 3.2 12.5 + - - +
897B ALA 4.4 9.2 - - - +
899B SER* 5.1 2.6 + - - -
937B THR* 2.8 49.0 + - + +
939B ASN* 2.9 28.1 + - - +
941B ALA* 4.6 11.3 + - - +
961B LYS* 4.8 10.4 + - - +
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Residues in contact with ARG 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B ILE* 2.9 17.0 + - - +
891B ALA 3.4 9.6 - - - +
893B ASN* 1.3 76.1 - - - +
895B LEU* 1.3 61.9 + - - +
896B GLY 3.4 0.7 + - - -
931B GLY 3.0 26.1 + - - -
932B LEU* 3.8 2.4 - - - +
933B GLN* 3.7 31.4 + - - +
936B ASP* 2.8 43.0 + - - +
1167B PRO* 3.8 16.1 - - - +
1168B GLY* 3.8 25.5 - - - +
1171B VAL* 4.2 14.7 - - + +
1175B TYR* 5.4 1.4 + - - -
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Residues in contact with LEU 895 (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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864B GLU* 4.7 0.7 - - - +
867B VAL* 3.4 30.6 - - + +
868B LYS* 4.3 9.0 - - - -
870B PHE* 5.8 0.2 - - + -
891B ALA 3.1 14.4 + - - +
892B MET* 3.2 39.7 + - + +
894B ARG* 1.3 75.9 - - - +
896B GLY* 1.3 60.2 + - - +
897B ALA* 3.8 7.0 - - + +
1171B VAL* 4.0 25.6 - - + +
1174B PHE* 3.8 24.0 - - + -
1175B TYR* 3.5 41.0 + - + +
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Residues in contact with GLY 896 (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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868B LYS* 3.9 30.4 - - - +
892B MET 3.1 3.0 + - - -
893B ASN* 3.2 14.3 + - - -
894B ARG 3.2 1.2 + - - -
895B LEU* 1.3 78.3 - - - +
897B ALA* 1.3 63.5 + - - +
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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
------------------------------------------------------------
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