Contacts of the helix formed by residues 881 - 896 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880A LEU* 1.3 74.0 - - - +
882A ARG* 1.3 59.9 + - - +
883A GLU* 3.6 4.1 + - - +
884A ALA* 3.1 17.0 + - - +
885A HIS* 2.9 27.4 + - - +
1151A GLY 2.9 25.1 + - - -
1152A VAL 2.9 12.8 + - - -
1154A THR 3.3 23.3 + - - -
1155A GLN* 3.8 4.6 - - - +
1160A ARG* 3.5 19.5 - - - +
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Residues in contact with ARG 882 (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 LEU* 3.8 25.6 - - + +
880A LEU 3.9 0.8 + - - -
881A SER* 1.3 72.7 - - - +
883A GLU* 1.3 67.3 + - - +
886A GLU* 2.8 66.9 + - - +
907A ASP* 3.7 9.9 + - - +
909A VAL* 4.2 6.3 - - - +
925A THR 5.5 0.4 + - - -
926A LEU* 3.7 13.1 - - - +
928A HIS* 3.2 31.6 + - - +
987A TYR* 3.2 49.5 + - + -
1155A GLN* 4.8 3.4 + - - -
1160A ARG* 3.8 19.8 - - - +
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Residues in contact with GLU 883 (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 SER* 3.1 4.7 - - - +
882A ARG* 1.3 78.9 - - - +
884A ALA* 1.3 57.4 + - - +
887A THR* 2.7 34.6 + - - -
928A HIS* 3.3 41.7 - - + +
929A LEU* 3.7 9.2 - - + +
1160A ARG* 2.6 69.0 + - - +
1163A PHE* 3.6 27.8 - - + -
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Residues in contact with ALA 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A LEU* 4.4 7.9 - - + -
881A SER* 3.1 16.8 + - - +
883A GLU* 1.3 78.4 - - - +
885A HIS* 1.3 63.3 + - - +
888A LEU* 3.4 9.5 + - - +
1135A GLU* 2.7 41.0 - - - +
1152A VAL* 3.9 24.9 - - + +
1163A PHE* 3.8 15.6 - - + -
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Residues in contact with HIS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A MET 2.9 29.1 + - - -
876A SER 3.7 1.6 + - - -
877A LEU* 3.5 37.1 + - + +
880A LEU* 4.1 14.8 - - + +
881A SER 2.9 17.3 + - - +
882A ARG 3.9 0.2 - - - +
884A ALA* 1.3 79.4 - - - +
886A GLU* 1.3 62.1 + - - +
888A LEU* 3.4 5.8 + - - +
889A ALA* 3.3 16.5 + - + +
900A ASN 4.2 4.3 + - - -
901A SER* 4.0 20.9 - - - -
905A GLY 5.4 1.5 + - - -
906A GLU* 4.0 9.1 + - - -
910A ARG* 2.7 41.7 + - - -
940A SER* 4.1 2.9 + - - -
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Residues in contact with GLU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A LEU* 5.1 0.3 - - - +
882A ARG* 2.8 57.4 + - - +
885A HIS* 1.3 69.6 - - - +
887A THR* 1.3 65.3 + - - +
889A ALA* 3.1 3.0 + - - +
890A ILE* 2.9 28.9 + - - +
907A ASP* 5.5 0.5 - - - +
910A ARG* 3.4 40.8 + - - +
926A LEU* 3.7 9.6 - - - +
928A HIS* 2.6 30.5 + - - -
929A LEU* 3.5 20.0 - - + +
938A ALA* 4.1 5.3 - - + +
987A TYR* 4.5 2.1 + - - -
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Residues in contact with THR 887 (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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883A GLU 2.7 21.2 + - - -
885A HIS 3.3 0.2 - - - -
886A GLU* 1.3 75.7 - - - +
888A LEU* 1.3 60.1 + - - +
890A ILE* 3.4 4.0 + - - +
891A ALA* 3.0 22.2 + - - +
929A LEU* 3.7 12.1 - - - +
930A HIS 5.8 0.5 + - - -
1135A GLU* 3.0 26.5 - - + +
1163A PHE* 3.4 13.4 - - + -
1165A GLY 4.2 4.4 + - - -
1166A VAL 3.7 15.3 - - - +
1167A PRO* 3.6 35.8 - - + +
1170A VAL* 4.5 1.8 - - + -
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Residues in contact with LEU 888 (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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872A THR* 4.2 19.5 - - + +
875A MET* 3.4 33.4 - - + -
880A LEU* 4.3 9.9 - - + -
884A ALA 3.4 13.4 + - - +
885A HIS* 3.6 7.6 - - - +
886A GLU 3.2 0.2 - - - -
887A THR* 1.3 79.1 - - - +
889A ALA* 1.3 57.4 + - - +
891A ALA* 3.1 5.9 + - - +
892A MET* 2.9 35.1 + - - +
899A SER* 4.5 0.9 - - - -
1131A ALA* 3.9 25.1 - - + +
1132A MET* 5.1 1.8 - - + -
1135A GLU* 3.4 31.4 + - + +
1170A VAL* 4.1 15.5 - - + -
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Residues in contact with ALA 889 (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 HIS* 3.3 4.2 + - + +
886A GLU 3.1 8.6 + - - +
888A LEU* 1.3 78.9 - - - +
890A ILE* 1.3 63.3 + - - +
892A MET* 3.3 0.9 + - - +
893A ASN* 3.0 30.3 + - - -
899A SER* 3.3 24.4 + - - +
910A ARG* 3.7 13.0 - - - +
937A THR 4.0 0.2 - - - -
938A ALA 3.2 29.6 - - - +
939A ASN 4.4 2.9 - - - +
940A SER* 4.8 0.9 - - - +
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Residues in contact with ILE 890 (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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886A GLU 2.9 18.1 + - - +
887A THR* 3.8 4.9 - - - +
889A ALA* 1.3 75.2 - - - +
891A ALA* 1.3 63.0 + - - +
893A ASN* 3.9 1.2 - - - +
894A ARG* 3.0 23.9 + - - +
914A LEU* 5.0 1.6 - - + -
926A LEU* 4.8 4.0 - - + -
929A LEU* 3.6 22.7 - - + -
932A LEU* 3.5 26.0 - - + -
936A ASP* 3.3 38.8 - - + +
937A THR 3.5 20.1 + - - +
938A ALA* 3.9 13.0 - - + +
1167A PRO* 3.7 20.9 - - + -
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Residues in contact with ALA 891 (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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887A THR 3.0 13.2 + - - +
888A LEU 3.5 4.5 - - - +
890A ILE* 1.3 78.1 - - - +
892A MET* 1.3 65.3 + - - +
894A ARG* 3.3 4.2 + - - +
895A LEU* 3.1 25.7 + - - +
1167A PRO* 3.4 27.3 - - + +
1170A VAL* 3.4 28.0 - - + -
1171A VAL* 3.6 11.7 - - + +
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Residues in contact with MET 892 (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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870A PHE* 3.7 30.5 - - + +
871A CYS 4.1 0.9 - - - -
872A THR* 3.7 25.4 - - - +
888A LEU* 2.9 24.3 + - - +
889A ALA 4.1 0.4 - - - +
891A ALA* 1.3 72.3 - - - +
893A ASN* 1.3 62.8 + - - +
895A LEU* 3.1 17.6 + - + +
897A ALA* 2.9 37.7 + - + -
898A LYS 3.6 31.0 - - - +
899A SER* 3.7 8.1 - - - +
1170A VAL* 4.5 4.0 - - - -
1174A PHE* 3.5 38.6 - - + -
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Residues in contact with ASN 893 (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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889A ALA* 3.0 18.4 + - - +
890A ILE 4.0 1.8 - - - +
892A MET* 1.3 76.6 - - - +
894A ARG* 1.3 64.5 + - - +
896A GLY* 3.2 12.7 + - - -
897A ALA 4.3 9.3 - - - +
899A SER* 5.1 2.6 + - - -
937A THR* 2.8 47.5 + - + +
939A ASN* 2.9 28.4 + - - +
941A ALA* 4.5 11.6 + - - +
961A LYS* 4.6 9.8 + - - +
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Residues in contact with ARG 894 (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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890A ILE* 3.0 16.9 + - - +
891A ALA 3.4 10.1 - - - +
893A ASN* 1.3 76.1 - - - +
895A LEU* 1.3 61.3 + - - +
896A GLY 3.5 0.3 + - - -
931A GLY 3.0 25.3 + - - -
932A LEU* 3.7 0.6 - - - +
933A GLN* 3.6 32.0 - - - +
936A ASP* 2.6 43.7 + - - +
1167A PRO* 3.8 13.4 - - - +
1168A GLY* 3.7 29.5 - - - +
1171A VAL* 4.2 14.8 - - + +
1175A TYR* 5.2 2.5 + - - -
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Residues in contact with LEU 895 (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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864A GLU* 4.7 2.6 - - - +
867A VAL* 3.6 29.6 - - + +
868A LYS* 4.7 6.8 - - - +
870A PHE* 6.1 0.2 - - + -
891A ALA 3.1 16.0 + - - +
892A MET* 3.1 36.0 + - + +
894A ARG* 1.3 81.5 - - - +
896A GLY* 1.3 58.5 + - - +
897A ALA* 3.9 3.1 - - + +
1171A VAL* 3.8 29.2 - - + +
1174A PHE* 3.9 22.2 - - + -
1175A TYR* 3.6 41.1 + - + +
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Residues in contact with GLY 896 (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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868A LYS* 3.9 30.8 - - - +
892A MET 3.1 2.6 + - - -
893A ASN* 3.2 13.4 + - - -
894A ARG 3.3 0.8 + - - -
895A LEU* 1.3 78.7 - - - +
897A ALA* 1.3 61.7 - - - +
898A LYS* 5.6 0.5 - - - +
961A LYS* 5.9 3.6 - - - -
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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