Contacts of the helix formed by residues 922 - 942 (chain B) in PDB entry 1OW8
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 922 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A MET 5.8 0.4 - - - -
1047A GLY* 6.4 0.4 - - - -
917B LEU* 5.7 0.5 - - - +
918B ASP 4.1 6.2 - - - +
919B ARG* 3.0 49.2 + - - +
920B SER 3.4 3.4 - - - -
921B ASN* 1.3 77.3 - - - +
923B LYS* 1.3 59.6 + - - +
924B VAL* 3.1 1.4 + - - +
925B TYR* 3.1 25.9 + - + +
926B GLU* 3.1 23.6 + - - +
1035B LEU* 4.7 0.2 - - - +
1042B ARG* 3.0 43.2 + - - +
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Residues in contact with LYS 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A MET* 5.5 3.5 - - + +
921B ASN 3.6 6.2 + - - +
922B ASP* 1.3 72.0 + - - +
924B VAL* 1.3 61.7 + - + +
925B TYR 3.3 0.7 - - - -
926B GLU* 3.5 27.5 + - - +
927B ASN* 2.9 60.4 + - - +
963B THR* 4.1 12.7 - - - +
967B THR* 3.9 25.1 + - + +
1042B ARG* 4.9 0.8 - - - +
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Residues in contact with VAL 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922B ASP* 3.4 6.5 - - - +
923B LYS* 1.3 77.4 - - + +
925B TYR* 1.3 61.0 + - - +
927B ASN* 3.8 1.9 - - - -
928B VAL* 2.9 42.0 + - + +
964B LEU* 3.9 7.8 - - + +
967B THR* 3.7 23.1 - - + +
968B VAL* 4.9 2.9 - - + -
971B THR* 3.9 14.8 - - + +
1034B LEU* 6.0 0.4 - - + -
1035B LEU* 3.8 19.5 - - + -
1038B ILE* 3.9 30.7 - - + -
1042B ARG* 3.9 20.6 - - - +
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Residues in contact with TYR 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913B PRO* 4.0 30.1 - - + +
919B ARG* 3.4 53.2 - - + +
922B ASP* 3.1 23.8 + - + +
924B VAL* 1.3 76.7 - - - +
926B GLU* 1.3 66.3 + - - +
928B VAL* 3.3 3.0 + - - +
929B THR* 2.8 40.4 + - - -
1035B LEU* 3.9 19.7 - - + +
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Residues in contact with GLU 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922B ASP 3.1 14.3 + - - +
923B LYS* 3.6 33.5 - - - +
924B VAL 3.2 0.4 - - - -
925B TYR* 1.3 82.4 - - - +
927B ASN* 1.3 64.8 + - - +
929B THR* 3.4 7.5 + - - +
930B GLY* 2.9 22.9 + - - -
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Residues in contact with ASN 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B LYS* 2.9 39.3 + - - +
924B VAL* 4.5 0.2 - - - -
925B TYR 3.1 0.2 - - - -
926B GLU* 1.3 87.2 - - - +
928B VAL* 1.3 65.0 + - - +
929B THR 3.1 0.9 - - - -
930B GLY* 3.1 3.6 + - - +
931B LEU* 3.1 24.6 + - - +
960B ALA* 4.7 2.4 - - - +
963B THR* 3.6 22.9 - - + +
964B LEU* 3.7 28.7 - - + +
967B THR* 2.8 34.1 + - - -
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Residues in contact with VAL 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B VAL* 2.9 26.4 + - + +
925B TYR 3.8 3.8 - - - +
927B ASN* 1.3 77.8 - - - +
929B THR* 1.3 64.2 + - - +
931B LEU* 3.1 4.8 + - - +
932B VAL* 3.0 26.7 + - + +
964B LEU* 3.7 21.5 - - + -
1031B ALA* 3.8 34.5 - - + +
1032B LYS* 4.3 13.7 - - + -
1034B LEU* 5.8 1.6 - - + -
1035B LEU* 4.2 28.5 - - + +
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Residues in contact with THR 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B TYR* 2.8 35.3 + - - -
926B GLU* 3.5 8.5 - - - +
928B VAL* 1.3 78.1 - - - +
930B GLY* 1.3 65.4 + - - +
932B VAL* 3.6 4.9 + - - +
933B LYS* 3.0 46.9 + - + +
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Residues in contact with GLY 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B GLU 2.9 15.7 + - - -
927B ASN* 3.1 6.2 + - - -
928B VAL 3.1 0.8 - - - -
929B THR* 1.3 80.9 - - - +
931B LEU* 1.3 59.7 + - - +
933B LYS* 3.7 6.8 - - - +
934B ALA* 3.2 20.3 + - - +
960B ALA* 4.3 6.3 - - - +
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Residues in contact with LEU 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B ASN 3.1 14.2 + - - +
928B VAL 3.1 2.0 + - - +
930B GLY* 1.3 75.4 - - - +
932B VAL* 1.3 70.3 + - + +
933B LYS 3.1 0.9 - - - -
934B ALA* 3.3 2.9 + - - +
935B VAL* 3.1 25.2 + - + +
957B VAL* 3.7 37.7 - - + +
960B ALA* 3.8 18.6 - - + +
961B LEU* 4.4 9.0 - - + +
964B LEU* 3.9 15.7 - - + -
1027B LEU* 4.4 21.1 - - + +
1028B ALA* 5.3 1.1 - - - -
1031B ALA* 3.4 33.7 - - + -
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Residues in contact with VAL 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B VAL* 3.0 19.5 + - + +
929B THR* 4.1 4.9 - - - +
931B LEU* 1.3 76.6 - - + +
933B LYS* 1.3 64.5 + - + +
935B VAL* 3.0 8.7 + - + +
936B ILE* 2.9 40.0 + - + +
1028B ALA* 3.8 37.2 - - + +
1031B ALA* 5.1 0.9 - - + -
1032B LYS* 4.4 22.2 - - + -
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Residues in contact with LYS 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B THR* 3.0 39.3 + - + +
930B GLY* 3.9 6.7 - - - +
931B LEU 3.1 0.4 - - - -
932B VAL* 1.3 76.8 - - + +
934B ALA* 1.3 62.8 + - - +
935B VAL 2.9 1.0 + - - -
936B ILE* 2.9 15.9 + - + +
937B GLU* 2.8 23.1 + - - +
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Residues in contact with ALA 934 (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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930B GLY 3.2 12.7 + - - +
931B LEU 3.3 8.5 + - - +
933B LYS* 1.3 77.4 - - - +
935B VAL* 1.3 57.0 + - - +
937B GLU* 3.7 8.9 - - - +
938B MET* 3.2 24.8 + - - +
953B MET 4.9 1.2 - - - +
956B GLU* 4.1 28.7 - - + +
957B VAL* 3.8 15.0 - - + +
960B ALA* 4.5 3.1 - - + -
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Residues in contact with VAL 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 3.1 21.8 + - + +
932B VAL* 3.0 11.1 + - - +
933B LYS 3.0 0.8 - - - -
934B ALA* 1.3 73.9 - - - +
936B ILE* 1.3 67.6 + - + +
938B MET* 3.5 5.2 + - - +
939B SER* 3.0 26.1 + - - +
957B VAL* 4.2 27.4 - - + -
1024B ALA* 3.4 42.6 - - + +
1025B HIS* 4.3 3.4 - - - +
1027B LEU* 5.1 1.3 - - + -
1028B ALA* 4.3 15.9 - - + +
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Residues in contact with ILE 936 (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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932B VAL* 2.9 39.1 + - + +
933B LYS* 3.5 14.8 - - + +
935B VAL* 1.3 75.9 - - + +
937B GLU* 1.3 69.5 + - - +
939B SER* 3.1 8.0 + - - +
940B SER* 2.9 26.5 + - - -
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Residues in contact with GLU 937 (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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933B LYS 2.8 13.3 + - - +
934B ALA* 3.7 12.8 - - - +
935B VAL 3.3 0.2 - - - -
936B ILE* 1.3 77.7 - - - +
938B MET* 1.3 65.6 + - - +
940B SER* 3.0 19.2 + - - -
941B LYS* 3.1 45.6 + - + +
953B MET* 5.7 5.8 - - + -
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Residues in contact with MET 938 (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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934B ALA 3.2 12.3 + - - +
935B VAL* 3.7 8.1 - - - +
936B ILE 3.2 0.2 - - - -
937B GLU* 1.3 79.8 - - - +
939B SER* 1.3 60.0 + - - +
941B LYS 3.2 1.7 + - - -
942B ILE* 2.9 45.1 + - + +
950B TYR* 5.6 0.2 - - + -
953B MET* 3.6 36.6 - - + +
954B VAL* 3.6 33.7 - - + -
957B VAL* 4.2 7.6 - - + -
997B LEU* 4.0 26.0 - - + -
1020B MET* 4.2 18.2 - - + +
1021B LEU* 5.0 4.0 - - - -
1024B ALA* 4.3 15.0 - - + -
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Residues in contact with SER 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935B VAL* 3.0 21.5 + - - +
936B ILE* 3.1 12.9 + - - +
938B MET* 1.3 77.4 - - - +
940B SER* 1.3 60.2 + - - +
942B ILE* 3.9 6.6 + - - +
943B GLN 5.2 0.5 + - - -
1021B LEU* 3.1 38.6 - - - +
1024B ALA* 6.2 1.1 - - - -
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Residues in contact with SER 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936B ILE* 2.9 20.6 + - - +
937B GLU* 3.0 18.7 + - - -
939B SER* 1.3 80.9 + - - +
941B LYS* 1.3 74.7 + - - +
942B ILE 3.7 0.2 + - - -
943B GLN* 5.0 1.0 + - - +
944B PRO* 5.4 2.3 - - - +
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Residues in contact with LYS 941 (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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937B GLU* 3.1 42.7 + - - +
940B SER* 1.3 87.3 - - - +
942B ILE* 1.3 65.6 + - - +
943B GLN 3.2 3.6 + - - -
944B PRO* 3.5 16.0 - - - +
945B ALA* 3.6 9.5 - - - +
949B GLU* 5.2 1.9 - - - +
953B MET* 3.7 27.8 - - + -
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Residues in contact with ILE 942 (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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938B MET* 2.9 25.3 + - + +
939B SER 3.9 4.7 + - - +
940B SER 3.4 2.6 - - - -
941B LYS* 1.3 79.2 - - - +
943B GLN* 1.3 68.8 + - + +
945B ALA* 3.1 8.9 + - - +
950B TYR* 4.1 17.0 - - + -
953B MET* 4.5 1.3 - - - -
1017B LYS* 2.7 51.6 + - + +
1020B MET* 3.4 40.6 - - + -
1021B LEU* 3.6 30.7 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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