Contacts of the helix formed by residues 922 - 941 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C LEU* 6.0 0.2 - - - +
918C ASP 4.5 5.0 + - - +
919C ARG* 3.1 48.1 + - - +
920C SER 3.5 0.2 - - - -
921C ASN* 1.3 73.8 - - - +
923C LYS* 1.3 61.5 + - - +
924C VAL* 3.0 15.3 + - - +
925C TYR* 3.2 15.5 + - + +
926C GLU* 3.2 19.8 + - - +
1035C LEU* 5.2 0.3 - - - +
1042C ARG* 2.9 41.2 + - - +
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Residues in contact with LYS 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921C ASN* 3.3 11.5 + - - +
922C ASP* 1.3 70.0 + - - +
924C VAL* 1.3 60.8 + - - +
926C GLU* 3.4 28.2 + - - +
927C ASN* 3.0 43.6 + - - +
963C THR* 5.0 5.5 - - - +
967C THR* 3.9 28.7 + - + -
970C GLU* 6.2 0.2 - - - -
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Residues in contact with VAL 924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922C ASP* 3.0 9.1 + - - +
923C LYS* 1.3 77.1 - - - +
925C TYR* 1.3 57.2 + - - +
927C ASN* 3.0 2.4 + - - +
928C VAL* 2.7 48.1 + - + +
964C LEU* 4.4 9.2 - - + -
967C THR* 3.9 19.3 - - + +
968C VAL* 4.3 13.0 - - + -
971C THR* 4.3 13.0 - - + +
1034C LEU* 5.7 0.4 - - + -
1035C LEU* 4.2 17.7 - - + +
1038C ILE* 4.3 23.3 - - + -
1042C ARG* 3.9 17.7 - - - +
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Residues in contact with TYR 925 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913C PRO* 3.7 38.9 - - + +
919C ARG* 3.3 46.2 - - + +
922C ASP* 3.2 23.5 + - + +
924C VAL* 1.3 80.5 - - - +
926C GLU* 1.3 58.4 + - - +
928C VAL* 4.1 1.3 - - - +
929C THR* 2.8 41.8 + - - -
1035C LEU* 3.6 22.6 - - + +
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Residues in contact with GLU 926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C ASP 3.2 11.6 + - - +
923C LYS* 3.4 31.5 - - - +
924C VAL 3.1 0.6 - - - -
925C TYR* 1.3 79.8 - - - +
927C ASN* 1.3 63.3 + - - +
929C THR* 3.3 7.1 + - - -
930C GLY* 2.8 25.5 + - - -
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Residues in contact with ASN 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923C LYS* 3.0 28.1 + - - +
924C VAL 3.0 0.2 + - - -
926C GLU* 1.3 80.5 - - - +
928C VAL* 1.3 61.0 + - - +
930C GLY* 3.1 3.2 + - - +
931C LEU* 2.8 29.3 + - - +
960C ALA 4.6 2.9 - - - +
963C THR* 3.2 26.6 - - + +
964C LEU* 3.6 26.0 - - + +
967C THR* 2.7 37.8 + - - -
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Residues in contact with VAL 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924C VAL* 2.7 26.1 + - + +
925C TYR 4.1 3.8 - - - +
927C ASN* 1.3 71.2 - - - +
929C THR* 1.3 57.9 + - - +
931C LEU* 2.8 5.3 + - - +
932C VAL* 2.8 45.7 + - + +
964C LEU* 3.9 23.8 - - + -
1031C ALA* 3.5 34.8 - - + +
1032C LYS* 4.2 11.4 - - + -
1034C LEU* 5.4 0.7 - - + -
1035C LEU* 4.0 26.2 - - + +
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Residues in contact with THR 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925C TYR* 2.8 35.5 + - - -
926C GLU* 3.5 6.5 - - - -
928C VAL* 1.3 80.1 - - - +
930C GLY* 1.3 62.6 + - - +
932C VAL* 4.1 6.2 - - - +
933C LYS* 3.1 52.3 + - + +
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Residues in contact with GLY 930 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C GLU 2.8 15.8 + - - -
927C ASN* 3.5 4.5 - - - -
928C VAL 3.0 0.4 - - - -
929C THR* 1.3 79.4 - - - +
931C LEU* 1.3 59.3 + - - +
933C LYS* 3.2 9.1 + - - +
934C ALA* 3.1 22.0 + - - +
960C ALA* 4.6 6.8 - - - +
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Residues in contact with LEU 931 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927C ASN 2.8 18.9 + - - +
928C VAL* 3.5 4.9 - - - +
930C GLY* 1.3 71.2 - - - +
932C VAL* 1.3 66.5 + - - +
934C ALA* 3.4 1.6 + - - +
935C VAL* 3.3 20.9 + - + +
957C VAL* 3.4 38.8 - - + +
960C ALA* 4.0 19.8 - - + +
961C LEU* 3.8 31.4 - - + +
964C LEU* 4.3 7.2 - - + -
990C LEU* 5.1 0.2 - - + -
1027C LEU* 4.2 17.5 - - + -
1028C ALA* 5.5 1.1 - - - -
1031C ALA* 3.6 26.7 - - + -
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Residues in contact with VAL 932 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928C VAL* 2.8 36.0 + - + +
929C THR* 4.1 6.1 - - - +
931C LEU* 1.3 71.9 - - - +
933C LYS* 1.3 64.3 + - - +
935C VAL* 3.2 3.6 + - - +
936C ILE* 3.0 39.8 + - + +
1028C ALA* 4.1 39.3 - - + +
1031C ALA* 4.6 2.5 - - + -
1032C LYS* 4.2 17.5 - - + +
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Residues in contact with LYS 933 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929C THR* 3.1 42.6 + - + +
930C GLY* 3.3 8.5 - - - +
931C LEU 3.1 0.2 - - - -
932C VAL* 1.3 80.0 - - - +
934C ALA* 1.3 55.6 + - - +
936C ILE* 3.4 15.0 + - + +
937C GLU* 3.1 24.9 + - - +
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Residues in contact with ALA 934 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930C GLY 3.1 13.5 + - - +
931C LEU 3.4 4.2 + - - +
932C VAL 3.3 0.2 - - - -
933C LYS* 1.3 73.6 - - - +
935C VAL* 1.3 63.3 + - - +
937C GLU* 3.5 10.0 + - - +
938C MET* 3.3 16.6 + - - +
953C MET 4.6 2.3 - - - +
956C GLU* 4.4 17.4 - - + +
957C VAL* 3.3 33.2 - - + +
960C ALA* 4.4 10.3 - - + -
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Residues in contact with VAL 935 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931C LEU* 3.3 12.8 + - + +
932C VAL 3.2 10.0 + - - +
934C ALA* 1.3 74.1 - - - +
936C ILE* 1.3 63.1 + - + +
938C MET* 3.1 3.4 + - - +
939C SER* 2.7 44.1 + - - -
957C VAL* 3.8 17.3 - - + -
1024C ALA* 3.5 42.6 - - + +
1025C HIS* 4.5 3.1 - - - +
1027C LEU* 4.2 17.0 - - + -
1028C ALA* 4.2 17.3 - - + +
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Residues in contact with ILE 936 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932C VAL* 3.0 31.8 + - + +
933C LYS* 3.6 15.3 - - + +
935C VAL* 1.3 81.9 - - + +
937C GLU* 1.3 60.6 + - - +
939C SER* 3.2 9.4 + - - +
940C SER* 3.0 29.2 + - - -
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Residues in contact with GLU 937 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933C LYS 3.1 13.4 + - - +
934C ALA* 3.5 13.9 - - - +
935C VAL 3.1 0.2 - - - -
936C ILE* 1.3 78.0 - - - +
938C MET* 1.3 63.0 + - - +
940C SER* 3.7 1.5 - - - -
941C LYS* 3.0 40.6 + - - +
953C MET* 4.8 8.7 - - + +
956C GLU* 5.4 6.3 - - - +
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Residues in contact with MET 938 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934C ALA 3.3 8.7 + - - +
935C VAL* 3.1 7.2 + - - +
937C GLU* 1.3 74.2 - - - +
939C SER* 1.3 59.6 + - - +
940C SER 2.8 15.1 + - - -
941C LYS 2.8 12.0 + - - -
942C ILE* 3.3 23.7 + - + +
953C MET* 3.2 46.2 - - + +
954C VAL* 3.3 30.5 - - + -
957C VAL* 4.2 9.2 - - + -
997C LEU* 4.1 24.5 - - + -
1020C MET* 4.6 10.8 - - + -
1021C LEU* 4.6 10.1 - - + -
1024C ALA* 4.2 13.5 - - + -
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Residues in contact with SER 939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935C VAL* 2.7 28.4 + - - +
936C ILE* 3.2 17.5 + - - +
938C MET* 1.3 74.1 - - - +
940C SER* 1.3 62.0 + - - +
941C LYS 3.6 0.2 - - - -
942C ILE* 4.6 2.3 - - - +
943C GLN* 5.6 2.9 + - - +
1021C LEU* 3.6 43.5 - - - +
1024C ALA* 5.5 1.8 - - - -
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Residues in contact with SER 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936C ILE* 3.0 22.3 + - - -
937C GLU* 3.7 1.6 - - - -
938C MET 2.8 4.8 + - - -
939C SER* 1.3 79.4 + - - +
941C LYS* 1.3 62.3 + - - +
943C GLN* 6.3 0.9 - - - -
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Residues in contact with LYS 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C GLU* 3.0 27.6 + - - +
938C MET 2.8 3.8 + - - -
940C SER* 1.3 82.9 - - - +
942C ILE* 1.3 56.5 + - - +
943C GLN* 2.6 21.7 + - - +
944C PRO* 3.2 39.9 - - - +
945C ALA* 4.3 11.7 - - + -
949C GLU* 5.2 4.2 + - - +
953C MET* 3.6 26.5 - - + -
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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
------------------------------------------------------------
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