Contacts of the helix formed by residues 933 - 947 (chain C) in PDB entry 3JW0
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 THR 933 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862C TRP* 3.6 9.7 - - - -
931C TYR* 3.6 1.2 - - - +
932C GLU* 1.3 90.3 - - + +
934C PHE* 1.3 59.0 + - - +
935C GLU* 3.6 3.9 + - - +
936C ASP* 2.6 35.2 + - + +
937C LEU* 2.9 28.4 + - - +
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Residues in contact with PHE 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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862C TRP* 3.7 68.0 - + + +
865C LYS* 4.0 17.9 - - + -
866C ALA* 3.9 17.9 - - + -
869C LEU* 3.8 27.1 - - + -
933C THR* 1.3 71.9 - - - +
935C GLU* 1.3 88.5 + - - +
937C LEU* 3.0 6.3 + - + +
938C ARG* 2.8 41.8 + - - +
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Residues in contact with GLU 935 (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 THR* 3.4 3.7 + - - +
934C PHE* 1.3 101.3 - - - +
936C ASP* 1.3 63.8 + - - +
938C ARG* 3.8 26.2 + - + +
939C GLU* 2.8 45.6 + - + +
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Residues in contact with ASP 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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913C PRO* 4.9 5.1 - - - +
931C TYR* 4.1 13.8 - - + -
932C GLU* 3.8 22.3 + - - +
933C THR* 2.6 40.9 + - - +
935C GLU* 1.3 81.1 - - - +
937C LEU* 1.3 58.5 + - - +
939C GLU* 4.0 10.4 - - - +
940C LYS* 3.4 32.2 + - - +
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Residues in contact with LEU 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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859C VAL* 3.7 39.7 - - + +
862C TRP* 4.2 9.9 - - + -
863C PHE* 4.0 15.3 - - + +
866C ALA* 4.0 21.8 - - + -
928C LEU* 4.3 10.8 - - + -
931C TYR* 3.5 29.8 - - + +
933C THR 2.9 11.0 + - - +
934C PHE* 3.4 10.5 - - + +
936C ASP* 1.3 75.4 - - - +
938C ARG* 1.3 72.8 + - - +
939C GLU 3.1 0.3 + - - -
940C LYS* 3.1 3.8 + - - +
941C LEU* 2.9 39.4 + - + +
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Residues in contact with ARG 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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866C ALA* 4.7 11.3 + - + +
869C LEU* 3.5 36.4 - - - +
934C PHE* 2.8 41.0 + - + +
935C GLU* 3.9 26.3 + - + +
937C LEU* 1.3 81.7 - - + +
939C GLU* 1.3 58.3 + - + +
941C LEU* 4.5 2.7 - - - -
942C LEU* 3.0 60.5 + - + +
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Residues in contact with GLU 939 (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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935C GLU* 2.8 40.4 + - + +
936C ASP* 4.0 11.2 - - - +
938C ARG* 1.3 78.7 - - + +
940C LYS* 1.3 66.0 + - + +
942C LEU* 4.2 3.1 - - - +
943C MET* 3.2 27.0 + - - +
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Residues in contact with LYS 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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913C PRO 3.8 9.8 + - - -
914C GLU* 2.8 30.4 + - - +
916C LEU* 3.3 28.9 - - + +
917C PRO* 3.4 6.9 - - - +
931C TYR* 3.0 36.6 - - + +
936C ASP* 3.4 20.6 + - - +
937C LEU 3.1 2.8 + - - +
939C GLU* 1.3 77.9 - - + +
941C LEU* 1.3 64.6 + - - +
943C MET* 4.3 0.4 - - - -
944C ALA 3.2 16.1 + - - -
34X GLU 5.4 0.8 + - - +
35X GLY* 2.9 26.0 + - - +
37X PRO* 4.8 0.2 - - - +
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Residues in contact with LEU 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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863C PHE* 3.8 33.9 - - + +
866C ALA* 4.4 13.2 - - + -
867C VAL* 5.5 0.4 - - + -
870C MET* 4.5 13.9 - - + -
878C LEU* 3.9 26.7 - - + -
881C PHE* 5.8 1.1 - - + -
917C PRO* 4.2 21.5 - - + -
926C LEU* 4.8 6.1 - - + -
928C LEU* 4.9 5.6 - - + -
931C TYR* 5.3 0.6 - - + -
937C LEU* 2.9 30.9 + - + +
938C ARG* 4.0 2.5 - - - +
940C LYS* 1.3 75.2 - - - +
942C LEU* 1.3 64.5 + - + +
943C MET 2.8 6.0 + - - -
944C ALA* 3.0 4.3 + - + +
945C VAL* 3.0 28.1 + - + +
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Residues in contact with LEU 942 (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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866C ALA* 6.5 0.2 - - + -
870C MET* 3.3 35.9 - - + -
874C LYS* 4.4 16.6 - - + -
938C ARG* 3.0 53.7 + - + +
939C GLU* 4.4 3.4 - - - +
941C LEU* 1.3 80.2 - - + +
943C MET* 1.3 57.4 + - - +
945C VAL* 3.9 4.8 - - + +
946C GLU* 2.9 35.8 + - + +
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Residues in contact with MET 943 (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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916C LEU* 4.3 11.7 - - + -
939C GLU 3.2 20.6 + - - +
940C LYS 3.7 5.6 - - - +
941C LEU 2.8 1.6 + - - -
942C LEU* 1.3 76.6 - - - +
944C ALA* 1.3 66.2 + - - +
946C GLU* 4.9 2.0 - - - -
947C ASN* 2.4 72.2 + - + +
7X THR* 5.0 2.5 - - + -
11X LYS* 5.8 0.4 - - - +
34X GLU* 3.8 30.7 - - - +
36X ILE* 3.6 38.4 - - + -
69X LEU* 5.4 0.7 - - + -
71X LEU* 4.8 1.8 - - + -
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Residues in contact with ALA 944 (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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881C PHE* 4.4 10.9 - - + -
916C LEU* 4.5 1.9 - - + +
917C PRO* 3.5 34.8 - - + +
940C LYS 3.2 4.4 + - - +
941C LEU* 3.0 5.2 + - + +
943C MET* 1.3 79.2 - - - +
945C VAL* 1.3 54.4 + - + +
947C ASN 3.6 1.4 - - - +
948C ALA* 2.7 36.4 + - - +
71X LEU* 4.5 4.0 - - - +
73X LEU* 3.8 26.7 - - + +
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Residues in contact with VAL 945 (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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870C MET* 4.1 12.1 - - + -
874C LYS* 3.8 12.3 - - + +
877C ARG* 3.2 53.0 + - + +
878C LEU* 3.5 41.7 - - + +
881C PHE* 5.0 11.4 - - + +
941C LEU* 3.0 21.2 + - + +
942C LEU* 3.9 6.5 - - - +
944C ALA* 1.3 79.3 - - - +
946C GLU* 1.3 63.0 + - + +
948C ALA* 3.4 6.9 - - - +
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Residues in contact with GLU 946 (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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873C GLU* 3.9 2.1 - - - +
874C LYS* 2.3 51.2 + - + +
877C ARG* 3.3 23.3 + - - +
942C LEU* 2.9 27.4 + - + +
943C MET* 4.0 2.0 - - - +
945C VAL* 1.3 70.1 - - + +
947C ASN* 1.3 58.3 + - - +
948C ALA 2.6 19.2 + - - +
8X LEU* 4.5 5.9 - - - +
9X THR* 3.6 26.9 + - + +
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Residues in contact with ASN 947 (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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943C MET* 2.4 49.9 + - + +
944C ALA 3.6 2.2 - - - -
946C GLU* 1.3 75.3 - - - +
948C ALA* 1.3 57.5 + - - +
7X THR* 3.4 21.6 + - - +
8X LEU* 3.9 14.6 - - + +
9X THR* 2.4 45.4 + - - +
11X LYS* 5.7 1.9 - - - +
34X GLU* 4.6 0.3 - - - +
69X LEU* 6.0 1.3 - - + +
71X LEU* 2.9 40.5 - - + +
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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
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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