Contacts of the strand formed by residues 938 - 946 (chain C) in PDB entry 1JZ3
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 ARG 938 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897C TRP* 3.6 12.0 - - + +
900C LEU 3.4 22.2 - - - +
902C PRO 2.9 26.2 + - - -
903C GLN* 3.6 5.5 - - - +
904C GLU* 3.5 18.3 - - - +
905C ASN* 3.6 10.3 - - - +
920C LEU* 3.8 10.3 - - - +
924C ASP 3.2 19.8 + - - -
925C MET* 3.7 35.2 - - - +
927C THR* 5.3 1.0 + - - -
936C GLY* 2.9 36.4 + - - -
937C LEU* 1.3 74.2 - - - +
939C CYS* 1.3 62.0 + - - +
941C THR* 4.0 1.3 + - - +
956C GLN* 3.2 2.9 - - - -
957C PHE* 2.9 53.9 + - + -
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Residues in contact with CYS 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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900C LEU* 3.1 23.8 + - - +
905C ASN* 2.9 34.7 + - - +
906C TYR* 3.7 17.9 - - - -
907C PRO* 3.8 14.8 - - - -
910C LEU* 3.8 16.4 - - + -
937C LEU* 3.8 16.4 - - - -
938C ARG* 1.3 72.2 - - - +
940C GLY* 1.3 66.9 + - - +
941C THR* 3.1 6.3 + - - -
956C GLN* 3.1 17.0 - - - +
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Residues in contact with GLY 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899C GLY* 3.2 16.3 - - - -
900C LEU* 3.7 10.4 + - - +
910C LEU* 5.6 0.2 - - - +
915C PHE* 3.5 17.0 - - - -
939C CYS* 1.3 72.7 - - - +
941C THR* 1.3 60.6 + - - +
942C ARG* 4.3 3.3 - - - -
954C ASP* 4.3 14.1 - - - -
955C PHE 4.0 1.1 - - - -
956C GLN* 2.9 13.6 + - - -
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Residues in contact with THR 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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897C TRP* 3.4 20.8 + - + -
898C LEU 3.4 7.2 - - - +
899C GLY* 3.7 1.0 - - - -
938C ARG 4.0 1.0 + - - -
939C CYS 3.3 12.8 + - - -
940C GLY* 1.3 75.0 - - - +
942C ARG* 1.3 59.3 + - - +
943C GLU 3.3 31.6 - - - +
944C LEU* 4.4 0.4 - - + -
954C ASP* 3.4 2.4 - - - -
955C PHE* 2.8 61.1 + - + +
957C PHE* 3.5 25.0 - - + -
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Residues in contact with ARG 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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721C ARG* 6.1 0.6 - - - +
724C GLU* 5.6 2.6 + - - -
898C LEU* 2.8 18.1 + - + +
915C PHE* 3.9 26.4 - - + -
940C GLY 4.3 4.7 - - - -
941C THR* 1.3 78.7 - - - +
943C GLU* 1.3 61.4 + - - +
952C ARG* 3.2 8.1 - - - +
953C GLY 2.7 51.2 + - - +
954C ASP* 3.6 17.7 - - - +
955C PHE* 4.4 1.1 - - - -
1013D ARG* 3.6 47.5 - - - +
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Residues in contact with GLU 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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897C TRP* 3.2 5.2 - - - +
898C LEU* 2.8 43.4 + - + +
917C ARG* 2.7 37.5 + - - -
941C THR* 3.3 4.9 - - - +
942C ARG* 1.3 82.1 - - - +
944C LEU* 1.3 62.6 + - - +
945C ASN* 2.9 12.9 + - - +
950C GLN* 3.5 33.6 + - + +
951C TRP 3.3 5.4 - - - -
952C ARG* 4.2 12.2 - - + +
1023C LYS* 5.7 0.5 - - - -
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Residues in contact with LEU 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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895C VAL* 3.8 19.1 - - + -
896C ASN 3.6 4.3 - - - +
897C TRP* 4.0 2.5 - - + -
941C THR* 4.4 1.3 - - + -
943C GLU* 1.3 76.9 - - - +
945C ASN* 1.3 70.8 + - - +
946C TYR* 5.4 0.2 - - + -
950C GLN* 3.3 3.8 - - - +
951C TRP* 2.9 59.4 + - + +
955C PHE* 3.8 15.9 - - + -
957C PHE* 3.7 48.9 - - + -
959C ILE* 5.1 4.3 - - + -
984C LEU* 4.2 15.9 - - + -
986C ILE* 4.2 10.3 - - + -
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Residues in contact with ASN 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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894C ARG 4.4 0.7 - - - +
895C VAL* 3.9 6.1 - - - +
896C ASN* 2.6 63.0 + - + +
917C ARG* 3.4 2.4 - - - +
943C GLU* 2.9 26.3 + - - +
944C LEU* 1.3 75.4 - - - +
946C TYR* 1.3 62.5 + - - +
947C GLY 5.8 0.4 - - - +
949C HIS 3.4 3.4 - - - +
950C GLN* 2.8 30.8 + - - +
951C TRP* 4.6 0.2 - - - -
1023C LYS* 3.1 27.0 - - + +
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Residues in contact with TYR 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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888C LEU* 4.0 16.6 - - + -
890C GLN* 3.9 13.0 - - + -
891C VAL* 3.6 1.0 - - - -
892C ALA* 2.8 41.4 + - + -
894C ARG 3.5 20.4 - - - -
895C VAL* 3.9 5.4 - - + -
922C LEU* 3.7 21.9 - - + +
944C LEU* 5.4 0.9 - - + -
945C ASN* 1.3 75.1 - - - +
947C GLY* 1.3 72.0 + - - +
948C PRO 3.2 0.2 - - - -
949C HIS* 2.9 33.3 + + - +
951C TRP* 3.8 15.2 - - + -
959C ILE* 3.6 22.0 - - + -
982C THR* 2.7 44.7 + - + +
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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
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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