Contacts of the strand formed by residues 1013 - 1022 (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 ARG1013 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870C VAL 3.4 3.6 - - - +
871C GLU* 4.0 26.8 + - + +
1011C ALA* 2.9 25.3 + - - +
1012C GLY* 1.3 86.0 - - - +
1014C TYR* 1.3 71.0 + - - +
721D ARG* 5.9 2.8 - - - +
724D GLU* 5.3 7.1 + - - -
942D ARG* 3.7 37.3 - - - +
954D ASP* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1014 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868C VAL 3.8 0.5 - - - +
869C ASP* 3.3 5.1 - - - +
870C VAL* 2.8 40.9 + - + +
872C VAL* 4.5 6.7 - - + -
882C ILE* 3.4 29.2 - - + -
989C PHE* 3.6 51.1 - + + -
1008C GLN 4.4 0.9 + - - -
1009C LEU* 3.1 33.8 - - + +
1010C SER 3.2 0.5 + - - -
1011C ALA* 2.8 45.5 + - + +
1012C GLY 3.8 8.5 - - - -
1013C ARG* 1.3 81.5 - - - +
1015C HIS* 1.3 60.5 + - - +
1016C TYR* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1015 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867C THR* 3.5 29.7 - - + +
868C VAL 3.2 5.6 + - - -
869C ASP* 2.4 30.9 + - - +
989C PHE* 3.2 21.8 - - - -
1014C TYR* 1.3 76.4 - - - +
1016C TYR* 1.3 73.4 + - - +
1017C GLN* 4.6 7.6 - - + +
867D THR* 5.8 0.2 - - + -
869D ASP* 3.4 16.3 + - - -
1015D HIS* 3.4 51.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1016 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C ASP* 4.7 1.0 + - - -
866C ILE 4.2 0.2 - - - +
867C THR* 3.8 0.3 - - - -
868C VAL* 2.8 71.5 + - + +
870C VAL* 4.8 1.7 - - + +
882C ILE* 4.0 21.8 - - + +
883C GLY* 3.3 30.4 + - - -
884C LEU* 3.4 16.8 - - + +
954C ASP 5.4 5.8 - - - +
955C PHE* 5.9 0.7 - - + -
986C ILE 4.9 0.9 - - - -
987C ASP 5.0 0.2 - - - -
988C GLY* 3.5 33.9 - - - -
989C PHE* 4.1 9.6 - + + -
1014C TYR 5.2 1.3 - - - -
1015C HIS* 1.3 88.0 + - - +
1017C GLN* 1.3 62.2 + - - +
1018C LEU* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1017 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865C ALA* 3.9 12.9 - - - +
866C ILE 2.4 55.8 + - - +
867C THR* 2.8 20.8 + - + +
953C GLY* 3.8 18.9 - - - -
954C ASP 4.3 3.8 + - - -
955C PHE* 6.0 0.2 - - - +
1015C HIS* 4.6 10.7 - - + +
1016C TYR* 1.3 78.7 - - - +
1018C LEU* 1.3 69.0 + - - +
1019C VAL* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1018 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864C MET 3.7 0.5 - - - +
865C ALA* 3.4 1.0 - - - -
866C ILE* 2.5 54.1 + - + +
868C VAL* 6.2 0.2 - - + -
884C LEU* 3.7 29.8 - - + -
951C TRP* 5.3 9.6 - - + -
952C ARG 3.4 3.8 - - - +
955C PHE* 3.5 39.0 - - + -
986C ILE* 3.7 33.0 - - + -
1016C TYR* 4.1 17.9 - - + -
1017C GLN* 1.3 81.1 + - - +
1019C VAL* 1.3 65.9 + - - +
1020C TRP 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1019 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C GLN* 3.9 24.0 - - + +
864C MET 3.3 8.7 - - - +
865C ALA* 4.0 17.3 - - + -
950C GLN 3.7 0.5 - - - +
951C TRP* 3.1 6.3 - - - +
952C ARG* 2.8 72.1 + - + +
1017C GLN* 5.1 7.9 - - + -
1018C LEU* 1.3 80.8 - - - +
1020C TRP* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1020 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C TRP* 5.8 0.5 - - - -
765C LEU* 4.7 0.9 - - + -
768C MET* 3.2 34.1 - - + +
776C LEU* 4.2 5.4 - - + -
780C LEU* 4.1 31.2 - - + -
862C GLY 4.3 0.5 - - - +
863C GLN* 3.8 0.3 - - - -
864C MET* 2.8 63.0 + - + +
866C ILE* 4.5 8.9 - - + +
886C CYS* 4.2 5.6 - - - -
888C LEU* 4.0 17.5 - - + -
949C HIS* 3.0 32.6 + + - +
950C GLN 3.5 6.5 - - - -
951C TRP* 3.1 43.4 - + + +
984C LEU* 5.7 0.7 - - + -
1018C LEU 4.1 0.4 - - - -
1019C VAL* 1.3 73.9 - - - +
1021C CYS* 1.3 91.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1021 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862C GLY 4.3 6.3 - - - +
863C GLN* 3.9 28.5 - - + -
949C HIS* 3.7 3.5 + - - -
950C GLN* 2.8 44.8 + - - -
952C ARG* 3.0 32.1 - - - +
1020C TRP* 1.3 85.8 - - - +
1022C GLN* 1.3 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1022 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753C ASN* 3.3 12.0 + - - +
754C LYS* 2.7 45.9 + - + +
770C ILE* 3.3 42.6 - - + +
862C GLY 5.1 2.2 + - - -
948C PRO* 3.4 16.3 + - - +
949C HIS* 6.0 1.1 - - - +
950C GLN* 4.6 0.6 - - - -
1021C CYS* 1.3 89.2 - - - +
1023C LYS* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
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