Contacts of the strand formed by residues 938 - 946 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897D TRP* 3.8 10.0 - - + +
900D LEU 3.5 22.7 - - - +
902D PRO 2.9 24.7 + - - -
903D GLN* 3.6 5.1 - - - +
904D GLU* 3.5 18.8 - - - +
905D ASN* 3.6 11.4 - - - +
920D LEU* 4.0 4.6 - - - +
924D ASP 3.2 20.0 + - - -
925D MET* 3.5 41.5 - - - +
927D THR* 5.1 1.8 + - - -
936D GLY* 2.7 47.0 + - - -
937D LEU* 1.3 72.1 - - - +
939D CYS* 1.3 62.9 + - - +
941D THR* 4.2 0.9 - - - +
956D GLN* 3.3 2.4 - - - +
957D PHE* 2.8 53.3 + - + -
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Residues in contact with CYS 939 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900D LEU* 3.2 24.0 + - + +
905D ASN* 2.7 38.4 + - - +
906D TYR* 3.9 4.9 - - - -
907D PRO* 3.8 30.5 - - - -
910D LEU* 3.9 16.2 - - + -
937D LEU* 4.0 10.3 - - - -
938D ARG* 1.3 75.0 - - - +
940D GLY* 1.3 69.2 + - - +
941D THR* 3.1 7.0 + - - -
956D GLN* 3.2 16.6 - - - +
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Residues in contact with GLY 940 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899D GLY* 3.2 15.2 - - - -
900D LEU* 4.4 9.6 - - - -
915D PHE* 3.5 15.9 - - - -
939D CYS* 1.3 77.3 - - - +
941D THR* 1.3 60.1 + - - +
942D ARG* 4.2 3.1 - - - -
954D ASP* 4.4 13.0 - - - -
955D PHE 4.1 0.9 - - - -
956D GLN* 2.9 11.7 + - - -
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Residues in contact with THR 941 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897D TRP* 3.5 14.4 + - + -
898D LEU 3.3 11.7 - - - +
899D GLY* 3.8 0.6 - - - -
938D ARG 3.9 1.0 + - - -
939D CYS 3.3 13.7 + - - -
940D GLY* 1.3 76.6 - - - +
942D ARG* 1.3 65.2 - - - +
943D GLU 3.5 20.9 - - - +
944D LEU 4.4 0.2 - - - +
953D GLY 3.6 0.5 - - - +
954D ASP* 3.3 5.0 + - - -
955D PHE* 2.9 60.5 + - + +
957D PHE* 3.4 27.4 - - + -
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Residues in contact with ARG 942 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871C GLU* 5.8 1.6 + - - -
1013C ARG* 3.7 44.8 - - - +
724D GLU* 5.6 3.2 + - - -
898D LEU* 2.8 22.4 + - + +
915D PHE* 3.9 25.8 - - + -
940D GLY 4.2 4.5 - - - -
941D THR* 1.3 80.5 - - - +
943D GLU* 1.3 60.2 - - - +
952D ARG* 3.4 7.3 - - - +
953D GLY 2.8 48.6 + - - +
954D ASP* 3.7 16.9 - - - +
955D PHE* 4.5 1.1 - - - -
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Residues in contact with GLU 943 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897D TRP* 3.2 5.7 - - - +
898D LEU* 2.8 45.4 + - + +
917D ARG* 2.8 28.5 + - - -
941D THR* 3.5 4.3 - - - +
942D ARG* 1.3 82.0 - - + +
944D LEU* 1.3 61.0 - - - +
945D ASN* 2.7 25.2 + - - +
950D GLN* 3.4 33.9 + - + +
951D TRP 3.3 7.0 - - - -
952D ARG* 4.1 11.6 - - + -
955D PHE* 4.5 0.2 - - - -
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Residues in contact with LEU 944 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895D VAL* 3.7 21.8 - - + -
896D ASN 3.7 4.5 - - - +
897D TRP* 4.0 2.0 - - + -
941D THR* 4.6 1.3 - - + -
943D GLU* 1.3 74.3 - - - +
945D ASN* 1.3 67.9 + - - +
946D TYR* 5.4 0.4 - - + -
950D GLN* 3.3 5.2 - - - +
951D TRP* 2.9 57.6 + - + +
955D PHE* 3.7 21.8 - - + -
957D PHE* 3.7 49.8 - - + -
959D ILE* 5.2 4.5 - - + -
984D LEU* 3.9 19.7 - - + -
986D ILE* 4.5 2.7 - - + -
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Residues in contact with ASN 945 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894D ARG 4.4 0.3 - - - +
895D VAL* 3.9 6.6 - - - +
896D ASN* 2.8 62.0 + - + +
917D ARG* 3.5 1.8 - - - +
943D GLU* 2.7 25.4 + - - +
944D LEU* 1.3 72.8 - - - +
946D TYR* 1.3 64.4 + - - +
947D GLY 5.5 2.0 - - - +
949D HIS 3.4 4.6 - - - +
950D GLN* 2.8 36.3 + - - +
1023D LYS 5.5 0.9 - - - -
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Residues in contact with TYR 946 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888D LEU* 3.8 21.1 - - + -
890D GLN* 3.9 18.6 - - + -
892D ALA* 3.0 36.3 + - + -
894D ARG 3.3 21.3 - - - -
895D VAL* 3.9 5.2 - - + -
922D LEU* 3.5 24.5 - - + +
944D LEU* 5.4 1.8 - - + -
945D ASN* 1.3 75.4 - - - +
947D GLY* 1.3 67.7 + - - +
948D PRO* 3.2 2.3 - - - +
949D HIS* 2.8 33.5 + + - +
951D TRP* 4.0 14.5 - - + -
959D ILE* 3.7 17.7 - - + -
982D THR* 2.5 46.6 + - + +
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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