Contacts of the strand formed by residues 881 - 888 (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 881 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783D GLN* 3.6 33.9 - - - +
784D PHE* 3.2 27.5 + - - +
785D THR 3.0 34.1 + - - +
786D ARG* 3.4 10.7 - - - +
879D PRO* 3.3 4.1 + - - +
880D ALA* 1.3 80.8 - - + +
882D ILE* 1.3 71.0 + - - +
934D GLU* 2.8 21.4 + - - -
937D LEU* 4.4 1.2 - - - +
958D ASN* 3.7 9.9 - - - +
964D GLN* 3.2 24.0 + - - -
985D ASN* 3.9 8.7 - - - +
987D ASP* 2.8 36.2 + - - +
989D PHE 3.4 12.8 - - - +
990D HIS* 3.4 19.4 - - + +
1009D LEU* 3.7 4.7 - - - -
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Residues in contact with ILE 882 (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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783D GLN 4.0 2.0 - - - -
784D PHE* 4.3 11.0 - - + -
870D VAL* 4.3 20.6 - - + -
872D VAL* 4.0 17.3 - - + -
879D PRO* 4.2 9.6 - - + -
881D ARG* 1.3 77.1 - - - +
883D GLY* 1.3 59.7 + - - +
987D ASP* 4.3 0.9 - - - -
988D GLY* 2.8 22.9 + - - -
989D PHE* 2.9 28.3 + - + +
1009D LEU* 4.1 9.0 - - + -
1014D TYR* 3.2 46.7 - - + -
1016D TYR* 3.9 18.3 - - + -
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Residues in contact with GLY 883 (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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782D ASP* 3.3 8.7 - - - +
783D GLN* 2.8 33.7 + - - -
784D PHE* 5.1 2.1 - - - -
882D ILE* 1.3 77.3 - - - +
884D LEU* 1.3 59.1 - - - +
986D ILE 3.3 12.3 - - - -
987D ASP* 3.6 10.4 + - - -
1016D TYR* 3.3 19.4 + - - -
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Residues in contact with LEU 884 (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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780D LEU* 3.9 34.3 - - + +
781D ARG 3.3 5.8 - - - +
782D ASP* 3.9 11.9 - - - +
783D GLN* 4.3 3.4 + - - +
854D LYS* 3.8 27.1 - - + -
856D TYR* 5.8 0.4 - - - +
866D ILE* 4.6 17.7 - - + -
868D VAL* 4.6 1.3 - - + -
883D GLY* 1.3 78.4 - - - +
885D ASN* 1.3 64.9 + - - +
984D LEU 4.0 0.2 - - - +
985D ASN* 3.6 1.0 - - - -
986D ILE* 2.8 37.7 + - + +
987D ASP* 4.8 1.2 - - - +
1016D TYR* 3.3 24.9 - - + +
1018D LEU* 4.0 24.2 - - + -
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Residues in contact with ASN 885 (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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778D THR* 5.9 1.4 - - - +
779D PRO 3.3 2.3 - - - +
780D LEU* 3.3 4.4 - - - -
781D ARG* 2.8 42.1 + - - +
782D ASP 5.0 0.9 - - - +
783D GLN* 3.6 25.8 + - + +
884D LEU* 1.3 78.6 - - - +
886D CYS* 1.3 66.0 + - - +
964D GLN* 4.9 4.4 - - - +
983D TRP* 3.6 28.4 - - - -
984D LEU 3.3 6.7 - - - +
985D ASN* 3.0 28.2 + - - +
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Residues in contact with CYS 886 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776D LEU* 4.2 5.2 - - + -
778D THR 3.5 14.1 - - - +
779D PRO 3.8 8.3 - - - +
780D LEU* 3.8 22.0 - - + -
885D ASN* 1.3 80.7 - - - +
887D GLN* 1.3 61.4 + - - +
888D LEU* 3.7 28.0 - - - -
982D THR 3.8 0.3 - - - +
983D TRP* 3.5 11.2 - - - -
984D LEU* 2.9 44.3 + - - +
1020D TRP* 4.1 10.5 - - - -
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Residues in contact with GLN 887 (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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776D LEU* 3.5 4.3 - - - +
777D LEU* 2.8 45.3 + - + +
778D THR* 3.4 35.2 + - - +
886D CYS* 1.3 76.5 - - - +
888D LEU* 1.3 65.6 + - - +
979D GLU* 3.8 6.0 + - - +
980D GLU* 2.2 49.1 + - - +
982D THR 3.5 7.0 - - - +
983D TRP* 3.4 39.4 - - + +
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Residues in contact with LEU 888 (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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775D GLN 3.5 4.9 - - - +
776D LEU* 4.0 6.3 - - + -
777D LEU* 3.8 3.3 - - - +
886D CYS* 3.7 24.2 - - - -
887D GLN* 1.3 76.4 - - - +
889D ALA* 1.3 60.7 + - - +
890D GLN* 4.2 12.6 - - + +
946D TYR* 3.8 31.2 - - + -
949D HIS* 4.1 13.2 - - + +
951D TRP* 4.0 18.6 - - + -
959D ILE* 5.2 0.9 - - + -
981D GLY* 3.3 4.5 - - - -
982D THR* 2.7 42.8 + - + +
984D LEU* 4.5 11.0 - - + -
1020D TRP* 4.0 24.5 - - + -
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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