Contacts of the strand formed by residues 754 - 759 (chain A) 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 LYS 754 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A GLU* 3.5 1.7 - - - +
751A LEU* 2.7 44.6 + - - +
752A GLY 3.0 0.4 - - - -
753A ASN* 1.3 103.1 + - - +
755A ARG* 1.3 67.2 - - - +
756A TRP* 3.5 28.7 - - + -
769A TRP 3.5 8.3 - - - +
770A ILE* 4.7 9.2 - - + -
861A SER 4.0 6.7 + - - -
862A GLY* 4.0 26.4 + - - +
1022A GLN* 3.7 34.8 - - + +
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Residues in contact with ARG 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A CYS* 6.5 0.7 - - + -
749A ILE 3.2 8.1 - - - +
750A GLU* 3.7 30.6 + - + +
753A ASN 4.2 1.6 + - - -
754A LYS* 1.3 81.9 - - - +
756A TRP* 1.3 68.5 - - - +
768A MET* 3.3 6.9 - - - +
769A TRP* 3.1 89.9 + - + +
771A GLY 3.5 21.0 + - - -
772A ASP* 3.6 19.0 + - - +
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Residues in contact with TRP 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A PHE 3.8 0.6 - - - +
748A CYS* 3.3 5.5 - - - +
749A ILE* 2.7 54.7 + - + +
751A LEU* 3.9 17.3 - - + -
754A LYS* 3.5 41.7 - - + -
755A ARG* 1.3 78.7 - - - +
757A GLN* 1.3 59.4 + - - +
758A PHE* 3.9 17.5 - - + -
765A LEU* 4.0 3.6 - - + -
767A GLN 3.8 4.3 - - - -
768A MET* 3.5 35.8 - - + -
769A TRP* 4.7 2.0 - - - -
858A ILE* 3.6 34.3 - - + -
862A GLY* 3.6 25.6 - - - -
864A MET* 3.7 30.7 - - + +
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Residues in contact with GLN 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 3.7 31.1 - - - +
747A PHE 3.4 3.6 - - - -
748A CYS* 3.7 20.1 - - - +
756A TRP* 1.3 74.8 - - - +
758A PHE* 1.3 63.6 + - - +
765A LEU* 3.6 3.1 - - - +
766A SER* 2.8 41.2 + - - +
767A GLN* 2.9 25.2 + - - +
769A TRP* 3.8 28.5 - - + -
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Residues in contact with PHE 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 3.2 8.4 - - - -
747A PHE* 2.7 50.8 + - + +
749A ILE* 3.6 31.6 - - + -
756A TRP* 3.9 13.9 - - + -
757A GLN* 1.3 76.6 - - - +
759A ASN* 1.3 62.8 + - - +
760A ARG* 3.6 0.9 + - - +
763A GLY 5.3 3.1 - - - -
764A PHE* 3.5 6.1 - - - +
765A LEU* 3.8 29.2 - - + -
836A ILE* 3.9 25.1 - - + -
838A THR* 5.6 0.7 - - + -
856A TYR* 3.5 57.2 - + + -
858A ILE* 4.0 3.4 - - + -
864A MET* 4.3 6.3 - - - -
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Residues in contact with ASN 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A MET* 3.6 24.6 + - - +
746A ASP* 3.8 8.9 + - - -
758A PHE* 1.3 71.0 - - - +
760A ARG* 1.3 53.5 + - - +
761A GLN* 2.7 18.2 + - - +
762A SER* 2.7 43.1 + - - +
763A GLY* 2.6 36.2 + - - -
764A PHE 3.0 11.3 + - - +
766A SER* 4.0 18.1 + - - +
825A CYS* 4.4 2.0 - - - -
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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