Contacts of the strand formed by residues 732 - 739 (chain A) in PDB entry 4Z96
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 LEU 732 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717A LEU* 4.1 20.0 - - + +
720A MET* 4.0 16.2 - - + -
721A CYS* 3.8 19.1 - - - -
726A PHE* 3.8 26.0 - - + -
730A THR* 3.6 13.1 + - + +
731A SER* 1.3 83.6 + - - +
733A ILE* 1.3 62.6 + - - +
734A LEU* 3.5 14.1 - - + -
749A TYR* 2.7 26.1 + - - -
768A PHE* 3.7 23.8 - - + -
769A GLN 3.2 21.5 - - - +
770A LYS* 4.0 2.7 - - - -
771A ASP* 4.5 1.3 - - - +
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Residues in contact with ILE 733 (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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732A LEU* 1.3 77.9 - - - +
734A LEU* 1.3 65.6 + - - +
735A TYR* 3.4 34.1 - - + +
745A ARG* 4.3 17.7 - - + -
749A TYR* 3.2 3.8 - - - +
767A VAL 3.7 0.5 - - - +
768A PHE* 3.0 4.5 - - - +
769A GLN* 2.7 67.3 + - + +
771A ASP* 3.8 33.0 - - + +
775A ASN* 5.7 0.2 - - - +
782A THR* 5.3 3.8 - - + -
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Residues in contact with LEU 734 (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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713A ILE* 3.7 26.5 - - + -
717A LEU* 3.7 15.3 - - + -
720A MET* 3.5 36.8 - - + -
732A LEU* 3.5 24.9 - - + -
733A ILE* 1.3 80.8 - - - +
735A TYR* 1.3 56.9 + - - +
745A ARG* 3.5 6.6 - - - +
746A ILE* 2.7 42.2 + - + +
749A TYR* 3.1 25.4 + - + +
766A ILE* 4.1 7.9 - - + -
767A VAL 3.4 2.7 - - - -
768A PHE* 3.8 9.9 - - + -
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Residues in contact with TYR 735 (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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733A ILE* 3.4 29.5 - - + +
734A LEU* 1.3 74.4 - - - +
736A GLU* 1.3 57.7 + - - +
743A THR* 3.7 28.3 - - + -
744A GLU 3.2 6.7 - - - +
745A ARG* 3.4 41.3 - - + -
746A ILE* 4.5 4.5 - - - -
766A ILE* 3.3 6.2 - - - +
767A VAL* 2.6 51.4 + - + +
769A GLN* 3.9 8.2 + - + -
782A THR* 3.1 33.2 - - - +
783A ALA* 3.7 29.6 - - + -
784A LYS* 3.8 18.6 - - + -
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Residues in contact with GLU 736 (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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735A TYR* 1.3 75.5 - - - +
737A GLU* 1.3 68.8 + - - +
738A VAL* 3.3 27.4 + - + +
743A THR* 3.6 1.8 - - - -
744A GLU* 2.7 45.3 + - + +
746A ILE* 4.4 3.2 - - + +
757A LEU* 3.8 45.6 - - + +
758A ASP 4.7 0.5 - - - +
764A ASP* 3.9 11.1 - - - +
765A ILE 3.3 13.0 - - - +
766A ILE* 4.4 2.0 - - + +
1109C LYS* 4.5 7.2 - - - -
1111C LYS* 3.3 27.5 + - - -
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Residues in contact with GLU 737 (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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581A ASN* 3.0 30.8 + - - +
582A ASP* 2.8 27.3 + - - +
634A ARG* 3.1 23.9 + - - +
690A LYS* 2.6 33.9 + - - +
735A TYR 3.9 2.0 + - - -
736A GLU* 1.3 75.3 - - - +
738A VAL* 1.3 59.5 + - - +
739A LYS 4.8 4.8 - - - +
740A PRO* 5.3 0.2 - - - +
742A LEU 4.3 2.9 - - - +
743A THR* 4.9 4.7 - - - +
765A ILE* 2.9 36.3 + - + +
767A VAL* 4.0 10.8 - - + +
787A PHE* 3.8 15.5 - - + -
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Residues in contact with VAL 738 (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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628A ARG* 5.5 0.9 + - - -
630A ASN* 3.9 10.5 + - - +
632A THR* 3.8 5.5 + - - +
634A ARG* 3.1 17.4 + - - +
736A GLU* 3.6 33.9 - - + +
737A GLU* 1.3 73.9 - - - +
739A LYS* 1.3 70.7 - - + +
742A LEU* 3.2 33.9 + - + +
744A GLU* 3.5 24.9 - - - +
1109C LYS* 3.9 19.3 - - + -
1111C LYS* 4.4 16.8 + - + +
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Residues in contact with LYS 739 (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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581A ASN* 4.0 10.2 + - - +
630A ASN* 3.7 32.2 - - + +
632A THR* 3.6 13.2 - - + -
634A ARG* 4.8 1.1 - - - +
737A GLU* 3.7 1.4 - - - +
738A VAL* 1.3 84.1 + - + +
740A PRO* 1.3 91.2 - - + +
741A ASN 3.3 0.6 + - - -
742A LEU* 2.9 40.6 + - + +
743A THR* 5.1 0.5 + - - -
1108C ASN* 3.3 24.7 + - - -
1109C LYS 4.3 5.9 + - - +
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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