Contacts of the helix formed by residues 722 - 728 (chain A) in PDB entry 3U44
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 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A TYR 3.0 14.5 + - - -
719A ARG* 4.1 16.6 + - - +
720A ASP 3.3 4.4 + - - +
721A THR* 1.3 79.9 - - - +
723A TYR* 1.3 59.3 + - - +
724A MET 3.3 2.2 - - - -
725A ASP* 3.3 26.4 + - + +
726A TYR* 2.9 29.9 + - - +
719B LYS* 4.1 7.1 - - - +
720B SER* 4.1 19.0 + - - +
723B GLN* 3.3 28.7 - - - +
758B GLN* 4.2 22.3 - - - +
762B LEU* 4.1 19.2 - - + +
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Residues in contact with TYR 723 (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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621A VAL* 4.3 1.0 - - - +
622A GLU* 3.0 40.9 + - - +
625A VAL* 3.5 24.5 - - + +
626A ALA* 4.4 5.6 - - + -
649A PRO* 4.7 19.5 - - + +
650A ILE* 3.8 31.2 - - + -
718A TYR* 3.6 13.5 + + + +
721A THR* 3.0 20.5 + - - +
722A LYS* 1.3 77.2 - - - +
724A MET* 1.3 57.9 + - - +
726A TYR* 3.2 10.1 + + + +
727A VAL* 2.8 51.2 + - + +
730A MET* 5.6 1.1 - - + -
740A LEU* 3.5 33.2 - - + -
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Residues in contact with MET 724 (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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718A TYR* 4.2 36.6 + - + +
722A LYS 3.3 0.2 - - - -
723A TYR* 1.3 79.2 - - - +
725A ASP* 1.3 66.2 + - - +
727A VAL* 3.5 0.9 + - - +
728A GLY 3.3 8.8 + - - -
737A GLN* 3.0 63.8 + - + +
740A LEU* 3.7 22.6 - - + +
741A ARG* 3.7 31.2 - - + +
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Residues in contact with ASP 725 (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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718A TYR 5.2 1.7 - - - +
719A ARG* 5.9 1.2 - - - -
722A LYS* 3.3 34.6 + - - +
723A TYR 3.2 0.2 - - - -
724A MET* 1.3 81.2 - - - +
726A TYR* 1.3 65.9 + - - +
728A GLY* 3.1 14.7 + - - -
729A GLY 3.8 2.4 + - - -
737A GLN* 4.3 3.4 + - - +
720B SER* 4.8 2.4 - - - +
723B GLN* 5.8 0.2 - - - +
724B SER* 2.7 46.4 + - - +
727B ALA* 4.1 11.8 - - - +
762B LEU* 3.7 16.5 - - + +
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Residues in contact with TYR 726 (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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649A PRO* 3.4 37.8 - - + +
721A THR 5.6 0.4 - - - +
722A LYS 2.9 17.7 + - - +
723A TYR* 3.5 10.3 - + + +
725A ASP* 1.3 77.3 - - - +
727A VAL* 1.3 59.2 + - + +
729A GLY* 2.9 17.7 + - - -
730A MET* 3.3 29.1 - - + +
761B LYS* 3.6 5.2 - - + -
762B LEU* 3.6 23.0 - - + +
764B SER* 3.5 24.9 + - - -
765B SER* 3.1 45.0 - - - -
768B PHE* 3.6 24.2 - + - +
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Residues in contact with VAL 727 (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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622A GLU* 3.5 12.6 - - + -
723A TYR* 2.8 68.2 + - + +
724A MET* 3.9 7.4 - - - +
725A ASP 3.3 0.4 - - - -
726A TYR* 1.3 71.9 - - + +
728A GLY* 1.3 59.9 + - - +
729A GLY 3.1 1.8 + - - -
730A MET* 3.4 22.2 - - + +
733A GLY* 3.2 15.2 - - - -
736A ARG* 3.1 42.2 - - + -
737A GLN* 4.2 1.3 - - + +
740A LEU* 4.0 5.6 - - + -
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Residues in contact with GLY 728 (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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724A MET 3.3 5.7 + - - -
725A ASP 3.1 7.2 + - - -
726A TYR 3.1 1.2 - - - -
727A VAL* 1.3 77.2 - - - +
729A GLY* 1.3 56.7 + - - +
730A MET 3.5 0.9 - - - -
733A GLY* 3.8 17.3 - - - -
734A LYS* 6.1 0.3 - - - +
737A GLN* 3.6 22.9 - - - -
728B SER* 3.5 25.1 - - - -
731B ARG* 3.6 12.3 - - - +
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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