Contacts of the strand formed by residues 721 - 728 (chain A) in PDB entry 1AMI
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 THR 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717A HIS* 2.8 44.5 + - + +
719A ASN* 2.7 28.1 + - - -
720A GLY* 1.3 75.9 - - - +
722A GLN* 1.3 69.8 + - - +
723A GLU* 5.2 3.1 - - + -
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Residues in contact with GLN 722 (chain A).
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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714A ILE* 3.6 21.8 - - + +
715A ILE 3.2 6.3 - - - +
716A LYS* 3.8 31.0 - - + +
720A GLY 3.5 9.1 + - - +
721A THR* 1.3 84.2 - - - +
723A GLU* 1.3 66.2 + - - +
724A THR* 6.0 0.2 - - - +
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Residues in contact with GLU 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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690A LYS* 3.4 44.3 - - + +
692A HIS* 5.7 0.2 - - - -
713A CYS 3.8 0.2 - - - +
714A ILE* 3.4 2.3 - - - -
715A ILE* 2.8 43.3 + - + +
717A HIS* 2.8 35.8 + - + +
721A THR* 5.2 3.8 - - + -
722A GLN* 1.3 76.5 - - - +
724A THR* 1.3 65.5 + - - +
725A ILE* 5.1 0.4 - - + -
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Residues in contact with THR 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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690A LYS* 5.1 2.4 + - - -
712A THR* 4.4 18.8 - - + -
713A CYS 3.3 7.4 - - - +
714A ILE* 3.8 18.6 - - + +
722A GLN* 6.0 0.2 - - - +
723A GLU* 1.3 74.6 - - - +
725A ILE* 1.3 78.0 + - - +
726A LEU* 5.4 2.7 - - + -
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Residues in contact with ILE 725 (chain A).
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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682A PHE* 4.0 32.5 - - + -
687A ASP* 3.4 31.4 - - + +
690A LYS* 3.8 13.9 - - + +
691A ILE* 4.4 6.1 - - + -
712A THR* 3.6 3.8 - - - -
713A CYS* 2.8 50.0 + - + +
715A ILE* 3.9 30.3 - - + -
723A GLU* 5.0 1.1 - - + -
724A THR* 1.3 83.6 - - - +
726A LEU* 1.3 64.9 + - - +
727A LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 726 (chain A).
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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682A PHE* 4.3 0.5 - - - -
683A ALA* 3.1 36.1 + - + +
684A ASP 4.7 0.5 + - - -
687A ASP* 5.0 2.2 + - - +
710A PRO* 4.1 26.5 - - + +
711A LEU 3.4 6.5 - - - +
712A THR* 3.6 30.7 - - + -
724A THR* 5.4 3.1 - - + -
725A ILE* 1.3 79.2 - - - +
727A LEU* 1.3 68.4 + - - +
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Residues in contact with LEU 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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660A ILE* 3.9 20.6 - - + -
680A LEU* 3.9 34.3 - - + -
681A THR 3.3 12.6 - - - +
682A PHE* 3.9 25.4 - - + -
699A ILE* 3.9 14.6 - - + -
710A PRO* 3.3 4.5 - - - +
711A LEU* 2.8 37.8 + - + +
713A CYS* 3.7 26.5 - - + +
725A ILE* 4.1 10.5 - - + -
726A LEU* 1.3 84.5 - - - +
728A ASN* 1.3 64.5 + - - +
729A HIS* 4.7 0.9 - - - -
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Residues in contact with ASN 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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680A LEU* 3.4 7.4 - - - +
681A THR* 2.8 44.9 + - - +
682A PHE 4.6 1.6 + - - -
683A ALA* 3.4 30.6 + - - +
710A PRO* 3.6 24.2 - - - +
726A LEU 4.3 0.4 + - - -
727A LEU* 1.3 74.4 - - - +
729A HIS* 1.3 64.0 + - - +
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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