Contacts of the strand formed by residues 722 - 729 (chain E) in PDB entry 1XSK
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 722 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717E ALA 3.5 1.7 - - - +
718E ARG* 4.5 0.2 - - - -
719E THR* 3.1 37.9 + - + +
720E GLY 3.6 0.8 - - - +
721E ASN* 1.3 82.7 + - - +
723E ILE* 1.3 63.7 + - - +
724E THR* 3.6 13.2 + - - +
769E THR* 4.6 13.9 - - + +
770E ILE 3.1 10.1 - - - +
771E THR* 3.9 15.8 + - - +
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Residues in contact with ILE 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690E LEU* 4.3 19.3 - - + -
693E LEU* 3.5 19.5 - - + -
716E ALA* 5.6 0.9 - - + -
717E ALA 3.1 2.9 - - - +
718E ARG* 3.2 40.8 - - + -
722E THR* 1.3 72.7 - - - +
724E THR* 1.3 62.7 + - - +
725E VAL* 3.9 5.4 + - + +
738E LEU* 4.7 6.5 - - + -
769E THR* 3.6 0.9 - - - -
770E ILE* 2.8 56.2 + - + +
772E LEU* 3.5 32.5 - - + -
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Residues in contact with THR 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715E LYS 3.6 0.9 - - - +
716E ALA* 3.1 5.9 - - - -
717E ALA* 2.7 44.7 + - - +
719E THR* 5.5 2.8 - - - +
722E THR* 3.6 13.0 + - - +
723E ILE* 1.3 72.7 - - - +
725E VAL* 1.3 63.6 - - - +
726E THR* 3.7 24.0 - - + +
767E ALA 6.1 0.4 - - - -
768E LEU 4.1 9.2 - - - +
769E THR* 4.5 10.4 - - + +
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Residues in contact with VAL 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E LEU* 6.1 0.2 - - + -
690E LEU* 6.3 1.3 - - + -
714E LEU* 4.0 26.0 - - + -
715E LYS 3.2 9.2 - - - +
716E ALA* 4.6 11.9 - - + -
723E ILE* 4.1 11.0 - - + +
724E THR* 1.3 78.3 - - - +
726E THR* 1.3 65.6 + - - +
734E TRP* 4.5 8.1 - - + -
736E LEU* 5.2 13.9 - - + -
766E ASN* 5.0 3.1 - - - +
767E ALA* 4.6 4.0 + - - -
768E LEU* 3.1 58.8 + - + +
770E ILE* 4.7 8.3 - - + -
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Residues in contact with THR 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713E THR 3.9 0.5 - - - +
714E LEU* 3.5 5.9 - - - +
715E LYS* 2.7 58.8 + - - +
724E THR* 3.7 21.8 - - + -
725E VAL* 1.3 79.6 - - - +
727E GLY* 1.3 58.4 + - - +
766E ASN* 4.8 4.3 - - - +
767E ALA* 6.4 0.9 - - - -
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Residues in contact with GLY 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712E PHE* 3.9 11.4 - - - -
713E THR 3.2 9.4 - - - -
714E LEU* 3.9 11.8 - - - +
726E THR* 1.3 76.9 - - - +
728E ALA* 1.3 61.6 + - - +
734E TRP* 5.7 0.9 - - - -
766E ASN* 3.8 29.6 + - - +
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Residues in contact with ALA 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711E ILE 4.6 0.2 - - - -
712E PHE* 3.0 10.0 - - - -
713E THR* 2.8 45.4 + - - +
727E GLY* 1.3 75.1 - - - +
729E GLY* 1.3 61.7 + - - +
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Residues in contact with GLY 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711E ILE 3.4 9.2 - - - -
712E PHE* 4.0 3.4 - - - -
728E ALA* 1.3 74.9 - - - +
730E GLU* 1.3 60.7 + - - +
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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