Contacts of the helix formed by residues 720 - 726 (chain A) in PDB entry 5UT1
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 PRO 720 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ILE* 5.1 1.6 - - + -
718A TRP 3.4 7.9 - - - +
719A VAL* 1.3 92.8 - - + +
721A PRO* 1.3 78.7 - - + +
722A GLU* 3.4 24.7 - - - +
723A CYS* 2.9 22.8 + - + -
724A ILE* 3.2 9.5 + - - +
734A THR* 3.7 36.1 - - + +
737A TRP* 3.7 22.4 - - + -
738A SER* 4.3 0.4 - - - +
766A TYR* 3.8 0.4 - - - -
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Residues in contact with PRO 721 (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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720A PRO* 1.3 87.5 - - + +
722A GLU* 1.3 62.4 + - - +
724A ILE* 3.2 4.7 + - - +
725A GLU* 3.0 26.4 + - - +
737A TRP* 3.5 31.0 - - + -
766A TYR* 3.4 26.7 - - + +
790A TYR* 3.5 43.5 - - + +
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Residues in contact with GLU 722 (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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720A PRO* 3.4 18.2 - - - +
721A PRO* 1.3 76.1 - - - +
723A CYS* 1.3 61.5 + - - +
725A GLU* 3.5 11.5 + - - +
726A ASN 3.0 13.0 + - - +
729A ASN* 2.8 47.4 + - + +
731A ASN* 6.0 0.5 - - - +
733A ALA* 4.8 0.5 - - - +
734A THR* 4.1 9.0 + - - -
790A TYR 4.8 1.3 - - - +
792A PRO* 3.7 23.4 - - + +
795A ARG* 2.8 46.2 + - - -
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Residues in contact with CYS 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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704A ILE* 4.0 18.2 - - + -
712A LEU* 4.5 3.3 - - - +
719A VAL* 3.7 16.6 - - + -
720A PRO* 2.9 19.7 + - + +
722A GLU* 1.3 80.1 - - - +
724A ILE* 1.3 62.5 + - - +
725A GLU 3.3 0.4 - - - -
726A ASN 3.6 5.2 - - - -
727A PRO* 3.0 31.5 - - + +
729A ASN 4.0 4.9 - - - -
730A LEU* 3.9 23.3 - - - -
734A THR* 3.6 24.2 - - - -
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Residues in contact with ILE 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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712A LEU* 3.6 39.6 - - + +
713A GLN* 4.1 8.1 - - + +
716A ILE* 3.8 26.0 - - + -
719A VAL* 3.7 14.1 - - + -
720A PRO 3.2 12.6 + - - +
721A PRO* 3.5 8.3 - - + +
723A CYS* 1.3 77.3 - - - +
725A GLU* 1.3 64.1 + - - +
726A ASN* 3.4 0.7 + - - -
727A PRO* 4.6 4.2 - - - +
763A LEU* 3.5 31.4 - - + -
766A TYR* 4.0 9.6 - - + -
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Residues in contact with GLU 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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721A PRO 3.0 11.4 + - - +
722A GLU* 3.8 15.7 - - - +
723A CYS 3.3 0.2 - - - -
724A ILE* 1.3 80.8 - - - +
726A ASN* 1.3 61.6 + - + +
727A PRO* 4.5 1.1 - - - +
729A ASN* 4.4 10.1 + - - -
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Residues in contact with ASN 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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722A GLU 3.0 7.1 + - - +
723A CYS* 3.3 3.7 - - - -
724A ILE 3.3 1.0 - - - -
725A GLU* 1.3 83.6 - - + +
727A PRO* 1.3 61.0 - - - +
728A LYS* 3.0 26.0 + - - +
729A ASN* 2.7 57.7 + - - +
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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