Contacts of the helix formed by residues 780 - 788 (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 LEU 780 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A ILE* 5.0 5.8 - - + -
650A LYS* 4.8 13.0 - - + +
651A LEU* 4.8 7.6 - - + -
654A ALA* 4.4 21.3 - - + -
743A LEU* 4.5 12.6 - - + -
746A ILE* 5.6 0.9 - - + -
747A CYS* 3.7 30.9 - - - -
777A ALA 4.8 1.4 + - - -
778A ALA 3.0 0.8 - - - -
779A GLU* 1.3 83.7 - - + +
781A ALA* 1.3 65.5 + - - +
782A ASN 3.3 2.7 - - - -
783A LEU* 3.1 13.6 + - + +
784A ILE* 3.0 29.3 + - + +
805A LEU* 3.9 17.9 - - + -
808A LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 781 (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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774A ALA* 3.7 33.2 - - + -
775A PRO* 4.4 2.6 - - + +
778A ALA* 2.9 18.8 + - + +
780A LEU* 1.3 77.6 - - - +
782A ASN* 1.3 68.4 + - - +
784A ILE* 3.2 13.9 + - - +
785A ASN* 3.0 33.3 + - - +
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Residues in contact with ASN 782 (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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778A ALA 4.7 0.4 + - - -
779A GLU 5.1 1.6 + - - -
780A LEU 3.3 0.8 - - - -
781A ALA* 1.3 80.9 - - - +
783A LEU* 1.3 57.1 + - - +
785A ASN* 3.3 8.8 + - - +
786A ASN* 2.9 42.0 + - - +
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Residues in contact with LEU 783 (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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743A LEU* 3.5 20.4 - - + -
780A LEU* 3.1 17.0 + - + +
782A ASN* 1.3 77.1 - - - +
784A ILE* 1.3 66.2 + - - +
786A ASN* 3.2 10.8 + - + +
787A CYS* 2.9 43.2 + - - -
796A PRO* 5.3 2.7 - - + -
801A ILE* 4.3 19.5 - - + +
804A ASP* 3.7 32.2 + - + +
805A LEU* 3.5 37.5 - - + -
808A LEU* 5.9 2.9 - - + -
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Residues in contact with ILE 784 (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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740A GLY* 3.7 19.3 - - - +
743A LEU* 3.6 28.7 - - + +
744A TRP* 3.7 38.1 - - + +
747A CYS* 4.5 1.1 - - - -
772A LEU* 4.9 1.1 - - + -
775A PRO* 4.2 16.4 - - + -
780A LEU* 3.0 30.3 + - + +
781A ALA* 3.4 11.4 - - - +
783A LEU* 1.3 77.1 - - - +
785A ASN* 1.3 67.8 + - - +
787A CYS* 3.3 2.1 + - - +
788A MET* 2.9 48.7 + - - +
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Residues in contact with ASN 785 (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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771A GLN* 4.0 30.0 + - + +
772A LEU 3.9 21.4 + - - +
774A ALA* 5.9 2.6 - - - +
781A ALA* 3.0 25.0 + - - +
782A ASN* 3.8 9.0 + - - +
784A ILE* 1.3 87.2 - - - +
786A ASN* 1.3 64.5 + - - +
788A MET* 3.2 22.5 + - - +
789A ASP* 3.8 2.4 + - - +
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Residues in contact with ASN 786 (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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782A ASN* 2.9 28.3 + - - +
783A LEU* 3.7 10.6 - - + +
785A ASN* 1.3 79.2 - - - +
787A CYS* 1.4 59.5 + - - +
789A ASP* 3.6 17.0 - - - +
794A HIS 4.9 0.7 - - - +
795A ARG* 4.3 0.2 - - - -
796A PRO* 3.4 26.0 - - + +
804A ASP* 5.2 6.3 + - - -
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Residues in contact with CYS 787 (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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736A LYS 3.3 17.5 - - - +
737A TRP* 3.4 7.3 + - - -
739A PHE* 3.9 16.4 - - - -
740A GLY* 3.8 9.9 - - - -
783A LEU* 2.9 33.1 + - - +
784A ILE 3.7 3.8 - - - +
786A ASN* 1.4 75.1 - - - +
788A MET* 1.3 59.2 + - - +
789A ASP 3.0 8.5 + - - -
795A ARG* 3.4 22.1 - - - -
796A PRO* 4.2 9.2 - - - -
801A ILE* 3.7 31.2 - - - -
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Residues in contact with MET 788 (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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717A PRO* 3.9 8.7 - - + +
737A TRP* 3.3 59.3 - - + +
740A GLY* 4.1 0.4 - - - -
741A THR* 3.3 28.3 - - - +
765A PHE* 5.8 2.5 - - + -
771A GLN* 2.9 34.3 + - - +
772A LEU* 3.7 40.4 - - + +
784A ILE* 2.9 33.4 + - - +
785A ASN* 3.2 7.1 + - - +
787A CYS* 1.3 72.8 - - - +
789A ASP* 1.3 59.7 + - - +
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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