Contacts of the helix formed by residues 758 - 768 (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 ASP 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756A ALA 3.9 3.2 + - - -
757A LEU* 1.3 73.7 - - - +
759A SER* 1.3 66.0 + - - +
760A GLN* 4.0 11.2 - - - +
761A ARG* 3.0 41.2 + - - +
762A LYS* 2.9 20.9 + - - +
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Residues in contact with SER 759 (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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710A ASP* 4.4 3.6 + - - +
713A GLN* 4.0 23.6 - - - +
714A GLU* 3.8 26.9 + - - +
758A ASP* 1.3 74.1 - - - +
760A GLN* 1.3 62.8 - - - +
762A LYS* 3.2 11.8 + - - +
763A LEU* 3.0 24.3 + - - +
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Residues in contact with GLN 760 (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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713A GLN* 5.2 0.4 - - - -
758A ASP* 3.2 13.6 + - - +
759A SER* 1.3 79.0 - - - +
761A ARG* 1.3 60.5 + - + +
763A LEU* 3.4 11.3 + - - +
764A GLN* 3.1 25.5 + - - +
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Residues in contact with ARG 761 (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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757A LEU* 3.9 32.6 - - + +
758A ASP* 3.0 31.9 + - - +
760A GLN* 1.3 77.0 - - + +
762A LYS* 1.3 60.3 + - - +
764A GLN* 3.3 7.4 + - + +
765A PHE* 2.9 28.1 + - - +
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Residues in contact with LYS 762 (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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713A GLN 3.5 18.2 - - - +
714A GLU* 3.8 15.3 - - - +
716A ILE* 3.4 51.4 - - + +
718A TRP* 6.2 0.7 - - - -
753A PRO 5.3 1.1 - - - -
754A LEU* 3.0 25.8 + - + +
755A SER* 4.2 8.7 + - - +
757A LEU* 2.4 41.6 + - + +
758A ASP 2.9 15.5 + - - +
759A SER* 3.2 11.4 + - - +
761A ARG* 1.3 77.9 - - - +
763A LEU* 1.3 62.8 + - - +
765A PHE* 3.1 21.8 + - - +
766A TYR* 3.2 5.4 + - - +
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Residues in contact with LEU 763 (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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713A GLN* 3.6 38.4 - - + +
716A ILE* 4.0 7.7 - - + +
724A ILE* 3.5 32.1 - - + -
759A SER 3.0 8.1 + - - +
760A GLN* 3.5 13.5 - - - +
762A LYS* 1.3 77.6 - - - +
764A GLN* 1.3 58.6 + - - +
766A TYR* 3.1 9.2 + - + +
767A GLU* 3.0 36.7 + - + +
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Residues in contact with GLN 764 (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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760A GLN 3.1 16.0 + - - +
761A ARG* 3.8 9.0 - - + +
762A LYS 3.3 0.4 - - - -
763A LEU* 1.3 73.2 - - - +
765A PHE* 1.3 60.7 + - - +
767A GLU* 3.8 18.6 - - - +
768A ASP* 2.8 65.3 + - - +
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Residues in contact with PHE 765 (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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717A PRO* 4.9 2.5 - - + -
737A TRP* 5.7 1.8 - + - -
754A LEU* 3.6 41.3 - - + -
757A LEU* 4.3 9.2 - - + -
761A ARG 2.9 13.3 + - - +
762A LYS* 3.1 14.8 - - - +
764A GLN* 1.3 76.6 - - - +
766A TYR* 1.3 82.5 + + - +
768A ASP 3.6 0.7 + - - -
769A ARG 3.1 15.9 + - - -
770A HIS* 3.2 65.7 + + + +
771A GLN* 3.6 23.1 - - - -
772A LEU* 4.0 10.8 - - + -
773A PRO* 5.9 0.9 - - + -
788A MET* 5.8 1.3 - - + -
790A TYR* 4.0 2.9 - - - -
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Residues in contact with TYR 766 (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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716A ILE* 3.7 33.0 - - + -
717A PRO* 3.2 17.9 - - + +
719A VAL 2.6 29.9 + - - -
720A PRO 3.8 0.2 - - - -
721A PRO* 3.4 32.0 - - + +
724A ILE* 4.0 8.7 - - + -
737A TRP* 3.3 32.6 + + - -
762A LYS 3.2 4.9 + - - +
763A LEU* 3.1 11.9 + - + +
765A PHE* 1.3 99.1 - + - +
767A GLU* 1.3 64.5 + - + +
769A ARG* 3.0 18.0 + - - +
790A TYR* 3.5 24.1 - + + -
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Residues in contact with GLU 767 (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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763A LEU* 3.0 26.7 + - + +
764A GLN* 3.1 28.7 + - - +
766A TYR* 1.3 77.4 - - + +
768A ASP* 1.3 61.5 + - - +
769A ARG* 3.2 9.4 + - - +
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Residues in contact with ASP 768 (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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764A GLN* 2.8 48.2 + - - +
767A GLU* 1.3 77.0 - - - +
769A ARG* 1.3 72.9 + - - +
770A HIS* 3.3 31.9 + - + +
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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