Contacts of the helix formed by residues 763 - 768 (chain D) in PDB entry 1UER
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 TYR 763 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D VAL 6.1 0.2 - - - -
623D THR* 5.5 2.9 - - - -
757D ASP 4.5 2.2 - - - -
758D VAL* 3.6 12.8 - - - -
759D TRP 3.6 19.7 - - - -
760D GLU* 3.5 25.6 + - + +
761D HIS 4.9 0.2 - - - -
762D ALA* 1.3 83.9 - - + +
764D TYR* 1.3 67.8 + + - +
765D LEU 3.4 2.5 - - - -
766D THR* 3.3 4.6 + - - -
767D TYR* 2.8 40.0 + - + +
768D GLN 3.2 25.4 - - - -
769D ASN* 4.8 1.9 + - - -
771D ARG* 3.0 51.1 + - + +
774D HIS* 3.4 42.8 - + + +
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Residues in contact with TYR 764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C PHE* 3.8 14.7 - - - +
427C HIS 5.0 0.3 + - - -
431C HIS* 2.7 32.3 + + - -
561C HIS* 3.5 33.3 + - + +
564C TYR* 4.3 25.4 - - + -
565C LEU* 3.6 36.1 - - + +
760D GLU* 2.8 41.1 + - + +
761D HIS 4.4 2.0 + - - -
763D TYR* 1.3 74.4 - + - +
765D LEU* 1.3 62.1 + - - +
768D GLN* 2.9 59.7 + - + +
769D ASN* 4.0 3.3 + - - -
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Residues in contact with LEU 765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564C TYR* 3.9 40.8 - - + +
565C LEU* 4.3 18.8 - - + +
568C GLN* 4.2 12.3 - - + +
620D SER* 5.2 2.2 - - - +
622D GLU* 4.5 12.3 - - + -
623D THR* 3.9 24.1 + - - +
626D PHE* 4.0 28.7 - - + -
761D HIS 5.5 1.3 + - - +
763D TYR 3.4 0.8 - - - -
764D TYR* 1.3 75.6 - - - +
766D THR* 1.3 58.7 + - - +
768D GLN* 3.1 12.8 + - - -
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Residues in contact with THR 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D PRO* 4.0 17.0 + - + +
618D VAL 4.9 1.5 + - - -
620D SER* 3.9 27.4 + - - -
623D THR* 4.5 3.4 + - - -
763D TYR* 3.3 3.2 + - - -
764D TYR 3.2 0.2 - - - -
765D LEU* 1.3 81.1 - - - +
767D TYR* 1.3 87.1 + - + +
768D GLN* 3.5 10.8 + - - +
770D ARG* 3.7 13.2 + - - +
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Residues in contact with TYR 767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D PRO 5.3 0.2 - - - -
618D VAL* 3.6 28.1 - - - +
763D TYR* 2.8 29.2 + - + +
766D THR* 1.3 89.9 - - + +
768D GLN* 1.3 72.2 + - - +
769D ASN 3.2 1.0 + - - -
770D ARG* 2.9 57.3 + - - +
773D ASP* 3.7 10.5 - - + -
774D HIS* 3.3 52.7 - - + -
777D ASP* 2.7 40.8 + - - +
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Residues in contact with GLN 768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLU* 5.9 1.9 + - - -
426C PHE* 3.5 49.7 - - + -
565C LEU* 4.2 11.4 - - + +
763D TYR* 3.2 24.1 - - - -
764D TYR* 2.9 53.3 + - + +
765D LEU 3.1 26.5 + - - -
766D THR 3.5 11.3 + - - +
767D TYR* 1.3 82.4 - - - +
769D ASN* 1.3 63.8 + - - +
770D ARG* 3.2 7.4 + - - -
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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