Contacts of the helix formed by residues 783 - 789 (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 ASP 783 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680D GLN 2.8 16.5 + - - +
682D ARG* 3.3 34.1 - - + +
685D LYS* 3.4 28.3 - - + +
781D ILE 3.4 1.6 + - - -
782D VAL* 1.3 70.1 - - - +
784D TRP* 1.3 57.3 + - - +
785D ASP* 2.9 23.9 + - - +
786D ILE* 3.0 46.0 + - + +
787D VAL* 3.4 6.9 + - - +
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Residues in contact with TRP 784 (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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685D LYS* 4.4 2.6 - - - +
686D GLY 3.7 23.0 - - - +
687D GLY 3.4 19.4 + - - -
688D ALA 3.9 15.5 - - - +
689D PRO* 3.6 21.8 - - + -
690D LYS* 6.1 0.2 - - + -
693D LEU* 4.0 8.7 - - + -
697D ILE* 5.2 2.0 - - + -
704D PHE* 3.3 35.3 - + - -
707D PHE* 4.8 6.7 - + - -
726D LEU* 5.1 7.6 - - + -
754D LEU* 4.2 17.3 - - + -
779D TRP* 3.9 17.8 + + - -
782D VAL* 3.3 22.0 + - + +
783D ASP* 1.3 68.3 + - - +
785D ASP* 1.3 58.0 + - - +
786D ILE 3.0 5.4 - - - -
787D VAL* 3.6 38.7 - - + +
788D GLU* 2.8 47.0 + - - +
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Residues in contact with ASP 785 (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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685D LYS* 6.0 2.0 - - + +
690D LYS* 5.1 7.8 - - - +
783D ASP* 2.9 13.7 + - - +
784D TRP* 1.3 79.5 - - - +
786D ILE* 1.3 64.2 + - + +
788D GLU* 3.1 20.5 - - - +
789D SER* 3.5 18.5 + - - -
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Residues in contact with ILE 786 (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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679D THR* 3.4 25.1 - - - +
680D GLN* 4.4 3.6 - - - -
682D ARG* 4.0 15.9 - - - +
783D ASP* 3.0 38.3 + - + +
785D ASP* 1.3 81.8 - - + +
787D VAL* 1.3 63.6 + - - +
788D GLU 3.2 0.2 - - - -
789D SER* 3.0 21.9 + - - +
790D ARG* 3.6 30.1 - - - +
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Residues in contact with VAL 787 (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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680D GLN* 4.5 10.5 - - + -
693D LEU* 3.4 18.5 - - + +
726D LEU* 5.3 0.9 - - + -
753D LEU* 3.7 29.6 - - + +
754D LEU* 3.9 26.7 - - + -
782D VAL* 4.1 11.7 - - + -
783D ASP 3.7 12.8 - - - +
784D TRP* 3.2 23.6 + - + +
786D ILE* 1.3 78.8 - - - +
788D GLU* 1.3 58.3 + - - +
790D ARG* 3.2 27.7 + - - +
791D TYR* 4.3 0.2 - - - +
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Residues in contact with GLU 788 (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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689D PRO* 3.3 7.3 - - - +
690D LYS* 2.4 47.9 + - - +
691D GLY* 5.7 0.2 - - - -
693D LEU* 3.4 30.0 - - + +
784D TRP* 2.8 26.5 + - - +
785D ASP* 3.1 24.5 - - - +
786D ILE 3.2 0.2 - - - -
787D VAL* 1.3 72.7 - - - +
789D SER* 1.3 59.6 + - - +
790D ARG 2.8 10.4 + - - -
791D TYR* 3.2 21.8 + - - +
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Residues in contact with SER 789 (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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785D ASP 3.5 13.6 + - - -
786D ILE* 3.0 15.8 + - - +
788D GLU* 1.3 75.9 - - - +
790D ARG* 1.3 59.6 + - - +
791D TYR 3.7 2.2 - - - -
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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