Contacts of the helix formed by residues 783 - 790 (chain D) in PDB entry 5YWB
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 THR 783 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782D ALA* 1.3 77.8 - - - +
784D VAL* 1.3 57.9 + - - +
785D GLU* 3.9 5.6 + - - +
786D GLU* 3.2 25.9 + - - +
787D ASN* 2.7 35.4 + - - -
820D GLN* 3.3 47.4 - - + +
821D THR 3.7 5.6 - - - -
822D GLN* 3.6 14.6 - - - +
823D ILE* 4.9 0.9 - - - -
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Residues in contact with VAL 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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783D THR* 1.3 71.5 - - - +
785D GLU* 1.3 67.9 + - - +
787D ASN* 3.1 6.9 + - - +
788D ILE* 3.0 47.6 + - + +
799D TYR* 5.2 3.4 - - - +
803D ILE* 5.6 0.4 - - + -
808D LEU* 5.3 0.2 - - + -
812D ILE* 3.8 32.3 - - + -
815D LEU* 5.0 4.0 - - + -
819D ASP* 4.0 13.0 - - - +
820D GLN* 4.5 2.0 - - - +
821D THR* 3.9 20.1 + - - +
823D ILE* 3.8 26.0 - - + -
830D LEU* 5.8 0.7 - - + -
838D ILE* 4.2 14.1 - - + -
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Residues in contact with GLU 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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783D THR* 3.4 4.2 + - - +
784D VAL* 1.3 76.8 - - - +
786D GLU* 1.3 57.0 + - - +
788D ILE* 3.3 1.7 + - - +
789D THR* 2.9 35.0 + - - +
794D PHE* 3.5 29.8 - - + -
799D TYR* 3.5 21.8 - - + +
819D ASP* 2.9 36.7 + - - +
820D GLN* 2.4 44.3 + - + +
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Residues in contact with GLU 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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780D LEU* 5.8 6.3 - - + +
782D ALA* 3.4 25.2 - - + +
783D THR* 3.2 24.9 + - - +
784D VAL 3.1 0.6 - - - -
785D GLU* 1.3 77.8 - - - +
787D ASN* 1.3 60.1 + - - +
789D THR* 3.0 8.0 + - - +
790D PHE* 3.0 29.3 + - - -
791D GLU 6.0 2.0 - - - +
794D PHE* 6.0 0.2 - - - -
1226D LYS* 5.5 4.9 + - - -
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Residues in contact with ASN 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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779D LEU* 3.5 7.6 - - - -
780D LEU* 2.7 53.0 + - - +
782D ALA* 3.9 10.7 + - - +
783D THR 2.7 29.9 + - - +
784D VAL* 3.1 9.1 + - - +
786D GLU* 1.3 75.5 - - - +
788D ILE* 1.3 60.7 + - - +
790D PHE* 4.4 3.3 - - - -
823D ILE* 4.3 7.5 - - + +
838D ILE* 4.4 13.2 - - + -
842D ARG* 3.2 49.3 + - - +
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Residues in contact with ILE 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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784D VAL* 3.0 34.0 + - + +
785D GLU 4.0 3.1 - - - +
787D ASN* 1.3 79.5 - - - +
789D THR* 1.3 61.6 + - - +
790D PHE* 4.8 0.2 - - - -
799D TYR* 4.4 17.5 - - + -
802D VAL* 4.5 5.2 - - + -
803D ILE* 3.6 28.5 - - + -
808D LEU* 4.5 7.2 - - + -
838D ILE* 4.7 11.2 - - + +
841D ALA* 3.8 39.0 - - + +
842D ARG* 4.2 10.2 - - - +
845D TYR* 3.1 34.1 - - + +
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Residues in contact with THR 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 GLU 2.9 20.8 + - - +
786D GLU* 3.0 14.4 + - - +
788D ILE* 1.3 78.0 - - - +
790D PHE* 1.3 68.0 + - - +
791D GLU 4.3 2.6 + - - -
792D SER* 3.5 25.1 + - - +
794D PHE* 3.5 39.5 - - + -
799D TYR* 5.2 2.7 - - + -
845D TYR* 3.8 20.5 - - + +
846D GLN* 2.8 23.4 + - - -
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Residues in contact with PHE 790 (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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778D TRP* 4.6 4.0 - + - -
780D LEU* 4.0 28.5 - - + -
786D GLU 3.0 11.0 + - - -
787D ASN* 4.4 3.8 - - - +
789D THR* 1.3 82.4 + - - +
791D GLU* 1.3 64.3 - - - +
792D SER 3.0 5.4 + - - -
842D ARG* 3.5 44.0 - - + -
846D GLN* 3.1 18.2 + - + +
1213D THR* 4.7 13.7 - - + -
1214D ILE* 4.7 5.6 - - + -
1217D PHE* 4.5 18.4 - + + -
1219D TYR* 3.3 36.8 - + + -
1223D PHE* 3.9 23.8 - + - -
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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